<PAGE>
                                                                     EXHIBIT 4.7


                          GENENCOR INTERNATIONAL, INC.

                        AMENDMENT NO. 3 TO NOTE AGREEMENT

                                                               As of May 5, 2000

TO EACH OF THE CURRENT NOTEHOLDERS
NAMED IN ANNEX 1 HERETO:

Ladies and Gentlemen:

     GENENCOR INTERNATIONAL, INC. (hereinafter, the "COMPANY"), together with
its successors and assigns, agrees with you as follows:

1.   PRELIMINARY STATEMENTS.

     1.1 NOTE ISSUANCE, ETC.

     The Company issued and sold $140,000,000 aggregate principal amount of its
6.82% Senior Notes due March 30, 2006 (as may be amended, restated or
otherwise modified from time to time, the "NOTES") pursuant to a Note Agreement
dated March 30, 1996 (as in effect immediately prior to giving effect to the
Amendments provided for by this Amendment Agreement, the "EXISTING NOTE
AGREEMENT"). The register for the registration and transfer of the Notes
indicates that the Persons named in Annex 1 hereto (collectively, the "CURRENT
NOTEHOLDERS") are currently the holders of the entire outstanding principal
amount of the Notes.

2.   DEFINED TERMS.

     Capitalized terms used herein and not otherwise defined herein have the
meanings ascribed to them in the Existing Note Agreement.

3.   AMENDMENTS.

     Subject to Section 5, the Existing Note agreement is amended as provided
for by this Amendment No. 3 to Note Agreement (this "AMENDMENT AGREEMENT") in
the manner specified in Exhibit A. The amendments referred to herein are
referred to herein, collectively, as the "Amendments".

4.   REPRESENTATIONS AND WARRANTIES OF THE COMPANY.

     To induce you to enter into this Amendment Agreement and to consent to the
Amendments, the Company represents and warrants as follows:

     4.1 ORGANIZATION, POWER AND AUTHORITY, ETC.

     The Company is a corporation duly incorporated and validly existing in good
standing under the laws of Delaware and has all requisite corporate power and
authority to enter into and perform its obligations under this Amendment
Agreement.





<PAGE>


     4.2 LEGAL VALIDITY.

     The execution and delivery of this Amendment Agreement by the Company and
compliance by the Company with its obligations hereunder: (a) are within the
corporate powers of the Company; and (b) are legal and do not conflict with,
result in any breach of, constitute a default under, or result in the creation
of any Lien upon any Property of the Company under the provisions of: (i) any
charter instrument or bylaw to which the Company is a party or by which the
Company or any of its Property may be bound; (ii) any order, judgment, decree or
ruling of any court, arbitrator or governmental authority applicable to either
the Company or its Property; or (iii) any agreement or instrument to which the
Company is a party or by which the Company or any of its Property may be bound
or any statute or other rule or regulation of any governmental authority
applicable to the Company or its Property, except where such conflict, breach or
default could not reasonably be expected to have a Material Adverse Effect.

     This Amendment Agreement has been duly authorized by all necessary action
on the part of the Company, has been executed and delivered by a duly authorized
officer of the Company, and constitutes a legal, valid and binding obligation of
the Company, enforceable in accordance with its terms, except that
enforceability may be limited by applicable bankruptcy, reorganization,
arrangement, insolvency, moratorium, or other similar laws affecting the
enforceability of creditors' rights generally and subject to the availability of
equitable remedies.

     4.3 NO DEFAULTS.

     No event has occurred and no condition exists that, upon the execution and
delivery of this Amendment Agreement, would constitute a Default or an Event of
Default.

5.   EFFECTIVENESS OF AMENDMENTS.

     The Amendments shall become effective as of the first date written above
(the "EFFECTIVE DATE") upon receipt by the Company of the written consent of the
Required Holders.

6.   EXPENSES.

     Whether or not the Amendments become effective, the Company will promptly
(and in any event within thirty days of receiving any statement or invoice
therefor) pay all fees, expenses and costs relating to this Amendment,
including, but not limited to, the reasonable fees of your special counsel,
Bingham Dana LLP, incurred in connection with the preparation, negotiation and
delivery of the Amendment Agreement and any other documents related thereto.
Nothing in this Section shall limit the Company's obligations pursuant to
Section 11B of the Existing Note Agreement.

7.   MISCELLANEOUS.

     7.1 PART OF EXISTING NOTE AGREEMENT; FUTURE REFERENCES, ETC.

     This Amendment Agreement shall be construed in connection with and as a
part of the Existing Note Agreement and, except as expressly amended by this
Amendment Agreement, all terms, conditions and covenants contained in the
Existing Note Agreement are hereby ratified




                                       2
<PAGE>


and shall be and remain in full force and effect. Any and all notices, requests,
certificates and other instruments executed and delivered after the execution
and delivery of this Amendment Agreement may refer to the Existing Note
Agreement without making specific reference to this Amendment Agreement, but
nevertheless all such references shall include this Amendment Agreement unless
the context otherwise requires.

     7.2 COUNTERPARTS.

     This Amendment Agreement may be executed in any number of counterparts,
each of which shall be an original but all of which together shall constitute
one instrument. Each counterpart may consist of a number of copies hereof, each
signed by less than all, but together signed by all, of the parties hereto.

     7.3 GOVERNING LAW.

     THIS AGREEMENT SHALL BE CONSTRUED AND ENFORCED IN ACCORDANCE WITH, AND THE
RIGHTS OF THE PARTIES SHALL BE GOVERNED BY, THE LAW OF THE STATE OF NEW YORK
EXCLUDING CHOICE-OF-LAW PRINCIPLES OF THE LAW OF SUCH STATE THAT WOULD REQUIRE
THE APPLICATION OF THE LAWS OF A JURISDICTION OTHER THAN NEW YORK.

   [Remainder of page intentionally left blank; next page is signature page.]












                                       3
<PAGE>




     If you are in agreement with the foregoing, please so indicate by signing
the acceptance below on the accompanying counterpart of this agreement and
returning it to the Company, whereupon it will become a binding agreement among
you and the Company.

                                        GENENCOR INTERNATIONAL, INC.

                                        BY:     /s/  Raymond J. Land
                                              ----------------------------------
                                        NAME:   Raymond J. Land
                                        TITLE:  Senior Vice President and
                                                Chief Financial Officer
















                                      A-1
<PAGE>



     The foregoing Amendment Agreement is hereby accepted as of the date first
above written.

                                       THE PRUDENTIAL INSURANCE COMPANY
                                       OF AMERICA


                                       BY:    /s/  Charles Y. King
                                             -----------------------------------
                                       NAME:  Charles Y. King
                                       TITLE: Vice President


                                       THE NORTHWESTERN MUTUAL LIFE
                                       INSURANCE COMPANY


                                       BY:    /s/  Richard A. Strait
                                             -----------------------------------
                                       NAME:  Richard A. Strait
                                       TITLE: Its Authorized Representative


                                       ALLMERICA FINANCIAL LIFE INSURANCE
                                       AND ANNUITY COMPANY
                                       By:  Allmerica Asset Management, Inc.

                                       BY:    /s/  Scott C. Hyney
                                             -----------------------------------
                                       NAME:  Scott C. Hyney
                                       TITLE: Vice President


                                       FIRST ALLMERICA FINANCIAL LIFE
                                       INSURANCE COMPANY
                                       By:  Allmerica Asset Management, Inc.

                                       BY:    /s/  Scott C. Hyney
                                             -----------------------------------
                                       NAME:  Scott C. Hyney
                                       TITLE: Vice President






                                      A-2
<PAGE>




                                       THE HANOVER INSURANCE COMPANY
                                       By: Allmerica Asset Management, Inc.

                                       BY:    /s/  Scott C. Hyney
                                             -----------------------------------
                                       NAME:  Scott C. Hyney
                                       TITLE: Vice President


                                       CITIZENS INSURANCE COMPANY OF
                                       AMERICA
                                       By: Allmerica Asset Management, Inc.

                                       BY:    /s/  Scott C. Hyney
                                             -----------------------------------
                                       NAME:  Scott C. Hyney
                                       TITLE: Vice President

                                       CONNECTICUT GENERAL LIFE INSURANCE
                                       COMPANY

                                       BY CIGNA INVESTMENTS, INC.


                                       BY:    /s/  Stephen H. Wilson
                                             -----------------------------------
                                       NAME:  Stephen H. Wilson
                                       TITLE: Managing Director


                                       CONNECTICUT GENERAL LIFE
                                       INSURANCE COMPANY ON BEHALF OF ONE OR
                                       MORE SEPARATE ACCOUNTS

                                       BY CIGNA INVESTMENTS, INC.


                                       BY:    /s/  Stephen H. Wilson
                                             -----------------------------------
                                       NAME:  Stephen H. Wilson
                                       TITLE: Managing Director





                                      A-3
<PAGE>




                                       LIFE INSURANCE COMPANY OF NORTH
                                       AMERICA

                                       BY CIGNA INVESTMENTS, INC.


                                       BY:    /s/  Stephen H. Wilson
                                             -----------------------------------
                                       NAME:  Stephen H. Wilson
                                       TITLE: Managing Director


                                       UNITED OF OMAHA LIFE INSURANCE
                                       COMPANY


                                       BY:    /s/  Curtis R. Caldwell
                                             -----------------------------------
                                       NAME:  Curtis R. Caldwell
                                       TITLE: First Vice President


                                       AMERICAN REPUBLIC INSURANCE
                                       COMPANY


                                       BY:
                                             -----------------------------------
                                       NAME:
                                       TITLE:


                                       COMPANION LIFE INSURANCE COMPANY


                                       BY:    /s/  Curtis R. Caldwell
                                             -----------------------------------
                                       NAME:  Curtis R. Caldwell
                                       TITLE: Authorized Signer


                                       BY:
                                             -----------------------------------
                                       NAME:
                                       TITLE:


                                      A-4
<PAGE>




                                       METROPOLITAN LIFE INSURANCE
                                       COMPANY


                                       BY:
                                             -----------------------------------
                                       NAME:
                                       TITLE:


                                       PACIFIC LIFE INSURANCE COMPANY


                                       BY:    /s/  Ronn Cornelius
                                             -----------------------------------
                                       NAME:  Ronn Cornelius
                                       TITLE: Assistant Vice Presidnt


                                       BY:    /s/  Diane W. Dales
                                             -----------------------------------
                                       NAME:  Diane W. Dales
                                       TITLE: Assistant Secretary


                                       GUARANTEE LIFE INSURANCE COMPANY


                                       BY:    /s/ Robert E. Whalen, II
                                             -----------------------------------
                                       NAME:  Robert E. Whelan, II
                                       TITLE: Vice President


                                       THE CANADA LIFE ASSURANCE
                                       COMPANY
                                       Cudd & Co. as Nominee

                                       BY:    /s/ Peter Coccia
                                             -----------------------------------
                                       NAME:  Peter Coccia
                                       TITLE: Partner




                                      A-5
<PAGE>




                                       CANADA LIFE INSURANCE COMPANY OF
                                       AMERICA
                                       Cudd & Co. as Nomoinee

                                       BY:    /s/ Peter Coccia
                                             -----------------------------------
                                       NAME:  Peter Coccia
                                       TITLE: Partner


                                       BERKSHIRE LIFE INSURANCE COMPANY


                                       BY:    /s/  Ellen I. Whittaker
                                             -----------------------------------
                                       NAME:  Ellen I Whittaker
                                       TITLE: Senior Investment Officer


                                       WOODMAN ACCIDENT AND LIFE
                                       COMPANY

                                       BY:    /s/  A.M.McCray
                                             -----------------------------------
                                       NAME:  A.M. McCray
                                       TITLE: Senior Director, Securities
                                              Investments And Assistant
                                              Treasurer




                                      A-6
<PAGE>



                                     ANNEX 1

                               CURRENT NOTEHOLDERS


The Prudential Insurance Company of America

The Northwestern Mutual Life Insurance Company

Allmerica Financial Life Insurance and Annuity Company

First Allmerica Financial Life Insurance Company

The Hanover Insurance Company

Citizens Insurance Company of America

Connecticut General Life Insurance Company

Life Insurance Company of North America

United of Omaha Life Insurance Company

American Republic Insurance Company

Companion Life Insurance Company

Metropolitan Life Insurance Company

Pacific Life Insurance Company

Guarantee Life Insurance Company

Canada Life Assurance Company of America

Canada Life Insurance Company of America

Berkshire Life Insurance Company

Woodmen Accident and Life Company






                                      A-7
<PAGE>



                                    EXHIBIT A

                                   AMENDMENTS

     (a) SECTION 10.B, Definition of Consolidated Net Worth. The definition of
Consolidated Net Worth shall be and is hereby amended and restated in its
entirety to read as follows:

     "CONSOLIDATED NET WORTH - means, at any time, the total shareholders'
     equity of the Company and its Subsidiaries, determined at such time in
     accordance with GAAP, but excluding therefrom the amount of share capital
     attributable to Redeemable Preferred Stock, provided, however, that for the
     period beginning December 31, 1999 and extending through and including
     September 30, 2000, Consolidated Net Worth shall include the Preferred
     Stock being reclassified as $147,925,000 of Redeemable Preferred Stock
     pursuant to the Company's S-1 filing dated as of May 5, 2000."



























                                      A-8