<SEC-DOCUMENT>0001209191-16-094263.txt : 20160129
<SEC-HEADER>0001209191-16-094263.hdr.sgml : 20160129
<ACCEPTANCE-DATETIME>20160129182155
ACCESSION NUMBER:		0001209191-16-094263
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20160127
FILED AS OF DATE:		20160129
DATE AS OF CHANGE:		20160129

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:			Nashat Amir
		CENTRAL INDEX KEY:			0001575843

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-37378
		FILM NUMBER:		161374914

	MAIL ADDRESS:	
		STREET 1:		10835 ROAD TO THE CURE
		STREET 2:		SUITE 205
		CITY:			SAN DIEGO
		STATE:			CA
		ZIP:			92121
</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>2016-01-27</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001575843</rptOwnerCik>
            <rptOwnerName>Nashat Amir</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>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>6.14</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2016-01-27</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>19428</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2026-01-27</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>19428</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>19428</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The shares subject to this option shall vest and become exercisable in 36 equal monthly installments beginning on February 27, 2016, such that this option will be fully exercisable on January 27, 2019.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Nancy Krueger, as Attorney-in-Fact</signatureName>
        <signatureDate>2016-01-29</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
