<SEC-DOCUMENT>0001209191-16-114247.txt : 20160414
<SEC-HEADER>0001209191-16-114247.hdr.sgml : 20160414
<ACCEPTANCE-DATETIME>20160414192045
ACCESSION NUMBER:		0001209191-16-114247
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20160413
FILED AS OF DATE:		20160414
DATE AS OF CHANGE:		20160414

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			aTYR PHARMA INC
		CENTRAL INDEX KEY:			0001339970
		STANDARD INDUSTRIAL CLASSIFICATION:	BIOLOGICAL PRODUCTS (NO DIAGNOSTIC SUBSTANCES) [2836]
		IRS NUMBER:				203435077
		STATE OF INCORPORATION:			DE

	BUSINESS ADDRESS:	
		STREET 1:		3545 JOHN HOPKINS COURT, STE #250
		CITY:			SAN DIEGO
		STATE:			CA
		ZIP:			92121
		BUSINESS PHONE:		858-731-8389

	MAIL ADDRESS:	
		STREET 1:		3545 JOHN HOPKINS COURT, STE #250
		CITY:			SAN DIEGO
		STATE:			CA
		ZIP:			92121

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			SCHIMMEL PAUL
		CENTRAL INDEX KEY:			0001236447

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-37378
		FILM NUMBER:		161572866

	BUSINESS ADDRESS:	
		STREET 1:		88 SIDNEY STREET
		CITY:			CAMBRIDGE
		STATE:			MA
		ZIP:			02139
		BUSINESS PHONE:		617-494-0171

	MAIL ADDRESS:	
		STREET 1:		88 SIDNEY ST
		CITY:			CAMBRIDGE
		STATE:			MA
		ZIP:			02139
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>doc4.xml
<DESCRIPTION>FORM 4 SUBMISSION
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2016-04-13</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001339970</issuerCik>
        <issuerName>aTYR PHARMA INC</issuerName>
        <issuerTradingSymbol>LIFE</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001236447</rptOwnerCik>
            <rptOwnerName>SCHIMMEL PAUL</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>3545 JOHN HOPKINS COURT, SUITE #250</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>SAN DIEGO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>92121</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2016-04-13</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>P</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>9835</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>3.85</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>249962</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F1"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>20412</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>634242</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">These shares are owned directly by Paul R. Schimmel Prototype PSP. The Reporting Person is the trustee of the Paul R. Schimmel Prototype PSP.</footnote>
        <footnote id="F2">These shares are owned directly by Schimmel Revocable Trust U/A Dtd 9/6/2000. The Reporting Person and his spouse are trustees of the Schimmel Revocable Trust U/A Dtd 9/6/2000.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>Nancy Krueger, as Attorney-in-Fact</signatureName>
        <signatureDate>2016-04-14</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
