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                                                                     Exhibit 4.2
                                                                     -----------


           SECOND AMENDED AND RESTATED CERTIFICATE OF INCORPORATION

                                      OF

                                MATRIXONE, INC.

              (Incorporated July 19, 1983 as Adra Systems, Inc.)

                                  * * * * * *


     I, Mark F. O'Connell, President and Chief Executive Officer of MatrixOne,
Inc. (the "Corporation"), a corporation organized and existing under and by
virtue of the General Corporation Law of the State of Delaware, do hereby
certify that the Certificate of Incorporation of MatrixOne, Inc., as amended,
originally incorporated under the name Adra Systems, Inc., has been further
amended, and restated as amended, in accordance with the provisions of Sections
242 and 245 of the General Corporation Law of the State of Delaware, and, as
amended and restated, is set forth in its entirety as follows:

     FIRST.  The name of the Corporation is MatrixOne, Inc.

     SECOND.  The address of the registered office of the Corporation in the
State of Delaware is 1209 Orange Street, Wilmington, County of New Castle,
Delaware 19801. The name of its registered agent at such address is The
Corporation Trust Company.

     THIRD.  The nature of the business or purposes to be conducted or promoted
is to engage in any lawful act or activity for which corporations may be
organized under the General Corporation Law of the State of Delaware.

     FOURTH.  The total number of shares of all classes of capital stock which
the Corporation shall have authority to issue is 105,000,000 shares, consisting
of 100,000,000 shares of Common Stock with a par value of $.01 per share (the
"Common Stock") and 5,000,000 shares of Preferred Stock with a par value of $.01
per share (the "Preferred Stock").

     A description of the respective classes of stock and a statement of the
designations, powers, preferences and rights, and the qualifications,
limitations and restrictions of the Preferred Stock and Common Stock are as
follows:

     A.   COMMON STOCK
          ------------

     1.   General.  All shares of Common Stock will be identical and will
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entitle the holders thereof to the same rights, powers and privileges. The
rights, powers and privileges of
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the holders of the Common Stock are subject to and qualified by the rights of
holders of the Preferred Stock.

     2.   Dividends.  Dividends may be declared and paid on the Common Stock
          ---------
from funds lawfully available therefor as and when determined by the Board of
Directors and subject to any preferential dividend rights of any then
outstanding Preferred Stock.

     3.   Dissolution, Liquidation or Winding Up. In the event of any
          --------------------------------------
dissolution, liquidation or winding up of the affairs of the Corporation,
whether voluntary or involuntary, each issued and outstanding share of Common
Stock shall entitle the holder thereof to receive an equal portion of the net
assets of the Corporation available for distribution to the holders of Common
Stock, subject to any preferential rights of any then outstanding Preferred
Stock.

     4.   Voting Rights.  Except as otherwise required by law or this Second
          -------------
Amended and Restated Certificate of Incorporation, each holder of Common Stock
shall have one vote in respect of each share of stock held of record by such
holder on the books of the Corporation for the election of directors and on all
matters submitted to a vote of stockholders of the Corporation. Except as
otherwise required by law or provided herein, holders of Common Stock shall vote
together with holders of the Preferred Stock as a single class, subject to any
special or preferential voting rights of any then outstanding Preferred Stock.
There shall be no cumulative voting.

     B.   PREFERRED STOCK
          ---------------

     The Preferred Stock may be issued in one or more series at such time or
times and for such consideration or considerations as the Board of Directors of
the Corporation may determine. Each series shall be so designated as to
distinguish the shares thereof from the shares of all other series and classes.
Except as otherwise provided in this Second Amended and Restated Certificate of
Incorporation, different series of Preferred Stock shall not be construed to
constitute different classes of shares for the purpose of voting by classes.

     The Board of Directors is expressly authorized to provide for the issuance
of all or any shares of the undesignated Preferred Stock in one or more series,
each with such designations, preferences, voting powers (or special,
preferential or no voting powers), relative, participating, optional or other
special rights and privileges and such qualifications, limitations or
restrictions thereof as shall be stated in the resolution or resolutions adopted
by the Board of Directors to create such series, and a certificate of said
resolution or resolutions (a "Certificate of Designation") shall be filed in
accordance with the General Corporation Law of the State of Delaware. The
authority of the Board of Directors with respect to each such series shall
include, without limitation of the foregoing, the right to provide that the
shares of each such series may be: (i) subject to redemption at such time or
times and at such price or prices; (ii) entitled to receive dividends (which may
be cumulative or non-cumulative) at such rates, on such conditions, and at such
times, and payable in preference to, or in such relation to, the dividends
payable on any other class or classes or any other series; (iii) entitled to
such rights upon the dissolution of, or upon any distribution of the assets of,
the Corporation; (iv) convertible into, or exchangeable for, shares of any other
class or classes of stock, or of any other series of the same
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or any other class or classes of stock of the Corporation at such price or
prices or at such rates of exchange and with such adjustments, if any; (v)
entitled to the benefit of such limitations, if any, on the issuance of
additional shares of such series or shares of any other series of Preferred
Stock; or (vi) entitled to such other preferences, powers, qualifications,
rights and privileges, all as the Board of Directors may deem advisable and as
are not inconsistent with law and the provisions of this Second Amended and
Restated Certificate of Incorporation.

     FIFTH.  The Corporation is to have perpetual existence.

     SIXTH.  The following provisions are included for the management of the
business and the conduct of the affairs of the Corporation, and for further
definition, limitation and regulation of the powers of the Corporation and of
its Board of Directors and stockholders:

     1.   The business and affairs of the Corporation shall be managed by or
under the direction of the Board of Directors of the Corporation.

     2.   The Board of Directors of the Corporation is expressly authorized to
adopt, amend or repeal the By-laws of the Corporation, subject to any limitation
thereof contained in the By-laws. The stockholders shall also have the power to
adopt, amend or repeal the By-laws of the Corporation; provided, however, that,
                                                       --------  -------
in addition to any vote of the holders of any class or series of stock of the
Corporation required by law or by this Second Amended and Restated Certificate
of Incorporation, the affirmative vote of the holders of at least sixty-six and
two-thirds percent (66 2/3%) of the voting power of all of the then outstanding
shares of the capital stock of the Corporation entitled to vote generally in the
election of directors, voting together as a single class, shall be required to
adopt, amend or repeal any provision of the By-laws of the Corporation.

     3.   Stockholders of the Corporation may not take any action by written
consent in lieu of a meeting.

     4.   Special meetings of stockholders may be called at any time only by the
President, the Chairman of the Board of Directors (if any) or a majority of the
Board of Directors. Business transacted at any special meeting of stockholders
shall be limited to matters relating to the purpose or purposes stated in the
notice of meeting.

     5.   The books of the Corporation may be kept at such place within or
without the State of Delaware as the By-laws of the Corporation may provide or
as may be designated from time to time by the Board of Directors of the
Corporation.

     SEVENTH.

     1.   Number of Directors.  The number of directors which shall constitute
          -------------------
the whole Board of Directors shall be determined by resolution of a majority of
the Board of Directors, but in no event shall the number of directors be less
than three. The number of directors may be decreased at any time and from time
to time by a majority of the directors then in office, but only to eliminate
vacancies existing by reason of the death, resignation, removal or expiration of
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the term of one or more directors. The directors shall be elected at the annual
meeting of stockholders by such stockholders as have the right to vote on such
election. Directors need not be stockholders of the Corporation.

     2.   Classes of Directors.  The Board of Directors shall be and is divided
          --------------------
into three classes: Class I, Class II and Class III. No one class shall have
more than one director more than any other class.

     3.   Election of Directors.  Elections of directors need not be by written
          ---------------------
ballot except as and to the extent provided in the By-laws of the Corporation.

     4.   Terms of Office.  Each director shall serve for a term ending on the
          ---------------
date of the third annual meeting following the annual meeting at which such
director was elected; provided, however, that each initial director in Class I
shall serve for a term ending on the date of the annual meeting next following
the end of the Corporation's fiscal year ending July 1, 2000; each initial
director in Class II shall serve for a term ending on the date of the annual
meeting next following the end of the Corporation's fiscal year ending June 30,
2001; and each initial director in Class III shall serve for a term ending on
the date of the annual meeting next following the end of the Corporation's
fiscal year ending June 29, 2002.

     5.   Allocation of Directors Among Classes in the Event of Increases or
          ------------------------------------------------------------------
Decreases in the Number of Directors.  In the event of any increase or decrease
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in the authorized number of directors, (i) each director then serving as such
shall nevertheless continue as director of the class of which he or she is a
member until the expiration of such director's current term or his or her prior
death, removal or resignation and (ii) the newly created or eliminated
directorships resulting from such increase or decrease shall be apportioned by
the Board of Directors among the three classes of directors so as to ensure that
no one class has more than one director more than any other class. To the extent
possible, consistent with the foregoing rule, any newly created directorships
shall be added to those classes whose terms of office are to expire at the
earliest dates following such allocation, unless otherwise provided for from
time to time by resolution adopted by a majority of the directors then in
office, though less than a quorum. No decrease in the number of directors
constituting the whole Board of Directors shall shorten the term of an incumbent
Director.

     6.   Tenure.  Notwithstanding any provisions to the contrary contained
          ------
herein, each director shall hold office until his or her successor is elected
and qualified, or until his or her earlier death, resignation or removal.

     7.   Vacancies.  Unless and until filled by the stockholders, any vacancy
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in the Board of Directors, however occurring, including a vacancy resulting from
an enlargement of the Board of Directors, may be filled only by vote of a
majority of the directors then in office, even if less than a quorum, or by a
sole remaining director. A director elected to fill a vacancy shall be elected
for the unexpired term of his or her predecessor in office, if applicable, and a
director chosen to fill a position resulting from an increase in the number of
directors shall hold office until the next election of the class for which such
director shall have been chosen and until his or her successor is elected and
qualified, or until his or her earlier death, resignation or removal.
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     8.   Quorum.  A majority of the total number of the whole Board of
          ------
Directors shall constitute a quorum at all meetings of the Board of Directors.
In the event one or more of the directors shall be disqualified to vote at any
meeting, then the required quorum shall be reduced by one for each such director
so disqualified; provided, however, that in no case shall less than one-third
(1/3) of the number so fixed constitute a quorum. In the absence of a quorum at
any such meeting, a majority of the directors present may adjourn the meeting
from time to time without further notice other than announcement at the meeting,
until a quorum shall be present.

     9.   Action at Meeting.  At any meeting of the Board of Directors at which
          -----------------
a quorum is present, the vote of a majority of those present shall be sufficient
to take any action, unless a different vote is specified by law or the
Corporation's By-laws.

     10.  Removal.  Any one or more or all of the directors may be removed with
          -------
cause only by the holders of at least sixty-six and two-thirds percent (66 2/3%)
of the shares then entitled to vote at an election of directors. Directors may
not be removed without cause.

     11.  Stockholder Nominations and Introduction of Business, Etc.  Advance
          ----------------------------------------------------------
notice of stockholder nominations for election of directors and other business
to be brought by stockholders before a meeting of stockholders shall be given in
the manner provided in the By-laws of the Corporation.

     12.  Rights of Preferred Stock.  The provisions of this Article are subject
          -------------------------
to the rights of the holders of any series of Preferred Stock from time to time
outstanding.

     EIGHTH.  No director (including any advisory director) of the Corporation
shall be personally liable to the Corporation or its stockholders for monetary
damages for breach of fiduciary duty as a director notwithstanding any provision
of law imposing such liability; provided, however, that, to the extent provided
by applicable law, this provision shall not eliminate the liability of a
director (i) for any breach of the director's duty of loyalty to the Corporation
or its stockholders, (ii) for acts or omissions not in good faith or which
involve intentional misconduct or a knowing violation of law, (iii) under
Section 174 of the General Corporation Law of the State of Delaware, or (iv) for
any transaction from which the director derived an improper personal benefit. No
amendment to or repeal of this provision shall apply to or have any effect on
the liability or alleged liability of any director for or with respect to any
acts or omissions of such director occurring prior to such amendment or repeal.

     NINTH.  The Board of Directors of the Corporation, when evaluating any
offer of another party (a) to make a tender or exchange offer for any equity
security of the Corporation or (b) to effect a business combination, shall, in
connection with the exercise of its judgment in determining what is in the best
interests of the Corporation as whole, be authorized to give due consideration
to any such factors as the Board of Directors determines to be relevant,
including, without limitation:

     (i)  the interests of the Corporation's stockholders, including the
   possibility that these interests might be best served by the continued
   independence of the Corporation;
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     (ii)  whether the proposed transaction might violate federal or state laws;

     (iii) not only the consideration being offered in the proposed transaction,
   in relation to the then current market price for the outstanding capital
   stock of the Corporation, but also to the market price for the capital stock
   of the Corporation over a period of years, the estimated price that might be
   achieved in a negotiated sale of the Corporation as a whole or in part or
   through orderly liquidation, the premiums over market price for the
   securities of other corporations in similar transactions, current political,
   economic and other factors bearing on securities prices and the Corporation's
   financial condition and future prospects; and

     (iv)  the social, legal and economic effects upon employees, suppliers,
   customers, creditors and others having similar relationships with the
   Corporation, upon the communities in which the Corporation conducts its
   business and upon the economy of the state, region and nation.

In connection with any such evaluation, the Board of Directors is authorized to
conduct such investigations and engage in such legal proceedings as the Board of
Directors may determine.

     TENTH.  The Corporation reserves the right to amend or repeal any provision
contained in this Second Amended and Restated Certificate of Incorporation in
the manner prescribed by the laws of the State of Delaware and all rights
conferred upon stockholders are granted subject to this reservation, provided,
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however, that in addition to any vote of the holders of any class or series of
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stock of the Corporation required by law, this Second Amended and Restated
Certificate of Incorporation or a Certificate of Designation with respect to a
series of Preferred Stock, the affirmative vote of the holders of shares of
voting stock of the Corporation representing at least sixty-six and two-thirds
percent (66 2/3%) of the voting power of all of the then outstanding shares of
the capital stock of the Corporation entitled to vote generally in the election
of directors, voting together as a single class, shall be required to (i) reduce
or eliminate the number of authorized shares of Common Stock or the number of
authorized shares of Preferred Stock set forth in Article FOURTH or (ii) amend
or repeal, or adopt any provision inconsistent with, Parts A and B of Article
FOURTH and Articles FIFTH, SIXTH, SEVENTH, EIGHTH, NINTH and this Article TENTH
of this Second Amended and Restated Certificate of Incorporation.

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     IN WITNESS WHEREOF, the undersigned has hereunto signed his name and
affirms that the statements made in this Second Amended and Restated Certificate
of Incorporation are true under the penalties of perjury this 6th day of March,
2000.


                                  /s/ Mark F. O'Connell
                                  ---------------------------------------------
                                  Name: Mark F. O'Connell
                                  Title: President and Chief Executive Officer



Attest:



/s/ Gordon H. Hayes, Jr.
-------------------------------
Name: Gordon H. Hayes, Jr.
Title: Secretary