Court Opinion

ID: 2653549
Source: CourtListenerOpinion
Date Created: 2014-02-18 16:27:02.241596+00
Date Added: 2024-06-11T09:11:24.072041
License: Public Domain

United States Court of Appeals
      for the Federal Circuit
                ______________________

   BUTAMAX(TM) ADVANCED BIOFUELS LLC,
             Plaintiff-Appellant,

                           v.

                     GEVO, INC.,
                  Defendant- Appellee.
                ______________________

                      2013-1342
                ______________________

    Appeal from the United States District Court for the
District of Delaware in No. 11-CV-0054, Judge Sue L.
Robinson.
                ______________________

              Decided: February 18, 2014
               ______________________

    LEORA BEN-AMI, Kirkland & Ellis, LLP, of New York,
New York, argued for plaintiff-appellant. With her on the
brief were THOMAS F. FLEMING, CHRISTOPHER T. JAGOE,
and PETER B. SILVERMAN.

    MICHELLE S. RHYU, Cooley, LLP, of Palo Alto, Califor-
nia, argued for defendant-appellee. With her on the brief
were STEPHEN C. NEAL, BENJAMIN G. DAMSTEDT, DANIEL
J. KNAUSS, of Palo Alto, California; and JAMES P. BROGAN,
of Broomfield, Colorado.
                 ______________________
2               BUTAMAX(TM) ADVANCED BIOFUELS   v. GEVO, INC.

    Before RADER, Chief Judge, LINN, and WALLACH, Circuit
                           Judges.
LINN, Circuit Judge.
     ButamaxTM Advanced Biofuels LLC (“Butamax”) owns
U.S. Pat. No. 7,851,188 (“’188 patent”) and No. 7,993,889
(“’889 patent”) (collectively, the “patents-in-suit”) and
appeals a final judgment entered against it following the
district court’s 1) claim construction and denial of Buta-
max’s motion for summary judgment of literal infringe-
ment of the asserted claims of the ’188 and ’889 patents
by Gevo, Inc. (“Gevo”), 2) grant of Gevo’s motion for sum-
mary judgment of noninfringement under the doctrine of
equivalents of the asserted claims of the ’188 and ’889
patents, 3) grant of Gevo’s motion for summary judgment
of invalidity of claims 12 and 13 of the ’889 patent for lack
of written description, and 4) judgment of invalidity of
claims 12 and 13 of the ’889 patent for lack of enablement.
Opinion, ButamaxTM Advanced Biofuels LLC v. Gevo, Inc.,
No. 11-54-SLR, 2013 WL 3914467 (D. Del. March 19,
2013) (“Opinion”). Because the district court erred in its
claim construction, this court vacates the district court’s
denial of Butamax’s motion for summary judgment of
infringement and its grant of Gevo’s motion of nonin-
fringement under the doctrine of equivalents. Because
the district court failed to recognize the existence of
genuine issues of material fact on Gevo’s motion for
summary judgment of invalidity as to claims 12 and 13 of
the ’889 patent, this court reverses the district court’s
grant of that motion. Finally, this court reverses the
grant of summary judgment of invalidity for lack of ena-
blement because that judgment appears to have been a
scrivener’s error.
BUTAMAX(TM) ADVANCED BIOFUELS    v. GEVO, INC.                3

                     I. BACKGROUND
                    A. The ’188 Patent
    The ’188 patent covers a recombinant microbial host
cell that uses a particular biosynthetic pathway to pro-
duce isobutanol, which is useful as a fuel or fuel additive.
Opinion at *3. The claimed biosynthetic pathway com-
prises essentially five steps. See ’188 Patent fig. 1.
   Claim 1 of the ’188 patent recites the first four steps:
       1. A recombinant microbial host cell compris-
   ing heterologous DNA molecules encoding poly-
   peptides that catalyze substrate to product
   conversions for each step below:
       i) pyruvate to acetolactate;
       ii) acetolactate to 2,3-dihydroxyisovalerate;
       iii)    2,3-dihydroxyisovalerate          to    α-
   ketoisovalerate; and
       iv) α-ketoisovalerate to isobutyraldehyde;
      wherein said microbial host cell produces iso-
   butanol; and wherein
       a) the polypeptide that catalyzes a substrate
   to product conversion of pyruvate to acetolactate
   is acetolactate synthase having the EC number
   2.2.1.6;
       b) the polypeptide that catalyzes a substrate
   to product conversion of acetolactate to 2,3-
   dihydroxyisovalerate is acetohydroxy acid isom-
   eroreductase having the EC number 1.1.1.86;
       c) the polypeptide that catalyzes a substrate to
   product conversion of 2,3-dihydroxyisovalerate to
   α-ketoisovalerate is acetohydroxy acid dehydra-
   tase having the EC number 4.2.1.9;
4             BUTAMAX(TM) ADVANCED BIOFUELS     v. GEVO, INC.

        d) the polypeptide that catalyzes a substrate
    to product conversion of α-ketoisovalerate to iso-
    butyraldehyde is branched-chain α-keto acid de-
    carboxylase having the EC number 4.1.1.72.
’188 Patent col. 335 ll. 21–44 (emphasis added). In the
fifth step, isobutyraldehyde is converted into isobutanol.
See ’188 Patent col. 336 ll. 43–48 (dependent claim 18,
reciting a method for producing isobutanol from the
recombinant microbial host cell of claim 1).
    Claim 15 depends from claim 1 and recites “[a] host
cell according to claim 1 wherein the acetohydroxy acid
isomeroreductase has an amino acid sequence selected
from the group consisting of SEQ ID NO:43, SEQ ID
NO:181, SEQ ID NO:183, and SEQ ID NO:185.” ’188
Patent col. 336 ll. 33–36. SEQ ID NO:183 is a sequence of
Methanococcus.
    This appeal primarily concerns step (ii): the conver-
sion of acetolactate (“AL”) to 2,3-dihydroxyisovalerate
(“DHIV”), catalyzed by the polypeptide enzyme acetohy-
droxy acid isomeroreductase (also known as keto-acid
reductoisomerase, or “KARI”) “having the EC number
1.1.1.86.” KARI assists reactions by rearranging (i.e.,
isomerizing) a reagent and also by “reducing” (the process
of adding electrons) this rearranged molecule. To accom-
plish the reduction, KARI needs a source for the added
electrons. This electron source is known as the “cofactor”
or “coenzyme.” Two such cofactors are NADH (nicotina-
mide adenine dinucleotide + hydrogen) and NADPH
(nicotinamide adenine dinucleotide phosphate + hydro-
gen).
    The ’188 patent’s specification provides “defini-
tions . . . to be used for the interpretation of the claims,”
including a definition of KARI:
    an enzyme that catalyzes the conversion of aceto-
    lactate to 2,3-dihydroxyisovalerate using NADPH
BUTAMAX(TM) ADVANCED BIOFUELS    v. GEVO, INC.           5

    (reduced nicotinamide adenine dinucleotide phos-
    phate) as an electron donor. Preferred acetohy-
    droxy acid isomeroreductases are known by the
    EC number 1.1.1.86 and sequences are available
    from a vast array of microorganisms, including
    but not limited to . . . Methanococcus maripalu-
    dis . . . .
’188 Patent col. 7 ll. 35–47.
     EC number 1.1.1.86, referenced in both this definition
and claim 1, is an Enzyme Commission number for an
enzyme known by the names KARI, “acetohydroxy acid
isomeroreductase,” and several other names. The EC
enzyme classification system was developed in the 1950s
to standardize enzyme nomenclature. Opinion at *15.
Notably, Rule 18 of the EC system states that “[f]or
oxidoreductases using NAD+ or NADP+ [the oxidized
states of NADH and NADPH, respectively], the coenzyme
should always be named as the acceptor” unless a certain
exception applies, which is irrelevant here. Id. However,
it also appears common to assign different EC numbers to
the same enzyme, where the difference between the
numbers is the identity of the cofactor named. Id. at 15
n.8. EC number 1.1.1.86 names only NADP+ as an accep-
tor, and neither party calls attention to another EC
number for KARI naming any other cofactor as an accep-
tor.
    Butamax alleges that Gevo infringes claim 1 of
the ’188 patent and claims 2–4, 13–15, 17, and 36 depend-
ent therefrom, as well as claim 18 and claims 19–25, and
34–35 dependent therefrom.
                     B. The ’889 Patent
    The ’889 patent issued from a divisional of the appli-
cation from which the ’188 patent issued. The patents’
specifications largely are identical, each for example
including the KARI definition quoted above. See ’889
6             BUTAMAX(TM) ADVANCED BIOFUELS      v. GEVO, INC.

Patent col. 7 ll. 8–20. The ’889 patent focuses on a meth-
od of producing isobutanol from a recombinant yeast
microorganism that expresses the five-step biosynthetic
pathway described above.
    Claim 1 of the ’889 patent states:
    1. A method for producing isobutanol comprising;
        a. providing a fermentation media comprising
    carbon substrate; and
        b. contacting said media with a recombinant
    yeast microorganism expressing an engineered
    isobutanol biosynthetic pathway wherein said
    pathway comprises the following substrate to
    product conversions;
        i. pyruvate to acetolactate (pathway step a);
        ii. acetolactate to 2,3-dihydroxyisovalerate
    (pathway step b);
        iii.    2,3-dihydroxyisovalerate        to      α-
    ketoisovalerate (pathway step c);
        iv. α-ketoisovalerate    to      isobutyraldehyde
    (pathway step d); and
        v. isobutyraldehyde to isobutanol (pathway
    step e);
        and wherein
         a) the substrate to product conversion of step
    (i) is performed by an acetolactate synthase en-
    zyme;
         b) the substrate to product conversion of step
    (ii) is performed by an acetohydroxy acid isomero-
    reductase enzyme;
BUTAMAX(TM) ADVANCED BIOFUELS    v. GEVO, INC.             7

         c) the substrate to product conversion of step
    (iii) is performed by an acetohydroxy acid dehy-
    dratase enzyme;
         d) the substrate to product conversion of step
    (iv) is performed by a decarboxylase enzyme; and
         e) the substrate to product conversion of step
    (v) is performed by an alcohol dehydrogenase en-
    zyme;
        whereby isobutanol is produced.
’889 Patent col. 325 ll. 14–43. As with the ’188 patent, the
primary issue with the ’889 patent on appeal involves step
(ii): the conversion of AL to DHIV using acetohydroxy
acid isomeroreductase enzyme, i.e., KARI. Unlike claim 1
of the ’188 patent, claim 1 of the ’889 patent does not refer
to any EC classification number.
    Butamax alleges that Gevo has infringed claim 1 of
the ’889 patent and claims 2–14 and 16–19 dependent
therefrom.
        C. The Parties and Previous Proceedings
    Butamax was formed in 2009 as a joint venture be-
tween E.I. du Pont de Nemours and Co. (“Du Pont”) and
BP Biofuels North America LLC. The applications that
led to the patents-in-suit are part of Du Pont’s previous
research and development into isobutanol production.
The patents-in-suit have been assigned to Butamax.
    Gevo was incorporated in 2005 as Methanotech, Inc.
and likewise pursues isobutanol production. Gevo uses
mutant KARI enzymes that when using NADH as a
cofactor exhibit significantly lower Km (Michaelis-Menten
constant) for the AL-to-DHIV conversion than when using
NADPH as a cofactor. This indicates that the reaction
rate with Gevo’s mutant enzymes is much faster with
NADH than with NADPH.
8             BUTAMAX(TM) ADVANCED BIOFUELS     v. GEVO, INC.

     On January 14, 2011, Butamax sued Gevo in the dis-
trict court and on September 22, 2011, moved for a pre-
liminary injunction predicated on the ’889 patent. The
district court construed the KARI term as “an enzyme
that is solely NADPH-dependent” and denied the motion.
Butamax(TM) Advanced Biofuels LLC v. Gevo, Inc., 486 F.
App’x 883 (Fed. Cir. 2012). This court affirmed the denial
of the preliminary injunction. Id. However, this court
noted that the district court’s construction of the KARI
term was “very questionable” and asked the district court
“to reconsider its construction when it holds the Markman
hearing.” Id.
    At the Markman hearing, the district court construed
the term as “an enzyme known by the EC number 1.1.1.86
that catalyzes the conversion of acetolactate to 2,3-
dihydroxyisovalerate and is NADPH-dependent.” Opin-
ion at *21. Additionally, adopting Butamax’s proposed
construction, the district court construed the ’889 patent’s
term “pathway step (a); . . . pathway step (b); . . . pathway
step (c); . . . pathway step (d); . . . pathway step (e)” to
mean “the pathway steps a-e are contiguous steps such
that the product of step a is the substrate for step b; the
product of step b is the substrate for step c; etc.” Id. at *
22.
    At the district court, Butamax moved for summary
judgment of infringement of the patents-in-suit and for a
judgment of no invalidity of the ’889 patent. Opinion at
*2. Gevo moved for summary judgment of invalidity and
non-infringement. Id. In a memorandum opinion, the
district court denied Butamax’s motion for summary
judgment of infringement. The district court granted
Gevo’s motion for summary judgment of noninfringement
as it related to the doctrine of equivalents, but otherwise
denied the motion. Each of Butamax’s motion of no
invalidity and Gevo’s motion for invalidity was granted by
the district court with respect to some claims and denied
with respect to others. Relevant to this appeal, the dis-
BUTAMAX(TM) ADVANCED BIOFUELS   v. GEVO, INC.            9

trict court granted Gevo’s invalidity motion and denied
Butamax’s motion of no invalidity with respect to claims
12 and 13 of the ’889 patent, finding the claims lacking in
written description support. Opinion at *52–53. The
district court issued an order reflecting the memorandum
opinion and also holding claims 12 and 13 the ’889 patent
invalid for lack of enablement, a ground not raised in the
motions of the parties.
    Butamax appeals the claim construction of the KARI
term, the denial of Butamax’s motion for summary judg-
ment of literal infringement, the grant of Gevo’s motion
for summary judgment of noninfringement under the
doctrine of equivalents, the grant of Gevo’s motion for
summary judgment of invalidity of claims 12 and 13 of the
’889 patent for inadequate written description, and the
order also holding those same claims invalid for lack of
enablement. This court has jurisdiction under 28 U.S.C.
§ 1295(a)(1).
                     II. DISCUSSION
                 A. Standards of Review
    “We review claim construction de novo.” Thorner v.
Sony Computer Entm’t Am. LLC, 669 F.3d 1362, 1365
(Fed. Cir. 2012).
     Summary judgment is granted “if the movant shows
that there is no genuine dispute as to any material fact
and the movant is entitled to judgment as a matter of
law.” Fed. R. Civ. P. 56(a). “This court reviews the dis-
trict court’s grant or denial of summary judgment under
the law of the regional circuit.” Lexion Med., LLC v.
Northgate Techs., Inc., 641 F.3d 1352, 1358 (Fed. Cir.
2011). The Third Circuit “review[s] an order granting
summary judgment de novo, applying the same standard
used by the District Court.” Azur v. Chase Bank, USA,
Nat’l Ass’n, 601 F.3d 212, 216 (3d Cir. 2010) (quotation
omitted).
10            BUTAMAX(TM) ADVANCED BIOFUELS    v. GEVO, INC.

    “[A] determination of infringement, both literal and
under the doctrine of equivalents, is a question of fact.”
Lockheed Martin Corp. v. Space Sys./Loral, Inc., 324 F.3d
1308, 1318 (Fed. Cir. 2003). “Summary judgment on the
issue of infringement is proper when no reasonable jury
could find that every limitation recited in a properly
construed claim either is or is not found in the accused
device either literally or under the doctrine of equiva-
lents.” PC Connector Solutions LLC v. SmartDisk Corp.,
406 F.3d 1359, 1364 (Fed. Cir. 2005).
                 B. Claim Construction
    The primary dispute between the parties concerns
whether the claimed KARI must be “NADPH-dependent.”
The district court considered the patents’ specifications,
prosecution histories, and the extrinsic evidence such as
expert testimony and the EC enzyme classification system
and other enzyme databases. It concluded that in the
“state of the art,” the “KARI enzyme known by the EC
number 1.1.1.86 was generally understood to be NADPH-
dependent.” Opinion at *20. This decision is premised in
large part on the district court’s conclusion that the
patentees acted as their own lexicographers in defining
KARI by reference to EC number 1.1.1.86 and the en-
zyme’s “use” of NADPH rather than use of NADH or both
NADPH and NADH. Id. at *19–20. The district court
therefore construed the KARI term as “an enzyme known
by the EC number 1.1.1.86 that catalyzes the conversion
of acetolactate to 2,3-dihydroxyisovalerate and is
NADPH-dependent.” Id. at *21.
    Butamax argues that the district court erred because
KARI’s plain meaning merely refers to an enzyme catalyz-
ing the AL to DHIV conversion and because the patentees
did not expressly relinquish any of that claim scope in the
specification or the prosecution history. Butamax con-
tends that the patentees in defining KARI did not clearly
express an intent to redefine KARI to be NADPH-
BUTAMAX(TM) ADVANCED BIOFUELS    v. GEVO, INC.           11

dependent. In support, Butamax points to the other
claims, the embodiments provided in the specifications,
and extrinsic evidence including contemporary scientific
literature, a database referenced in EC number 1.1.1.86,
and Gevo’s use of EC number 1.1.1.86 to describe its own
enzymes.
    Gevo disagrees, arguing that the district court con-
strued the term correctly. Gevo contends that the specifi-
cations’ definition of KARI demonstrates that the
patentees did clearly express an intent to specify KARI as
NADPH-dependent, and points to other aspects of the
specifications as well as the prosecution histories in
support. Gevo further contends that extrinsic evidence,
such as EC number 1.1.1.86 and its references, the EC
rules, and Butamax’s internal documents and subsequent
patent applications indicate that the claimed KARI must
be NADPH-dependent.
   Generally, claim terms are:
   given their ordinary and customary meaning as
   understood by a person of ordinary skill in the art
   when read in the context of the specification and
   prosecution history. There are only two excep-
   tions to this general rule: 1) when a patentee sets
   out a definition and acts as his own lexicographer,
   or 2) when the patentee disavows the full scope of
   a claim term either in the specification or during
   prosecution.
Thorner, 669 F.3d at 1365 (citation omitted). “To act as
its own lexicographer, a patentee must ‘clearly set forth a
definition of the disputed claim term’ other than its plain
and ordinary meaning.” Id. at 1365 (quoting CCS Fitness,
Inc. v. Brunswick Corp., 288 F.3d 1359, 1366 (Fed. Cir.
2002)). “It is not enough for a patentee to simply disclose
a single embodiment or use a word in the same manner in
all embodiments, the patentee must ‘clearly express an
intent’ to redefine the term.” Id. (citing Helmsderfer v.
12             BUTAMAX(TM) ADVANCED BIOFUELS     v. GEVO, INC.

Bobrick Washroom Equip., Inc., 527 F.3d 1379, 1381 (Fed.
Cir. 2008)).
               i. KARI’s Ordinary Meaning
    The initial inquiry is whether the plain meaning of
KARI indicates that the enzyme is NADPH-dependent.
While the district court found that “the scientific refer-
ences almost exclusively characterize KARI enzymes as
NADPH-dependent,” Opinion at *19, there is nothing in
the record to indicate that persons of ordinary skill in the
art in 2005 understood the plain meaning to be limited to
dependence on NADPH as a cofactor. Gevo conceded as
much at the district court, acknowledging that under
KARI’s plain meaning, the enzyme converts AL to DHIV
“using NADH or NADPH as a cofactor.” See Joint Appen-
dix (“J.A.”) 10240.
    We agree that the plain meaning of KARI itself im-
poses no limitation on the cofactor or source of electrons
for the AL to DHIV conversion. The question then be-
comes whether the asserted claims are limited, as Gevo
contends, to the use of NADPH only based principally on
the “explicit definition” set forth in the patents-in-suit.
See J.A. 10241.
             ii. The Specifications and Claims
           a. The Patentees’ Definition of KARI
    The patents provide definitions of several terms, not-
ing that “[t]he following definitions and abbreviations are
to be used for the interpretation of the claims and specifi-
cation.” ’188 Patent col. 7 ll. 12–14. 1 As described above,
the patents subsequently define KARI as:

     1  Because the specifications of the patents-in-suit
largely are identical, the court for brevity will cite only to
the ’188 patent.
BUTAMAX(TM) ADVANCED BIOFUELS    v. GEVO, INC.           13

    an enzyme that catalyzes the conversion of aceto-
    lactate to 2,3-dihydroxyisovalerate using NADPH
    (reduced nicotinamide adenine dinucleotide phos-
    phate) as an electron donor. Preferred acetohy-
    droxy acid isomeroreductases are known by the
    EC number 1.1.1.86 and sequences are available
    from a vast array of microorganisms, including
    but not limited to . . . Methanococcus maripalu-
    dis . . . .
’188 Patent col. 7 ll. 35–47.
     It cannot be disputed that the patentees offered a def-
inition of KARI. It is disputed, however, whether this
definition “clearly expresses an intent” to redefine KARI
in a way that differs from the plain and ordinary meaning
identified above and, if so, the extent of any such differ-
ence. Gevo contends that the phrase “using NADPH . . .
as an electron donor” is a clear expression of the patent-
ees’ intent to exclude KARI that are not “NADPH-
dependent.”
    Butamax disagrees and asserts that the fact that an
enzyme can catalyze the conversion of AL to DHIV “using
NADPH” does not, on its own, indicate that the enzyme
cannot also use other cofactors, such as NADH, to cata-
lyze that conversion.
    Gevo argues that Butamax’s interpretation reads out
an important aspect of the patentees’ definition of KARI
because all KARI are capable of using NADPH as a cofac-
tor. Thus, Gevo argues it would have been completely
unnecessary for the patents to have referred to “using
NADPH” in the first instance. Gevo also argues that the
phrase “using NADPH” must be understood in light of
other aspects of the specifications. Gevo first contends
that the specifications use the term “use(s) NADPH”
interchangeably with the phrase “NADPH-dependent.”
Gevo points to this passage:
14             BUTAMAX(TM) ADVANCED BIOFUELS   v. GEVO, INC.

     [A]lcohol dehydrogenase VI (ADH6) and Ypr1p . . .
     use NADPH as electron donor. An NADPH-
     dependent reductase, YqhD, . . . has also been re-
     cently identified in E. coli . . . .
’188 Patent col. 12 ll. 50–60. The patents further describe
ADH6 as “NADPH-dependent cinnamyl alcohol dehydro-
genase.” Id. at col. 4 ll. 60–62. However, “[i]t is not
enough for a patentee to simply disclose a single embodi-
ment or use a word in the same manner in all embodi-
ments.” Thorner, 669 F.3d at 1365.
    We agree with Butamax and find no reason to con-
strict the phrase “using NADPH” to mean “only use
NADPH” or “NADPH-dependent.” We also disagree with
Gevo’s argument that such an interpretation reads out an
important part of the patentees’ definition. The patents’
definition at least excludes as-yet-undiscovered KARI
enzymes that could catalyze the conversion of AL to DHIV
without using NADPH at all. Moreover, the description of
specific types of KARI as NADPH-dependent does not
clearly express an intent to redefine all KARI “using
NADPH” as KARI that must be NADPH-dependent.
    Next, Gevo points to the patents’ descriptions of other
enzymes that use or utilize either NAD+ or “NADH . . .
and/or NADPH” as an electron donor. Id. at col. 8 ll. 14–
16, 25–29. Gevo contends that the patentees knew how to
describe enzymes that used NADH or both NADH and
NADPH and that the patentees instead chose to define
KARI as using only NADPH.
    Butamax counters that the patents’ descriptions of
other enzymes “using” or “utilizing” various cofactors
merely is a reference to particular EC numbers or the
assays for the enzymes in question. For example, Buta-
max contends that the standard assay for KARI is the
Arfin-Umbarger assay, which “uses” NADPH to measure
KARI activity by monitoring the consumption of NADPH
in the presence of acetolactate and the enzyme in ques-
BUTAMAX(TM) ADVANCED BIOFUELS    v. GEVO, INC.           15

tion. Appellant’s Br. 14. The patents’ Example 2 express-
ly teaches to measure KARI activity “using the method
described by Arfin and Umbarger,” ’188 Patent col. 33 ll.
45–47. Example 10 teaches using the same method. Id.
at col. 39 ll. 4–5. Butamax also argues that the patents’
reference to “using NADPH” merely matches the descrip-
tion of the enzyme in EC number 1.1.1.86, which notes
the use of NADP+ but is silent as to NAD+ or NADH.
Butamax notes that the other enzymes in question from
the specifications have multiple EC numbers—each
referring to NADH, NADPH, or both NADH and
NADPH—and/or have multiple different assays for their
identification—each assay using a different cofactor.
Thus, Butamax argues that the patentees merely referred
the other cofactors where appropriate. Appellant’s Br. 45.
    We agree with Butamax that the references to other
enzymes as either using NAD+ or using NADH and/or
NADPH do not imply that the patentees intended to limit
KARI’s use of NADH. The patentees’ description of KARI
merely corresponds with the Arfin-Umbarger assay and
the description of KARI in EC Number 1.1.1.86.
     b. Reference to EC Number 1.1.1.86 in Claim 1
    The ’188 patent’s claim 1 explicitly states that the en-
zyme in question is “acetohydroxy acid isomeroreductase
having the EC number 1.1.1.86.” ’188 Patent col. 335 ll.
33–36. As described above, EC number 1.1.1.86 identifies
NADP+ as the cofactor, but does not itself mention NAD+
or NADH. See Appellee’s Br. 45. The EC rules provide
that for an enzyme “using” both NADH and NADPH, the
entry should “always” name both cofactors. Gevo con-
tends that this confirms that a person of ordinary skill in
the art understood KARI having EC number 1.1.1.86 to be
NADPH-dependent.
   It must first be appreciated that the EC nomenclature
was drafted to categorize naturally-occurring enzymes
and that new EC numbers generally are not created for
16            BUTAMAX(TM) ADVANCED BIOFUELS    v. GEVO, INC.

modified forms of enzymes that might rely on different
cofactors. See J.A. 17810–11. The nomenclature is also
not necessarily complete. In 2005, for example, it was
known that some KARI, such as KARI from at least some
species of Methanococcus, can use either cofactor effective-
ly. Significantly, Methanococcus was explicitly recited in
Butamax’s own definition as a preferred KARI and recited
in dependent claim 15. ’188 Patent col. 7 ll. 40–47.
    Butamax points to additional evidence showing per-
sons of skill in the art would have understood that EC
number 1.1.1.86 enzymes need not be NADPH-dependent.
The EC number 1.1.1.86 entry contains a link to the
BRENDA database (Braunchschweig Enzyme Database),
which contains a reference to a mutated KARI enzyme in
which NADH “can substitute for NADPH.” Appellant’s
Br. 16. The district court discounted this lone reference
because it was the only reference out of many indicating
that NADH could be substituted and because the specific
enzyme in question was a “quadruplet mutant.” Opinion
at *19–20.
    However, even a single reference to mutant KARI un-
der EC number 1.1.1.86 is particularly important here
because the accused enzymes also are mutants. Butamax
points to evidence that Gevo in approximately 2008—
prior to the litigation—described its own mutant enzymes
by reference to EC number 1.1.1.86. See, e.g., Appellant’s
Br. 25; J.A. 9804. And of course Gevo contends that its
enzymes are not NADPH-dependent. Though this evi-
dence identified by Butamax did not exist until years
after the patents-in-suits were filed in 2005, the BRENDA
entry for EC number 1.1.1.86 referred to a mutant KARI
that was not NADPH-dependent and was known prior to
2005, and Gevo years later indicated that EC number
1.1.1.86 still “would have been the best way [they] knew
how” to describe its own mutant enzyme. Appellant’s Br.
25 (citing testimony of Gevo’s former Executive Vice
President of Technology).      See e.g., ASM Am., Inc. v.
BUTAMAX(TM) ADVANCED BIOFUELS   v. GEVO, INC.           17

Genus, Inc., 401 F.3d 1340, 1347 (Fed. Cir. 2005) (conclud-
ing that extrinsic evidence that post-dated the patent
filing date nonetheless was helpful in determining how a
person of ordinary skill in the art would have understood
the claim term at the time it was filed).
    For the foregoing reasons, the Court cannot conclude
that the reference to EC number 1.1.1.86 is an expression
of a clear intent to redefine KARI to be NADPH-
dependent.
    c. Preferred Embodiments and Dependent Claims
    Other aspects of the patents raise further doubt of
any express intent to redefine KARI in the limited way
adopted by the district court. As above, the patents
specifically list “Methanococcus maripaludis . . . SEQ ID
NO: 183” as a source organism for the preferred
KARI. ’188 patent at col. 7 ll. 35–47. Moreover, depend-
ent claim 15 of the ’188 patent claims that KARI. ’188
Patent col. 336 ll. 33–36. Butamax contends that it would
be wrong to conclude that KARI from this organism are
NADPH-dependent, pointing to evidence that at least
some Methanococcus KARI are “able to utilize NADH as
well as NADPH” and have “broad specificity for NADPH
and NADH.” Further, Butamax notes that “NADH sup-
ported 60% of the methanococcal activity obtained with
NADPH.” See R. Xing & W. Whitman, Characterization
of Enzymes of the Branched-Chain Amino Acid Biosyn-
thetic Pathway in Methanococcus spp, 173(6) J. Bacteriol-
ogy 2086–92 (1991) (“Xing”).
     The district court discounted Xing because it provided
no references or data to support these findings. Opinion
at *19 (noting that Xing “included a single conclusory
sentence with no data or other literature references to
support it”). However, Xing’s accuracy is not in dispute.
Indeed, Gevo’s 2007 Pat. App. No. 61/016,483 cites to Xing
for this very proposition. Gevo does note that the patents
identify the KARI of Methanococcus maripaludis while
18             BUTAMAX(TM) ADVANCED BIOFUELS    v. GEVO, INC.

Xing examined the KARI of Methanococcus aeolicus, a
different species of Methanococcus. However, there is no
genuine dispute that Methanococcus maripaludis exhibits
similar characteristics. See Appellant’s Reply Br. 9.
    The district court’s claim construction, without justifi-
cation, excludes a preferred embodiment, which in this
case also is the subject of dependent claim 15, and this
court “normally do[es] not interpret claim terms in a way
that excludes embodiments disclosed in the specification.”
Oatey Co. v. IPS Corp., 514 F.3d 1271, 1276 (Fed. Cir.
2008).
                  iii. Prosecution History
    Gevo also contends that the prosecution history evinc-
es an express intent to redefine KARI to be NADPH-
dependent. The Patent Office separately rejected Buta-
max’s claims for lack of enablement and for lack of writ-
ten description, and Gevo contends that the patentees’
responses demonstrated that the claimed KARI are
NADPH-dependent.
    In the application leading to the ’188 patent, the Pa-
tent Office rejected for inadequate written description a
then-pending claim which stated:
         A recombinant microbial host cell comprising
     at least one DNA molecule encoding a polypeptide
     that catalyzes a substrate to product conversion
     selected from the group consisting of:
        i) pyruvate to acetolactate (pathway step a)
         ii) acetolactate to 2,3-dihydroxyisQvalerate
     (pathway step b)
         iii)    2,3-dihydroxyisovalerate      to      a-
     ketoisovalerate (pathway step c)
         iv) a-ketoisovalerate   to   isobutyraldehyde,
     (pathway step d), and
BUTAMAX(TM) ADVANCED BIOFUELS   v. GEVO, INC.           19

       v) isobutyraldehyde to isobutanol; (pathway
   step e)
       wherein the at least one DNA molecule is het-
   erologous to said microbial host cell and wherein
   said microbial host cell produces isobutanol.
J.A. 6906. The Patent Office concluded that “[o]ne skilled
in the art would require additional guidance, such as
information regarding the specific identity and structure
of the polypeptides that catalyze[]” the conversions in the
claim. J.A. 6927. The patentees responded, amending
the claim to refer to the EC numbers of the various en-
zymes, submitting a copy of the EC nomenclature rules,
and pointing to the specific examples of the enzymes in
the specification (including SEQ ID No: 183—
Methanococcus maripaludis—as an example of KARI).
J.A. 7095. The Patent Office concluded that this suffi-
ciently described the claimed inventions but concluded
that the claim lacked enablement for its full scope. J.A.
7117. The patentees disagreed, contending that the EC
numbers, together with the level of ordinary skill in the
art (including knowledge reflected in the BRENDA data-
base) did enable skilled artisans to identify appropriate
enzymes, and the examiner eventually withdrew the
rejection. J.A. 7209, 7251.
    In the application leading to the ’889 patent, a then-
pending claim similarly was rejected for lack of enable-
ment. J.A. 7572–73. The patentees again amended, this
time naming the enzymes used in each claimed step
without referring to any EC numbers. J.A. 7585. The
patentees argued that “[t]he specific enzymes that cata-
lyze the steps of the pathway recited in the claims are
described in the application in an abundance of detail,”
and went on to discuss Table 2 as a particular example.
J.A. 7583.
    In the prosecution history, the patentees defended
their claims by referring the Patent Office to the EC
20            BUTAMAX(TM) ADVANCED BIOFUELS    v. GEVO, INC.

numbers and the examples of the enzymes provided in the
specifications. For the reasons stated above, these refer-
ences do not clearly express an intent by the patentees to
redefine KARI to be NADPH-dependent. Indeed, the
patentees specifically named Methanococcus maripaludis
KARI as an example during the prosecution history, a
KARI that appears to “use” NADH.
    Accordingly, the court does not consider the prosecu-
tion history to warrant any limitation of the claimed
KARI as being NADPH-dependent.
                  iv. Extrinsic Evidence
    Gevo also relies on extrinsic evidence to support its
arguments. EC number 1.1.1.86 was discussed above.
Gevo further points to Butamax’s internal documents and
subsequent patent applications. For example, based on
its research, Butamax filed a patent application in 2008
which stated that “discovery of a KARI enzyme that can
use NADH as a cofactor as opposed to NADPH would be
an advance in the art.” J.A. 8794. Gevo contends that
this application and the related evidence demonstrate
that Butamax itself recognized that the earlier-filed
patents-in-suit did not encompass KARI that use NADH.
    However, as discussed above, the ordinary meaning of
KARI is not cofactor dependent, and this subsequent
extrinsic evidence does not clearly express an intent at the
time of the invention to redefine KARI to use one cofactor
over another. The subsequent discovery of the beneficial
results obtained by the use of NADH does not support the
conclusion that it was understood to be excluded as a
cofactor at the time the patents-in-suit were filed.
                  v. Claim Construction
    For all of the foregoing reasons, the term “acetohy-
droxy acid reductoisomerase” is construed as “an enzyme,
whether naturally occurring or otherwise, known by the
BUTAMAX(TM) ADVANCED BIOFUELS    v. GEVO, INC.           21

EC number 1.1.1.86 that catalyzes the conversion of
acetolactate to 2,3-dihydroxyisovalerate.”
                     C. Infringement
    Butamax contends that this court, under the more ac-
curate claim construction, should reverse the district
court’s ruling that denied Butamax’s motion for summary
judgment of literal infringement. Gevo disagrees, con-
tending that 1) there remains a dispute concerning the
“contiguous” pathway term and 2) there remains a dis-
pute as to the accused enzymes’ “use” of NADPH.
    The continuous pathway term relates only to the ’889
patent and does not present a genuine issue of material
fact on this record. Butamax provided expert testimony,
and Gevo failed to present any contention, interrogatory,
or expert testimony challenging Butamax’s contention
that the limitation was met.
     As to the dispute over whether Gevo’s enzymes use
detectable levels of NADPH, Gevo argues on appeal that
there is a distinction between in vivo and in vitro use that
gives rise to a genuine issue of material dispute. Howev-
er, Gevo does not appear to have argued at any point
before the district court that the construction of KARI
requires focusing on use of a specific cofactor in vivo as
opposed to in vitro. This court declines to consider what
appears to be a new claim construction argument raised
for the first time on appeal.
    Gevo further contends that Butamax’s in vitro testing
of Gevo’s enzymes, showing them to use NADPH, may be
unreliable. Appellee’s Br. 61. Gevo’s argument however,
is not that the results of the testing were inaccurate, but
rather that a person of ordinary skill in the art would not
draw the same conclusions from the experiments as the
conclusions drawn by Butamax’s expert. Whether Gevo’s
arguments create a genuine issue of material fact under
22              BUTAMAX(TM) ADVANCED BIOFUELS    v. GEVO, INC.

the claim construction set forth in this opinion is best left
to the district court on remand.
    The court accordingly vacates the district court’s de-
nial of Butamax’s motion for summary judgment of
infringement of claims 1, 2–4, 13–15, 17–25, and 34–36 of
the ’188 patent and claims 1, 2–14, and 16–19 of the ’889
patent and directs the district court to reconsider the
question under this court’s new claim construction.
                         D. Invalidity
     i. Written Description of Claims 12 and 13 of the ’889
                            Patent
      Claim 12 of the ’889 patent states:
      12. The recombinant yeast microorganism of claim
      1 wherein the said microorganism further com-
      prises inactivated genes thereby reducing yield
      loss from competing pathways for carbon flow.
      Claim 13 of the ’889 patent states:
      13. The recombinant yeast microorganism of claim
      12, wherein said inactivated genes reduce py-
      ruvate decarboxylase activity.
    The district court found that both claims were inade-
quately described and thus invalid because the specifica-
tion does not sufficiently describe how to inactivate genes
to disable the competing synthetic pathway.
      When determining whether a specification con-
      tains adequate written description, one must
      make an “objective inquiry into the four corners of
      the specification from the perspective of a person
      of ordinary skill in the art.” [Citation.] Because
      the specification is viewed from the perspective of
      one of skill, in some circumstances, a patentee
      may rely on information that is “well-known in
BUTAMAX(TM) ADVANCED BIOFUELS       v. GEVO, INC.             23

    the art” for purposes of meeting the written de-
    scription requirement.
Boston Scientific Corp. v. Johnson & Johnson, 647 F.3d
1353, 1366 (Fed. Cir. 2011) (citation omitted).
    The district court concluded that while the patent’s
specification “may be interpreted as identifying both the
[ ] problem and the solution, it does not even begin to
describe how to put into practice the solution.” Opinion at
*52. Butamax disagrees, but its evidence in support of its
arguments is weak. First, Butamax contends that the
patent does teach how to deactivate the pathway in
question. In support, Butamax cites to multiple aspects of
the specification, but each describes only a desire to
deactivate the genes rather than how to actually do it.
See, e.g., ’889 Patent col. 1 ll. 63–65 (“[t]here is a need . . .
for an environmentally responsible, cost-effective process
for the production of isobutanol as a single product”), col.
16 ll. 55–57 (“[t]he microbial host has to be manipulated
in order to inactivate competing pathways for carbon flow
by deleting various genes”), col. 12 ll. 12–17 (“[t]o prevent
misdirection of pyruvate away from isobutanol produc-
tion, a decarboxylase with decreased affinity for pyruvate
is desired”) (all emphasis added).
    Next, Butamax contends that irrespective of what is
explicitly taught in the specification itself, it was well-
known in the art how to deactivate the genes that express
the pathway. Butamax points to the testimony of Gevo’s
own experts, Dr. Stephanopolous and Dr. Kirsch, contend-
ing that they agreed that it was “conventional” in 2005 to
deactivate the pathway. However, the expert testimony
on which Butamax relies merely agrees that, in light of
the specification, it would have been understood that such
deactivation was desirable. See, e.g., Appellant’s Br. 68
(Dr. Stephanopolous agreeing that “the concept” of deac-
tivating the pathway was conventional by 2005, that it
was “nothing new” to “want to get rid of competing path-
24            BUTAMAX(TM) ADVANCED BIOFUELS    v. GEVO, INC.

ways,” that the patents “tell you [you] want to delete” the
competing pathway, and that the patent “tells you you’re
knocking out” that pathway); see also, e.g., Appellant’s Br.
69 (Dr. Kirsch agreeing that the patents teach that “you
want to knock out” the competing pathway) (emphasis
added).
     Butamax also relies on extrinsic evidence purportedly
teaching how to deactivate the pathway. Butamax sub-
mitted the declaration of Alexander M. Klibanov, who
opined that it would have been well-known to a person of
ordinary skill in the art how to deactivate the genes,
citing to seven references that purportedly describe organ-
isms with reduced or inactivated pyruvate decarboxylase
activity. Appellant’s Br. 67; J.A. 3141. The district court
does not appear to have addressed Mr. Klibanov’s testi-
mony or six of the references he cited. The seventh refer-
ence, Dickinson, was addressed by the district court,
which agreed that Dickinson discloses yeast with deac-
tivated genes associated with pyruvate decarboxylase
activity as described in claim 13. Opinion at *53. Howev-
er, the district court concluded that Dickinson was not
appropriately incorporated by reference into the ’889
patent for this point and even if it had been, that Dickin-
son effectively teaches away from claim 13 because in
deactivating those genes responsible for expressing the
pathway, isobutanol production was “virtually abolished.”
Id.
    Notwithstanding the shortcomings of the foregoing,
Butamax has identified sufficient evidence that at least
creates a genuine dispute of material fact. Gevo makes
much of the fact that Dickinson, though cited in the ’889
patent, was not cited in connection with the deactivation
of this pathway and was not incorporated by reference
into the patent. Nonetheless, Dickinson’s teachings still
reflect what was known in the art. See Falko-Gunter
Falkner v. Inglis, 448 F.3d 1357, 1368 (Fed. Cir. 2006)
(holding that where “accessible literature sources clearly
BUTAMAX(TM) ADVANCED BIOFUELS    v. GEVO, INC.            25

provided” a description of the teachings at issue, the
written description requirement does not require their
incorporation by reference). Dickinson does show that
persons of ordinary skill in the art could deactivate the
pathway in question, and though it appears that accord-
ing to Dickinson the claimed invention would not have
worked particularly well (isobutanol production would be
“virtually abolished”), the evidence at least creates a
genuine dispute as to whether a person of ordinary skill
in the art would have understood the patentees to have
possessed the invention on some level (isobutanol produc-
tion would not necessarily have been completely abol-
ished). Further, Mr. Klibanov opined that deactivation of
the genes associated with the pathway was well-known in
the art, and cited Dickinson as well as six other references
in support. Gevo’s experts disagree with Mr. Klibanov
and his interpretation of these references, but this merely
indicates the existence of a genuine dispute of material
fact.
     Though not addressed by the district court, Gevo rais-
es an argument that there can be no genuine dispute of
material fact because a subsequent Butamax patent
application demonstrates conclusively that the ’889
patent lacks an adequate written description of these
claims. Butamax filed a continuation-in-part of the
applications leading to the ’188 and ’889 patents, this
time providing additional detail on the deactivation of
certain genes. See U.S. Pat. App. No. 12/966,333. The
Patent Office concluded that the ’889 patent was not—on
its own—invalidating prior art to this application because
the ’889 patent “do[es] not teach the disruption of endoge-
nous pyruvate decarboxylase genes.” J.A. 17353. Howev-
er, the issue here is not just whether the ’889 patent itself
teaches the disruption such that the patent itself would
be invalidating prior art on that point. There is a genuine
dispute with respect to whether in 2005 it was generally
well-known in the art how to deactivate the genetic path-
26              BUTAMAX(TM) ADVANCED BIOFUELS   v. GEVO, INC.

way such that a person of ordinary skill in the art reading
the ’889 patent would understand the patentees to have
possessed the invention claimed in claims 12 and 13.
    For these reasons, the district court’s grant of Gevo’s
motion for summary judgment of invalidity of claims 12
and 13 for lack of adequate written description is re-
versed.
     ii. Enablement of the ’889 Patent’s Claims 12 and 13
    In its order, the district court summarily concluded
that claims 12 and 13 were invalid for lack of enablement.
However, its memorandum opinion does not reflect that
judgment, nor did Gevo move for invalidity of those claims
on this basis. On appeal, Gevo does not defend the judg-
ment. It thus appears that the judgment was a scrive-
ner’s error, and this court reverses the judgment that the
claims are invalid for lack of enablement.
                      III. CONCLUSION
     For the forgoing reasons, this court vacates the dis-
trict court’s denial of Butamax’s motion for summary
judgment of literal infringement of the asserted claims of
the ’188 and ’889 patents and remands the question of
infringement to the district court for reconsideration
under the claim construction set forth herein. Further,
this court likewise vacates and remands the district
court’s grant of Gevo’s motion for summary judgment of
noninfringement under the doctrine of equivalents. The
court further reverses the district court’s grant of Gevo’s
motion for summary judgment of invalidity for lack of
written description of claims 12 and 13 of the ’889 patent
and the district court’s order that those same claims are
invalid for lack of enablement.
  REVERSED-IN-PART, VACATED-IN-PART, AND
                REMANDED
BUTAMAX(TM) ADVANCED BIOFUELS   v. GEVO, INC.   27

                     IV. COSTS
   Costs are awarded to Butamax.