aTYR PHARMA INC 10-Q

Item 5. Other Information Our officers (as defined in Rule 16a-1(f) under the Exchange Act) have historically entered into sell-to-cover arrangements pursuant to Rule 10b5-1 authorizing the pre-arranged sale of shares to satisfy our tax withholding obligations arising exclusively from the vesting of time-vesting or performance-vesting restricted stock units and the related issuance of shares. The amount of shares to be sold to satisfy our tax withholding obligations under these arrangements has been dependent on future events which cannot be known in advance, including the future trading price of our shares. The expiration date relating to these arrangements has been dependent on future events which cannot be known in advance, including the final vest date of the applicable time-vesting or performance-vesting restricted stock units and the officer’s termination of service. 62 Item 6. Exhibits Index to Exhibits Incorporated by Reference Exhibit Number Exhibit Title Form File No. Exhibit Filing Date 3.1 Restated Certificate of Incorporation of the Registrant 10-Q 001-37378 3.1 November 14, 2022 3.2 Certificate of Amendment to Restated Certificate of Incorporation of the Registrant 8-K 001-37378 3.1 June 28, 2019 3.3 Certificate of Amendment to Restated Certificate of Incorporation of the Registrant 10-Q 001-37378 3.3 May 12, 2020 3.4 Certificate of Amendment to Restated Certificate of Incorporation of the Registrant 8-K 001-37378 3.1 May 4, 2021 3.5 Certificate of Amendment to Restated Certificate of Incorporation of the Registrant 8-K 001-37378 3.1 April 29, 2022 3.6 Certificate of Amendment to Restated Certificate of Incorporation of the Registrant 8-K 001-37378 3.1 May 19, 2023 3.7 Amended and Restated Bylaws of the Registrant 10-Q 333-203272 3.6 November 14, 2022 4.1 Specimen Common Stock Certificate S-1/A 333-203272 4.1 April 27, 2015 10.1* 2022 Inducement Plan, as amended 10-Q 001-37378 10.2 August 7, 2025 31.1 Certification of Principal Executive Officer required by Rule 13a-14(a) or Rule 15d-14(a) of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 — — — Filed herewith 31.2 Certification of Principal Financial Officer required by Rule 13a-14(a) or Rule 15d-14(a) of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 — — — Filed herewith 32.1# Certification of Principal Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002 — — — Furnished herewith 32.2# Certification of Principal Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002 — — — Furnished herewith 101.INS Inline XBRL Instance Document – the instance document does not appear in the Interactive Data File because XBRL tags are embedded within the Inline XBRL document — — — Filed herewith 101.SCH Inline XBRL Taxonomy Extension Schema With Embedded Linkbase Document — — — Filed herewith 104 Cover Page Interactive Data File (embedded within the Inline XBRL document) — — — Filed herewith * Indicates a management contract or compensatory plan, contract or arrangement. # The information in Exhibits 32.1 and 32.2 shall not be deemed “filed” for purposes of Section 18 of the Exchange Act, or otherwise subject to the liabilities of that section, nor shall it be deemed incorporated by reference in any filing under the Securities Act or the Exchange Act (including this Quarterly Report), unless the Registrant specifically incorporates the foregoing information into those documents by reference. 63 SIGNAT URES Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized. aTyr Pharma, Inc. Date: November 6, 2025 By: /s/ Sanjay S. Shukla Sanjay S. Shukla, M.D., M.S. President, Chief Executive Officer and Director (Principal Executive Officer) By: /s/ Jill M. Broadfoot Jill M. Broadfoot Chief Financial Officer (Principal Financial and Accounting Officer) 64