<SEC-DOCUMENT>0000899243-15-001072.txt : 20150710
<SEC-HEADER>0000899243-15-001072.hdr.sgml : 20150710
<ACCEPTANCE-DATETIME>20150710185701
ACCESSION NUMBER:		0000899243-15-001072
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20150708
FILED AS OF DATE:		20150710
DATE AS OF CHANGE:		20150710

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:			FALBERG KATHRYN E
		CENTRAL INDEX KEY:			0001206977

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-37378
		FILM NUMBER:		15984530

	MAIL ADDRESS:	
		STREET 1:		3400 CENTRAL AVENUE
		CITY:			SANTA CLARA
		STATE:			CA
		ZIP:			95051
</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>2015-07-08</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001206977</rptOwnerCik>
            <rptOwnerName>FALBERG KATHRYN E</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O ATYR PHARMA, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>3545 JOHN HOPKINS COURT, SUITE #250</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>14.96</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2015-07-08</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>6286</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2025-07-08</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>6286</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>6286</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Such Option shall vest on the earlier of (i) the first anniversary of the grant date or (ii) the date of the next annual meeting of the stockholders (currently scheduled for May 2016).</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Nancy Krueger, as Attorney-in-Fact</signatureName>
        <signatureDate>2015-07-10</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
