<PAGE>   1
                                                                    EXHIBIT 3.2



                               SECOND AMENDMENT TO
                           SECOND AMENDED AND RESTATED
                        AGREEMENT OF LIMITED PARTNERSHIP
                      OF EOP OPERATING LIMITED PARTNERSHIP

         THIS SECOND AMENDMENT TO SECOND AMENDED AND RESTATED AGREEMENT OF
LIMITED PARTNERSHIP OF EOP OPERATING LIMITED PARTNERSHIP (this "AMENDMENT"),
dated September 8, 2000, is entered into by EQUITY OFFICE PROPERTIES TRUST, a
Maryland real estate investment trust, as the general partner (the "GENERAL
PARTNER") of EOP Operating Limited Partnership, a Delaware limited partnership
(the "PARTNERSHIP"), for itself and on behalf of itself and the Limited Partners
of the Partnership, and those persons whose signatures are set forth on the
signature page attached hereto.

         WHEREAS, on the date hereof, WRC TRADE CENTER LLC ("CONTRIBUTOR"), is
receiving 227,011 Class B Units of limited partnership interest in the
Partnership ("OP UNITS"), based on a price per Unit of $30.3688, in exchange for
its interest in certain real property and related personal property known as the
World Trade Center - East Building, Seattle, Washington (the "PROJECT") pursuant
to a closing under, and as more particularly described in, that certain
Contribution Agreement (the "CONTRIBUTION AGREEMENT") dated July 7, 1998, by and
between the Contributor and EOP-WTC LLC, a Delaware limited liability company
(the "ACQUIROR") of which the Partnership is the sole member;

         WHEREAS, Contributor has assigned the OP Units to its constituent
members, Wright Runstad Associates Limited Partnership, a Washington limited
partnership ("WRALP") and Walter R. Ingram, an individual;

         WHEREAS, WRALP has assigned its OP Units to its constituent partners,
EOP Office Company, a Delaware corporation, R2N LLC, a Washington limited
liability company, and Wright Runstad & Co., a Washington corporation;

         WHEREAS, R2N LLC and Wright Runstad & Co. (together with WRALP, the
"INTERMEDIATE EQUITY HOLDERS") have assigned their OP Units to their constituent
members and shareholders, as applicable, who, together with Walter R. Ingram and
EOP Office Company, desire to become Limited Partners of the Partnership, and
whose signatures appear on the signature page attached hereto and whose names
are set forth on Schedule 1 hereto (the "EQUITY HOLDERS");

         WHEREAS, pursuant to the authority granted to the General Partner under
the Second Amended and Restated Agreement of Limited Partnership of EOP
Operating Limited Partnership dated as of June 19, 2000, (the "PARTNERSHIP
AGREEMENT"), the General Partner desires to amend the Partnership Agreement to
reflect (i) the admission of the Contributor as an Additional Limited Partner,
(ii) the admission of the Intermediate Equity Holders as Substituted Limited
Partners, and (iii) the admission of the Equity Holders as Substituted Limited
Partners, and (ii) certain agreements by and among the Contributor, the Acquiror
and the Partnership as to certain other matters set forth on Exhibit B to this
Amendment; and

         WHEREAS, the Contributor, the Intermediate Equity Holders, and the
Equity Holders desire to become parties to the Partnership Agreement and to be
bound by all of the terms,




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conditions and other provisions of this Amendment, the Exhibits hereto, and the
Partnership Agreement;

         NOW, THEREFORE, in consideration of the premises set forth above and
for other good and valuable consideration, the receipt and sufficiency of which
hereby are acknowledged, the General Partner hereby amends the Partnership
Agreement as follows:

         1. RESTATEMENT OF EXHIBIT A. Exhibit A to the Partnership Agreement
hereby is amended to reflect the admission of the Contributor as an Additional
Limited Partner to the Partnership and the transfer of the OP Units received by
the Contributor to the Intermediate Equity Holders and one of the Equity
Holders, as applicable. Exhibit A to the Partnership Agreement is amended
further to reflect the admission of the Intermediate Equity Holders as
Substituted Limited Partners of the Partnership and the transfer of the OP Units
received by the Intermediate Equity Holders from the Contributor to the Equity
Holders. Exhibit A to the Partnership Agreement is amended further as a result
of such transfer to reflect the admission of the Equity Holders as Substituted
Limited Partners of the Partnership. Exhibit A attached to this Amendment
contains the name, address, Capital Account, number of Partnership Units and
Percentage Interest of such Additional Limited Partner and Substituted Limited
Partners admitted to the Partnership hereby and shall be deemed attached to, and
an addendum of, Exhibit A to the Partnership Agreement for all relevant
purposes.

         2. AMENDMENT AND RESTATEMENT OF EXHIBIT E. Exhibit E to the Partnership
Agreement is hereby amended by attaching and adding Exhibit B to this Amendment,
which sets forth specific agreements regarding certain additional rights and
obligations of the Contributor, the Intermediate Equity Holders, and the Equity
Holders, as Exhibit E-8 to the Partnership Agreement.

         3. DEFINED TERMS. All capitalized terms used in this Amendment and not
otherwise defined shall have the meanings assigned to them in the Partnership
Agreement or the Contribution Agreement, as applicable. Except as modified
herein, all terms and conditions of the Partnership Agreement shall remain in
full force and effect, which terms and conditions the General Partner hereby
ratifies and affirms.

         4. TIME IS OF THE ESSENCE. Time is of the essence of each and every
provision of this Amendment.

         IN WITNESS WHEREOF, the undersigned has executed this Amendment as of
the date first set forth above.


                                    EQUITY OFFICE PROPERTIES TRUST, a Maryland
                                    real estate investment trust, the General
                                    Partner of EOP Operating Limited Partnership
                                    and on behalf of existing Limited Partners


                                    By: /s/ LAURA GERARD HASSAN
                                       ----------------------------------------
                                    Name:   LAURA GERARD HASSAN
                                         --------------------------------------
                                    Title:  VICE PRESIDENT
                                          -------------------------------------


                                        2

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                                  CONTRIBUTOR:

                                  WRC TRADE CENTER LLC, a Washington limited
                                  liability company

                                  By: Wright Runstad Associates Limited
                                      Partnership, a Washington limited
                                      partnership

                                      By: Wright Runstad & Company, its general
                                          partner


                                          By: /s/ WALTER R. INGRAM
                                             --------------------------------
                                             Its: EXECUTIVE VICE PRESIDENT & CFO
                                                 ----------------------------


                                  INTERMEDIATE EQUITY HOLDERS:

                                  WRIGHT RUNSTAD ASSOCIATES LIMITED PARTNERSHIP,
                                  a Washington limited partnership

                                      By: Wright Runstad & Company, its general
                                          partner

                                          By: /s/ WALTER R. INGRAM
                                             ---------------------------------
                                             Its: EXECUTIVE VICE PRESIDENT & CFO
                                                 -----------------------------


                                  WRIGHT RUNSTAD & COMPANY, a Washington
                                  corporation

                                          By: /s/ WALTER R. INGRAM
                                             ---------------------------------
                                             Its: EXECUTIVE VICE PRESIDENT & CFO
                                                 -----------------------------



                                  R2N LLC, a Washington limited liability
                                  company

                                          By: /s/ WALTER R. INGRAM
                                             ---------------------------------
                                             Its: MEMBER
                                                 -----------------------------

                                        3

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                                   EQUITY HOLDERS:

                                   /s/ WALTER R. INGRAM
                                   -------------------------------------
                                   WALTER R. INGRAM


                                   /s/ H. JON RUNSTAD
                                   -------------------------------------
                                   H. JON RUNSTAD


                                   /s/ DOUGLAS E. NORBERG
                                   -------------------------------------
                                   DOUGLAS E. NORBERG


                                   /s/ JON F. NORDBY
                                   -------------------------------------
                                   JON F. NORDBY




                                   EOP OFFICE COMPANY, a Delaware Corporation


                                       By: /s/ ALFRED L. LANGTRY III
                                          ------------------------------
                                       Name:   ALFRED L. LANGTRY III
                                            ----------------------------
                                       Its:
                                           -----------------------------

                                        4

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                                   SCHEDULE 1

                                (EQUITY HOLDERS)



Walter R. Ingram

H. Jon Runstad

Douglas E. Norberg

Jon F. Nordby

EOP Office Company



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                                                                       EXHIBIT A



<TABLE>
<CAPTION>

                                                         CLASS B UNITS
                                                         -------------

                                                            INITIAL
                                        PARTNERSHIP         CAPITAL       PERCENTAGE
NAME AND ADDRESS OF PARTNER               UNITS             ACCOUNT        INTEREST
---------------------------             -----------         -------       ----------
<S>                                     <C>                 <C>           <C>


</TABLE>



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                                                                       EXHIBIT B



                                   EXHIBIT E-8

             (SEATTLE WORLD TRADE CENTER -- EAST BUILDING AGREEMENT)


         BACKGROUND

         On September 8, 2000, in connection with the closing of the
Contribution Agreement by and between WRC Trade Center LLC, a Washington limited
liability company, ("Contributor") and EOP-WTC LLC, a Delaware limited liability
company, ("Acquiror") dated July 7, 1998, Contributor received 227,011 Class B
Units of limited Partnership Interest in the Partnership (the "WTC Units"),
based on a price per Unit of $30.3688, in exchange for its interest in the
"Project," as defined in the Contribution Agreement. In connection with the
issuance of the WTC Units, the Second Amendment to the Agreement was executed
adding this Exhibit E-8 to the Agreement, setting forth specific agreements
regarding additional rights and obligations of the Equity Holders, who were
assigned the WTC Units by the Contributor and the Intermediate Equity Holders as
described more fully in the Second Amendment to the Agreement, with respect to
the WTC Units. Such specific agreements are set forth below.

         All Capitalized terms used and not otherwise defined in this Exhibit
E-8 have the meanings assigned in the Agreement or the Second Amendment, as
applicable.

         SPECIFIC AGREEMENTS

1.       ADMISSION TO PARTNERSHIP. The Contributor is admitted to the
         Partnership as an Additional Limited Partner in accordance with Section
         12.2 of the Agreement and agrees to become a party to the Agreement and
         to be bound by all of the terms, conditions and other provisions of the
         Agreement, including, but not limited to, the power of attorney set
         forth in Section 15.11 of the Agreement. The General Partner has
         consented to the transfer of a portion of the WTC Units from the
         Contributor to the Intermediate Equity Holders, who have agreed to
         become parties to the Agreement and to be bound by all of the terms,
         conditions and other provisions of the Agreement, including, but not
         limited to, the power of attorney set forth in Section 15.11 of the
         Agreement. The General Partner has consented to the transfer the WTC
         Units from the Contributor and the Intermediate Equity Holders, as
         applicable, to the Equity Holders as reflected on Schedule 1 to the
         Second Amendment to the Agreement. Accordingly, the Equity Holders are
         admitted to the Partnership as Substituted Limited Partners in
         accordance with Section 11.4 of the Agreement and agree to become
         parties to the Agreement and to be bound by all of the terms,
         conditions and other provisions of the Agreement, including, but not
         limited to, the power of attorney set forth in Section 15.11 of the


<PAGE>   8



         Agreement. The Contributor and the Intermediate Equity Holders are no
         longer Limited Partners of the Partnership.

2.       LOCK-UP PERIOD. For a period equal to one year following the Closing
         Date (the "Lock-Up Period"), none of the Equity Holders shall, in any
         way or to any extent, redeem (pursuant to the Agreement or otherwise),
         sell, transfer, assign, pledge or encumber or otherwise convey any or
         all of the WTC Units delivered to Contributor pursuant to the
         Contribution Agreement and subsequently assigned to such Equity
         Holders. Notwithstanding the foregoing, during and after the Lock-Up
         Period, an Equity Holder shall have the right to (i) pledge or encumber
         the WTC Units (or Conversion Shares, if applicable) to a financial
         institution or other commercial lender for the purpose of securing an
         extension of credit to such Equity Holder by such financial institution
         or other commercial lender and (ii) assign all or any portion of its
         WTC Units, together with any and all other rights and obligations of
         such Equity Holder pursuant to this Exhibit E-8 and the Agreement, to
         one or more of the constituent partners or shareholders, members,
         partners or beneficiaries the such Equity Holder on the date hereof,
         whether direct or indirect, without the need for the consent of the
         General Partner or any other Limited Partner and without being subject
         to the right of first refusal set forth in Section 11.3.A(a) of the
         Agreement, but in each case subject to the restrictions and conditions
         set forth in Sections 11.3.C, 11.3.D, 11.3.E, 11.6.E and 11.6.F of the
         Agreement and subject to the requirement that each such assignee
         receiving any of such WTC Units and/or Conversion Shares is an
         "Accredited Investor," as such term is defined in Regulation D
         promulgated under the Securities Act of 1933, as amended. Upon the
         delivery of written notice of such an assignment to the General
         Partner, each assignee of WTC Units pursuant to the immediately
         preceding sentence shall be admitted to the Partnership as a
         Substituted Limited Partner owning the WTC Units so assigned and having
         all of the rights of a Limited Partner under the Agreement, the Second
         Amendment thereto and this Exhibit E-8, subject only to such assignee
         executing and delivering to the Partnership an acceptance of all of the
         terms and conditions of the Agreement and such other documents or
         instruments as the General Partner may reasonably require to effect
         such admission, in accordance with Section 11.4.B of the Agreement.
         Each permitted assignee of any of the WTC Units, issued to the
         Contributor pursuant to the Contribution Agreement, that is admitted as
         a Substituted Limited Partner in accordance with this Section 2 or
         Article XI of the Agreement, for so long as such Person owns any such
         WTC Units, is referred to in this Exhibit E-8 as an "INDIRECT EQUITY
         HOLDER." Upon satisfaction of the condition described in the second
         sentence of this Section 2, the General Partner shall amend Exhibit A
         to the Agreement in the manner described in Section 11.4.C of the
         Agreement. For purposes of Section 8.6 of the Agreement, each Indirect
         Equity Holder shall be entitled to exercise its right to require the
         Partnership to redeem all or any portion of the WTC Units assigned to
         it by the Contributor at any time on or after the first anniversary of
         the issuance of the WTC Units to Contributor pursuant to the closing
         under the Contribution Agreement.

3.       SALE OF THE PROJECT. For a period of two years following the Closing
         Date, the Partnership and the General Partner shall not, without the
         prior written consent of the

<PAGE>   9


         affected Equity Holder(s): (a) sell or otherwise dispose of the Project
         (other than through a deed in lieu of foreclosure, a foreclosure
         action, or an act of eminent domain) unless such sale or disposition
         qualifies for non-recognition of gain under the Code (for example, by
         means of exchanges contemplated under Code sections 351, 354, 355, 368,
         721, 1031, or 1033), in such manner as the Code provides from time to
         time and the Equity Holders recognize no gain as a result thereof or
         (b) cause a voluntary distribution of property that would cause the
         Equity Holders to recognize income or gain pursuant to the provisions
         of either or both of sections 704(c)(1)(B) and 737 of the Code.

4.       ALLOCATIONS. Notwithstanding any contrary provision in the Agreement,
         for a period of two years following the Closing Date, for purposes of
         allocating items of income, gain, loss and deduction with respect to
         the Property in the manner required by Section 704(c) of the Code, the
         Partnership shall employ, and shall cause any entity controlled by the
         Partnership which holds title to any of the Property to employ, the
         "traditional method" without curative allocations as set forth in
         Regulation Section 1.704-3(b).

5.       EQUITY HOLDERS TO PROVIDE INFORMATION. Each Equity Holder agrees that
         it shall deliver (or shall cause each of its partners, shareholders and
         members, as applicable, to deliver) to the General Partner or to any
         other party designated by the General Partner, any documentation that
         may be required under the Agreement or the Declaration of Trust of the
         General Partner and such other information as may reasonably be
         requested by the General Partner at such time as any WTC Units are
         exchanged for Shares of the General Partner (the "CONVERSION SHARES")
         pursuant to Section 8.6 of the Agreement.