Opinion ID: 2653549
Heading Depth: 4
Heading Rank: 2

Heading: Reference to EC Number 1.1.1.86 in Claim 1

Text: The ’188 patent’s claim 1 explicitly states that the enzyme 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 contends 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 effectively. 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 persons 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 –20. However, even a single reference to mutant KARI under 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 evidence 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) (concluding 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.