<SEC-DOCUMENT>0001209191-17-031640.txt : 20170511
<SEC-HEADER>0001209191-17-031640.hdr.sgml : 20170511
<ACCEPTANCE-DATETIME>20170511190144
ACCESSION NUMBER:		0001209191-17-031640
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20170509
FILED AS OF DATE:		20170511
DATE AS OF CHANGE:		20170511

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:			Hatfield Jeffrey S.
		CENTRAL INDEX KEY:			0001609879

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-37378
		FILM NUMBER:		17835869

	MAIL ADDRESS:	
		STREET 1:		11080 ROSELLE STREET
		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>2017-05-09</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001609879</rptOwnerCik>
            <rptOwnerName>Hatfield Jeffrey S.</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>3.15</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2017-05-09</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>20000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2027-05-09</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>20000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>20000</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 on the earlier of (i) May 09, 2018 or (ii) the date of the 2018 Annual Meeting of Stockholders, subject to the recipient's continued service on the Issuer's Board of Directors.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>Nancy Krueger, as Attorney-in-Fact</signatureName>
        <signatureDate>2017-05-11</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
