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P41250 (SYG_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 125. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (7) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Glycine--tRNA ligase

EC=6.1.1.14
Alternative name(s):
Diadenosine tetraphosphate synthetase
Short name=AP-4-A synthetase
Glycyl-tRNA synthetase
Short name=GlyRS
Gene names
Name:GARS
OrganismHomo sapiens (Human)
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length739 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the attachment of glycine to tRNA(Gly). Is also able produce diadenosine tetraphosphate (Ap4A), a universal pleiotropic signaling molecule needed for cell regulation pathways, by direct condensation of 2 ATPs. Ref.12

Catalytic activity

ATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-tRNA(Gly).

Subunit structure

Homodimer. Ref.10 Ref.11

Subcellular location

Cytoplasm. Mitochondrion Ref.7.

Tissue specificity

Widely expressed, including brain and spinal cord. Ref.13

Involvement in disease

Defects in GARS are the cause of Charcot-Marie-Tooth disease type 2D (CMT2D) [MIM:601472]. CMT2D is a form of Charcot-Marie-Tooth disease, the most common inherited disorder of the peripheral nervous system. Charcot-Marie-Tooth disease is classified in two main groups on the basis of electrophysiologic properties and histopathology: primary peripheral demyelinating neuropathy or CMT1, and primary peripheral axonal neuropathy or CMT2. Neuropathies of the CMT2 group are characterized by signs of axonal regeneration in the absence of obvious myelin alterations, normal or slightly reduced nerve conduction velocities, and progressive distal muscle weakness and atrophy. CMT2D is characterized by a more severe phenotype in the upper extremities (severe weakness and atrophy, absence of tendon reflexes) than in the lower limbs. CMT2D inheritance is autosomal dominant. Ref.13

Defects in GARS are the cause of distal spinal muscular neuropathy type 5 (HMN5) [MIM:600794]; also known as distal hereditary motor neuropathy type V (DSMAV). HMN5 is an autosomal dominant distal hereditary motor neuropathy (dHMN) with a phenotype similar to CMTD2. The main characteristic that distinguishes these disorders is the less severe distal sensory involvement in HMN5 patients. Ref.13

Sequence similarities

Belongs to the class-II aminoacyl-tRNA synthetase family.

Contains 1 WHEP-TRS domain.

Biophysicochemical properties

Kinetic parameters:

KM=1.3 µM for tRNA(Gly(GCC)) Ref.10

KM=15 µM for glycine

Sequence caution

The sequence AAA57001.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

The sequence AAA86443.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 739739Glycine--tRNA ligase
PRO_0000072998

Regions

Domain63 – 11957WHEP-TRS
Nucleotide binding331 – 3333ATP
Nucleotide binding341 – 3466ATP
Nucleotide binding457 – 4582ATP
Nucleotide binding580 – 5834ATP
Region346 – 3505Substrate binding
Region576 – 5805Substrate binding

Sites

Binding site2131Substrate
Binding site2991Substrate
Binding site4351Substrate; via carbonyl oxygen

Amino acid modifications

Modified residue2041N6-acetyllysine Ref.8
Modified residue2191N6-acetyllysine Ref.8
Modified residue4531Phosphotyrosine By similarity
Modified residue5011N6-acetyllysine Ref.8

Natural variations

Natural variant421P → A. Ref.1 Ref.2 Ref.3 Ref.5 Ref.6
Corresponds to variant rs1049402 [ dbSNP | Ensembl ].
VAR_054865
Natural variant1251E → G in CMT2D; phenotype overlapping with DSMA-V. Ref.13
Corresponds to variant rs28936972 [ dbSNP | Ensembl ].
VAR_018718
Natural variant1831L → P in HMN5. Ref.13
VAR_018719
Natural variant2681T → I.
Corresponds to variant rs2230310 [ dbSNP | Ensembl ].
VAR_054866
Natural variant2941G → R in CMT2D. Ref.13
VAR_018720
Natural variant3881R → Q.
Corresponds to variant rs17159287 [ dbSNP | Ensembl ].
VAR_054867
Natural variant5801G → R in HMN5; higher dimerization stability but loss of activity. Ref.11 Ref.13
Corresponds to variant rs28937323 [ dbSNP | Ensembl ].
VAR_018721

Experimental info

Mutagenesis6351S → L: Reduced activity. Ref.10
Sequence conflict9 – 1810Missing in BAG58412. Ref.3
Sequence conflict2051D → G in BAG51964. Ref.3
Sequence conflict5301M → I in AAA86443. Ref.2
Sequence conflict6341L → S in BAG51964. Ref.3

Secondary structure

................................................................................................... 739
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P41250 [UniParc].

Last modified November 30, 2010. Version 3.
Checksum: E4C001CEBF985C59

FASTA73983,166
        10         20         30         40         50         60 
MPSPRPVLLR GARAALLLLL PPRLLARPSL LLRRSLSAAS CPPISLPAAA SRSSMDGAGA 

        70         80         90        100        110        120 
EEVLAPLRLA VRQQGDLVRK LKEDKAPQVD VDKAVAELKA RKRVLEAKEL ALQPKDDIVD 

       130        140        150        160        170        180 
RAKMEDTLKR RFFYDQAFAI YGGVSGLYDF GPVGCALKNN IIQTWRQHFI QEEQILEIDC 

       190        200        210        220        230        240 
TMLTPEPVLK TSGHVDKFAD FMVKDVKNGE CFRADHLLKA HLQKLMSDKK CSVEKKSEME 

       250        260        270        280        290        300 
SVLAQLDNYG QQELADLFVN YNVKSPITGN DLSPPVSFNL MFKTFIGPGG NMPGYLRPET 

       310        320        330        340        350        360 
AQGIFLNFKR LLEFNQGKLP FAAAQIGNSF RNEISPRSGL IRVREFTMAE IEHFVDPSEK 

       370        380        390        400        410        420 
DHPKFQNVAD LHLYLYSAKA QVSGQSARKM RLGDAVEQGV INNTVLGYFI GRIYLYLTKV 

       430        440        450        460        470        480 
GISPDKLRFR QHMENEMAHY ACDCWDAESK TSYGWIEIVG CADRSCYDLS CHARATKVPL 

       490        500        510        520        530        540 
VAEKPLKEPK TVNVVQFEPS KGAIGKAYKK DAKLVMEYLA ICDECYITEM EMLLNEKGEF 

       550        560        570        580        590        600 
TIETEGKTFQ LTKDMINVKR FQKTLYVEEV VPNVIEPSFG LGRIMYTVFE HTFHVREGDE 

       610        620        630        640        650        660 
QRTFFSFPAV VAPFKCSVLP LSQNQEFMPF VKELSEALTR HGVSHKVDDS SGSIGRRYAR 

       670        680        690        700        710        720 
TDEIGVAFGV TIDFDTVNKT PHTATLRDRD SMRQIRAEIS ELPSIVQDLA NGNITWADVE 

       730 
ARYPLFEGQE TGKKETIEE 

« Hide

References

« Hide 'large scale' references
[1]"Human glycyl-tRNA synthetase. Wide divergence of primary structure from bacterial counterpart and species-specific aminoacylation."
Shiba K., Schimmel P., Motegi H., Noda T.
J. Biol. Chem. 269:30049-30055(1994) [PubMed: 7962006] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], VARIANT ALA-42.
[2]"Cloning, sequencing and bacterial expression of human glycine tRNA synthetase."
Williams J.H., Osvath S.R., Khong T.-F., Pearse M.J., Power D.A.
Nucleic Acids Res. 23:1307-1310(1995) [PubMed: 7753621] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], VARIANT ALA-42.
[3]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed: 14702039] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT ALA-42.
Tissue: Embryo and Hippocampus.
[4]"The DNA sequence of human chromosome 7."
Hillier L.W., Fulton R.S., Fulton L.A., Graves T.A., Pepin K.H., Wagner-McPherson C., Layman D., Maas J., Jaeger S., Walker R., Wylie K., Sekhon M., Becker M.C., O'Laughlin M.D., Schaller M.E., Fewell G.A., Delehaunty K.D., Miner T.L. expand/collapse author list , Nash W.E., Cordes M., Du H., Sun H., Edwards J., Bradshaw-Cordum H., Ali J., Andrews S., Isak A., Vanbrunt A., Nguyen C., Du F., Lamar B., Courtney L., Kalicki J., Ozersky P., Bielicki L., Scott K., Holmes A., Harkins R., Harris A., Strong C.M., Hou S., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Leonard S., Rohlfing T., Rock S.M., Tin-Wollam A.-M., Abbott A., Minx P., Maupin R., Strowmatt C., Latreille P., Miller N., Johnson D., Murray J., Woessner J.P., Wendl M.C., Yang S.-P., Schultz B.R., Wallis J.W., Spieth J., Bieri T.A., Nelson J.O., Berkowicz N., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Bedell J.A., Mardis E.R., Clifton S.W., Chissoe S.L., Marra M.A., Raymond C., Haugen E., Gillett W., Zhou Y., James R., Phelps K., Iadanoto S., Bubb K., Simms E., Levy R., Clendenning J., Kaul R., Kent W.J., Furey T.S., Baertsch R.A., Brent M.R., Keibler E., Flicek P., Bork P., Suyama M., Bailey J.A., Portnoy M.E., Torrents D., Chinwalla A.T., Gish W.R., Eddy S.R., McPherson J.D., Olson M.V., Eichler E.E., Green E.D., Waterston R.H., Wilson R.K.
Nature 424:157-164(2003) [PubMed: 12853948] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed: 15489334] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT ALA-42.
Tissue: Eye and Muscle.
[6]"Primary structure and functional expression of human glycyl-tRNA synthetase, an autoantigen in myositis."
Ge Q., Trieu E.P., Targoff I.N.
J. Biol. Chem. 269:28790-28797(1994) [PubMed: 7961834] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 3-739, VARIANT ALA-42.
[7]"Complex organisation of the 5'-end of the human glycine tRNA synthetase gene."
Mudge S.J., Williams J.H., Eyre H.J., Sutherland G.R., Cowan P.J., Power D.A.
Gene 209:45-50(1998) [PubMed: 9524218] [Abstract]
Cited for: SUBCELLULAR LOCATION.
[8]"Lysine acetylation targets protein complexes and co-regulates major cellular functions."
Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T., Olsen J.V., Mann M.
Science 325:834-840(2009) [PubMed: 19608861] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-204; LYS-219 AND LYS-501, MASS SPECTROMETRY.
[9]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed: 21269460] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[10]"Crystal structure of human wildtype and S581L-mutant glycyl-tRNA synthetase, an enzyme underlying distal spinal muscular atrophy."
Cader M.Z., Ren J., James P.A., Bird L.E., Talbot K., Stammers D.K.
FEBS Lett. 581:2959-2964(2007) [PubMed: 17544401] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS) OF 55-739, SUBUNIT, MUTAGENESIS OF SER-635, BIOPHYSICOCHEMICAL PROPERTIES.
[11]"Long-range structural effects of a Charcot-Marie-Tooth disease-causing mutation in human glycyl-tRNA synthetase."
Xie W., Nangle L.A., Zhang W., Schimmel P., Yang X.-L.
Proc. Natl. Acad. Sci. U.S.A. 104:9976-9981(2007) [PubMed: 17545306] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.85 ANGSTROMS) OF 55-739, VARIANT ARG-580, SUBUNIT.
[12]"Crystal structures and biochemical analyses suggest a unique mechanism and role for human glycyl-tRNA synthetase in Ap4A homeostasis."
Guo R.-T., Chong Y.E., Guo M., Yang X.-L.
J. Biol. Chem. 284:28968-28976(2009) [PubMed: 19710017] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS) OF 55-739 IN COMPLEX WITH ATP; SUBSTRATE AND SUBSTRATE ANALOGS, FUNCTION.
[13]"Glycyl tRNA synthetase mutations in Charcot-Marie-Tooth disease type 2D and distal spinal muscular atrophy type V."
Antonellis A., Ellsworth R.E., Sambuughin N., Puls I., Abel A., Lee-Lin S.Q., Jordanova A., Kremensky I., Christodoulou K., Middleton L.T., Sivakumar K., Ionasescu V., Funalot B., Vance J.M., Goldfarb L.G., Fischbeck K.H., Green E.D.
Am. J. Hum. Genet. 72:1293-1299(2003) [PubMed: 12690580] [Abstract]
Cited for: VARIANTS CMT2D GLY-125 AND ARG-294, VARIANTS HMN5 PRO-183 AND ARG-580, TISSUE SPECIFICITY.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
D30658 mRNA. Translation: BAA06338.1.
U09510 mRNA. Translation: AAA86443.1. Different initiation.
AK074524 mRNA. Translation: BAG51964.1.
AK295490 mRNA. Translation: BAG58412.1.
AC005154 Genomic DNA. No translation available.
AC006969 Genomic DNA. No translation available.
AC004976 Genomic DNA. Translation: AAC71652.1.
BC007722 mRNA. Translation: AAH07722.1.
BC007755 mRNA. Translation: AAH07755.1.
U09587 mRNA. Translation: AAA57001.1. Different initiation.
IPIIPI00783097.
PIRA55314.
RefSeqNP_002038.2. NM_002047.2.
UniGeneHs.404321.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2PMEX-ray2.90A55-739[»]
2PMFX-ray2.85A55-739[»]
2Q5HX-ray3.00A55-739[»]
2Q5IX-ray2.80A55-739[»]
2ZT5X-ray2.50A55-739[»]
2ZT6X-ray3.08A55-739[»]
2ZT7X-ray2.70A55-739[»]
2ZT8X-ray3.35A55-739[»]
2ZXFX-ray3.40A55-739[»]
ProteinModelPortalP41250.
SMRP41250. Positions 65-108, 117-727.
ModBaseSearch...

Protein-protein interaction databases

IntActP41250. 4 interactions.
MINTMINT-1395438.
STRINGP41250.

PTM databases

PhosphoSiteP41250.

Polymorphism databases

DMDM21264523.

Proteomic databases

PRIDEP41250.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000389266; ENSP00000373918; ENSG00000106105.
GeneID2617.
KEGGhsa:2617.
UCSCuc003tbm.1. human.

Organism-specific databases

CTD2617.
GeneCardsGC07P030600.
H-InvDBHIX0006570.
HGNCHGNC:4162. GARS.
HPAHPA017896.
HPA019097.
MIM600287. gene.
600794. phenotype.
601472. phenotype.
neXtProtNX_P41250.
Orphanet99938. Autosomal dominant Charcot-Marie-Tooth disease type 2D.
139536. Distal hereditary motor neuropathy type 5.
PharmGKBPA28575.
GenAtlasSearch...

Phylogenomic databases

eggNOGprNOG14046.
HOGENOMHBG319978.
HOVERGENHBG036190.
InParanoidP41250.
OMAGSITWAD.
OrthoDBEOG4RV2QV.
PhylomeDBP41250.

Enzyme and pathway databases

BRENDA6.1.1.14. 2681.
ReactomeREACT_71. Gene Expression.

Gene expression databases

ArrayExpressP41250.
BgeeP41250.
CleanExHS_GARS.
GenevestigatorP41250.
GermOnlineENSG00000106105. Homo sapiens.

Family and domain databases

InterProIPR002314. aa-tRNA-synt_IIb_cons-dom.
IPR006195. aa-tRNA-synth_II.
IPR004154. Anticodon-bd.
IPR009068. S15_NS1_RNA-bd.
IPR002315. tRNA-synt_gly.
IPR000738. WHEP-TRS.
[Graphical view]
Gene3DG3DSA:3.40.50.800. Anticodon_bd. 1 hit.
G3DSA:1.10.287.10. S15_NS1_RNA_bd. 1 hit.
KOK01880.
PANTHERPTHR10745. tRNA-synt_gly. 1 hit.
PfamPF03129. HGTP_anticodon. 1 hit.
PF00587. tRNA-synt_2b. 1 hit.
PF00458. WHEP-TRS. 1 hit.
[Graphical view]
PRINTSPR01043. TRNASYNTHGLY.
SMARTSM00991. WHEP-TRS. 1 hit.
[Graphical view]
SUPFAMSSF52954. Anticodon_bd. 1 hit.
TIGRFAMsTIGR00389. GlyS_dimeric. 1 hit.
PROSITEPS50862. AA_TRNA_LIGASE_II. 1 hit.
PS00762. WHEP_TRS_1. 1 hit.
PS51185. WHEP_TRS_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

DrugBankDB00145. Glycine.
NextBio10303.
PMAP-CutDBP41250.
SOURCESearch...

Entry information

Entry nameSYG_HUMAN
AccessionPrimary (citable) accession number: P41250
Secondary accession number(s): B3KQA2, B4DIA0, Q969Y1
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: November 30, 2010
Last modified: January 25, 2012
This is version 125 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Relevant documents

Aminoacyl-tRNA synthetases

List of aminoacyl-tRNA synthetase entries

Human chromosome 7

Human chromosome 7: entries, gene names and cross-references to MIM

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families