IMMEDIATE RELEASE Contact: Mark Johnson Sr. Director, Investor Relations mjohnson@atyrpharma.com 858-223-1163 aTyr Pharma Announces Fourth Quarter and Year-End 2016 Operating Results - Resolaris TM , in multiple rare myo

aTyr Pharma Announces Fourth Quarter and Year-End 2016 Operating Results

SAN DIEGO - March 16, 2017 - aTyr Pharma, Inc. (Nasdaq: LIFE), a biotherapeutics company engaged in the discovery and development of Physiocrine-based therapeutics to address severe, rare diseases, today announced operating results for the fourth quarter and year ended December 31, 2016.

"During the past year, we made significant progress in our mission to develop and ultimately deliver innovative therapeutics, based on novel immunological pathways, to patients with severe and rare diseases. Last year, we announced data from four separate clinical trials for Resolaris for the treatment of patients in three rare myopathy indications where immune cells play a role," said John Mendlein, PhD, CEO of aTyr Pharma. "In addition, we advanced our Stalaris program for rare lung diseases pre-clinically and plan to initiate clinical development in the second half of 2017. Finally, we created a third program based on our proprietary immunological pathways involving Physiocrine biology in a distinctly different therapeutic area, code named Project ORCA', and will announce more details later this year."

Resolaris Program Highlights

Resolaris represents a potentially first-in-class intravenous protein therapeutic candidate for the treatment of rare myopathies where T-cells in the muscle contribute to disease. Resolaris is a 57kD protein secreted from human muscle cells. aTyr's initial Phase 1b/2 clinical trials focused on adult limb girdle muscular dystrophy 2B (LGMD2B), adult facioscapulohumeral muscular dystrophy (FSHD), and early onset FSHD indications with little to no treatment options available.

Resolaris Signals of Clinical Activity

Resolaris Mechanism of Action and Safety

"Our clinical data and mechanism work suggest that Resolaris, as an immune modulator of activated T-cells, has been generally well-tolerated with no signs of general immunosuppression as well as promising signals of clinical activity in improved muscle function across multiple and genetically distinct T-cell mediated myopathies," commented Sanjay Shukla, MD, MS, chief medical officer of aTyr Pharma. "This supports our hypothesis that Resolaris, a potential modulator of activated T-cells in muscle, may be broadly applicable to rare myopathies with an immune component."

Stalaris Program Highlights

Stalaris is an engineered Physiocrine-based protein candidate that fuses an immuno-modulatory region of Resokine to the Fc domain of a human antibody. aTyr believes Stalaris has the potential to augment aspects of the Resokine pathway to provide therapeutic benefit to patients with rare pulmonary diseases with an immune component, such as T-cells.

Project ORCA Program Highlights

Intellectual Property Update

Fourth Quarter 2016 Financial Results

Research and development expenses were $9.1 million and $12.7 million for the quarters ended December 31, 2016 and 2015, respectively. The decrease of $3.6 million was due primarily to a $4.5 million decrease related to cGMP manufacturing of Resolaris, a $0.8 million decrease in non-cash stock-based compensation. These decreases were partially offset by a $1.7 million increase in cGMP manufacturing development costs for Stalaris. aTyr has substantially completed its cGMP manufacturing runs for Resolaris at commercial scale to support future clinical trials and does not anticipate additional commercial scale runs in 2017.

General and administrative expenses were $3.4 compared to $3.8 million for the quarters ended December 31, 2016 and 2015, respectively. The decrease was primarily related to non-cash stock-based compensation.

Full Year 2016 Financial Results

Research and development expenses were $42.8 million and $34.5 million for the years ended December 31, 2016 and 2015, respectively. The increase of $8.3 million was due primarily to a $3.2 million increase in development costs for Resolaris, a $2.4 million increase in manufacturing development costs for Stalaris, a $2.0 million increase in other pre-clinical development costs, a $1.2 million increase related cGMP manufacturing of Resolaris and a $0.9 million increase related to compensation expenses resulting from increased headcount in research and development functions, net of a $0.6 million reduction of non-cash stock-based compensation. These increases were offset by a decrease related to a one-time $1.4 million non-cash expense for the assignment of certain intellectual property rights in the prior year period.

General and administrative expenses were $15.1 million and $13.1 million for the years ended December 31, 2016 and 2015, respectively. The increase of $2.0 million was due primarily to a $1.8 million increase in personnel costs resulting from increased headcount, inclusive of $0.8 million of non-cash stock-based compensation.

As of December 31, 2016, aTyr had $76.1 million in cash, cash equivalents and investments and 23.7 million shares of common stock outstanding.

aTyr continues to expect that its cash, cash equivalents and investments will be sufficient to fund its anticipated operations into the third quarter of 2018.

aTyr Pharma is engaged in the discovery and clinical development of innovative medicines for patients suffering from severe, rare diseases using its knowledge of Physiocrine biology, a newly discovered set of physiological pathways. To date, the company has generated three innovative therapeutic candidate programs based on its knowledge of Physiocrine biology in three different therapeutic areas. aTyr has built an intellectual property estate, to protect its pipeline, comprising over 175 issued patents or allowed patent applications that are owned or exclusively licensed, including over 300 potential Physiocrine-based protein compositions. aTyr's key programs are currently focused on severe, rare diseases characterized by immune imbalance for which there are currently limited or no treatment options. For more information, please visit http://www.atyrpharma.com.

Forward-Looking Statements

This press release contains forward-looking statements within the meaning of the Private Litigation Reform Act. Forward-looking statements are usually identified by the use of words such as "anticipates," "believes," "estimates," "expects," "intends," "may," "plans," "projects," "seeks," "should," "will," and variations of such words or similar expressions. We intend these forward-looking statements to be covered by such safe harbor provisions for forward-looking statements and are making this statement for purposes of complying with those safe harbor provisions. These forward-looking statements, including statements regarding the potential of Resolaris or Stalaris , the ability of the Company to undertake certain development activities (such as clinical trial enrollment and the conduct of clinical trials) and accomplish certain development goals, the timing of initiation of additional clinical trials and of reporting results from our clinical trials and reflect our current views about our plans, intentions, expectations, strategies and prospects, which are based on the information currently available to us and on assumptions we have made. Although we believe that our plans, intentions, expectations, strategies and prospects as reflected in or suggested by those forward-looking statements are reasonable, we can give no assurance that the plans, intentions, expectations or strategies will be attained or achieved. Furthermore, actual results may differ materially from those described in the forward-looking statements and will be affected by a variety of risks and factors that are beyond our control including, without limitation, risks associated with the discovery, development and regulation of our Physiocrine-based product candidates, as well as those set forth in our most recent Annual Report on Form 10-K for the year ended December 31, 2016 and in our other SEC filings. Except as required by law, we assume no obligation to update publicly any forward-looking statements, whether as a result of new information, future events or otherwise.