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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN GLYCYL-TRNA SYNTHETASE (GLYRS) IN COMPLEX WITH AP4A (COCRYSTALLIZED WITH ATP)
 
Authors :  R. T. Guo, X. L. Yang, P. Schimmel
Date :  19 Sep 08  (Deposition) - 25 Aug 09  (Release) - 25 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Ligase, Ap4A, Glycine, Atp, Gly-Amp, Trna, Aminoacyl-Trna Synthetase, Atp-Binding, Charcot-Marie-Tooth Disease, Disease Mutation, Nucleotide-Binding, Phosphoprotein, Protein Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. T. Guo, Y. E. Chong, M. Guo, X. L. Yang
Crystal Structures And Biochemical Analyses Suggest Unique Mechanism And Role For Human Glyrs In Ap4A Homeostasis
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCYL-TRNA SYNTHETASE
    ChainsA
    EC Number6.1.1.14
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21A
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 55-739
    GeneGARS
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGLYCINE-TRNA LIGASE, GLYRS

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1B4P1Ligand/IonBIS(ADENOSINE)-5'-TETRAPHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1B4P2Ligand/IonBIS(ADENOSINE)-5'-TETRAPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:146 , ARG A:159 , ASP A:193 , LEU A:226 , ARG A:277 , GLU A:279 , ILE A:287 , ARG A:288 , VAL A:289 , PHE A:292 , MET A:294 , ASN A:381 , GLU A:382 , GLU A:403 , ILE A:404 , VAL A:405 , GLY A:406 , GLY A:526 , ARG A:529 , HOH A:918 , HOH A:919 , HOH A:920 , HOH A:1021BINDING SITE FOR RESIDUE B4P A1101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZT5)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:265 -Pro A:266
2Thr A:626 -Pro A:627

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (15, 15)

Asymmetric Unit (15, 15)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_018718E125GGARS_HUMANDisease (CMT2D)28936972AE71G
02UniProtVAR_018719L183PGARS_HUMANDisease (HMN5A)137852644AL129P
03UniProtVAR_073188D200NGARS_HUMANDisease (CMT2D)  ---AD146N
04UniProtVAR_074016D200YGARS_HUMANDisease (CMT2D)  ---AD146Y
05UniProtVAR_073189S265FGARS_HUMANDisease (CMT2D)  ---AS211F
06UniProtVAR_054866T268IGARS_HUMANPolymorphism2230310AT214I
07UniProtVAR_074017M292RGARS_HUMANDisease (CMT2D)  ---AM238R
08UniProtVAR_018720G294RGARS_HUMANDisease (CMT2D)137852643AG240R
09UniProtVAR_073190P298LGARS_HUMANDisease (CMT2D)137852648AP244L
10UniProtVAR_073191I334FGARS_HUMANDisease (CMT2D)  ---AI280F
11UniProtVAR_054867R388QGARS_HUMANPolymorphism17159287AR334Q
12UniProtVAR_073192H472RGARS_HUMANDisease (HMN5A)  ---AH418R
13UniProtVAR_018721G580RGARS_HUMANDisease (HMN5A)28937323AG526R
14UniProtVAR_073194S635LGARS_HUMANPolymorphism201358272AS581L
15UniProtVAR_073195G652AGARS_HUMANDisease (CMT2D)  ---AG598A

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (15, 30)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_018718E125GGARS_HUMANDisease (CMT2D)28936972AE71G
02UniProtVAR_018719L183PGARS_HUMANDisease (HMN5A)137852644AL129P
03UniProtVAR_073188D200NGARS_HUMANDisease (CMT2D)  ---AD146N
04UniProtVAR_074016D200YGARS_HUMANDisease (CMT2D)  ---AD146Y
05UniProtVAR_073189S265FGARS_HUMANDisease (CMT2D)  ---AS211F
06UniProtVAR_054866T268IGARS_HUMANPolymorphism2230310AT214I
07UniProtVAR_074017M292RGARS_HUMANDisease (CMT2D)  ---AM238R
08UniProtVAR_018720G294RGARS_HUMANDisease (CMT2D)137852643AG240R
09UniProtVAR_073190P298LGARS_HUMANDisease (CMT2D)137852648AP244L
10UniProtVAR_073191I334FGARS_HUMANDisease (CMT2D)  ---AI280F
11UniProtVAR_054867R388QGARS_HUMANPolymorphism17159287AR334Q
12UniProtVAR_073192H472RGARS_HUMANDisease (HMN5A)  ---AH418R
13UniProtVAR_018721G580RGARS_HUMANDisease (HMN5A)28937323AG526R
14UniProtVAR_073194S635LGARS_HUMANPolymorphism201358272AS581L
15UniProtVAR_073195G652AGARS_HUMANDisease (CMT2D)  ---AG598A

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZT5)

(-) Exons   (14, 14)

Asymmetric Unit (14, 14)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003892661aENSE00000832199chr7:30634297-30634759463GARS_HUMAN1-74740--
1.3ENST000003892663ENSE00001698528chr7:30638412-30638513102GARS_HUMAN75-108340--
1.4ENST000003892664ENSE00001722229chr7:30639563-30639665103GARS_HUMAN109-143351A:64-8926
1.5ENST000003892665ENSE00001788958chr7:30640675-30640816142GARS_HUMAN143-190481A:89-13648
1.6bENST000003892666bENSE00000674849chr7:30642650-3064273889GARS_HUMAN190-220311A:136-16631
1.7ENST000003892667ENSE00000674850chr7:30643112-3064318877GARS_HUMAN220-245261A:166-19126
1.8ENST000003892668ENSE00000674851chr7:30649201-30649346146GARS_HUMAN246-294491A:192-24049
1.9ENST000003892669ENSE00000674852chr7:30651712-30651861150GARS_HUMAN294-344511A:240-29051
1.11ENST0000038926611ENSE00000674853chr7:30655512-30655674163GARS_HUMAN344-398551A:290-34455
1.12ENST0000038926612ENSE00000674854chr7:30656730-30656894165GARS_HUMAN399-453551A:345-39955
1.13aENST0000038926613aENSE00001505312chr7:30661009-30661116108GARS_HUMAN454-489361A:400-43132
1.14bENST0000038926614bENSE00001505311chr7:30661933-30662078146GARS_HUMAN490-538490--
1.15ENST0000038926615ENSE00000674858chr7:30665850-3066593586GARS_HUMAN538-567301A:512-5132
1.17cENST0000038926617cENSE00001788803chr7:30668176-30668285110GARS_HUMAN567-603371A:513-54937
1.18bENST0000038926618bENSE00001796643chr7:30671064-3067115794GARS_HUMAN604-635321A:550-58132
1.19dENST0000038926619dENSE00000674864chr7:30671863-30672053191GARS_HUMAN635-698641A:581-64464
1.20bENST0000038926620bENSE00001907883chr7:30673351-30673649299GARS_HUMAN699-739411A:645-67329

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:530
 aligned with GARS_HUMAN | P41250 from UniProtKB/Swiss-Prot  Length:739

    Alignment length:610
                                   127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727
           GARS_HUMAN   118 IVDRAKMEDTLKRRFFYDQAFAIYGGVSGLYDFGPVGCALKNNIIQTWRQHFIQEEQILEIDCTMLTPEPVLKTSGHVDKFADFMVKDVKNGECFRADHLLKAHLQKLMSDKKCSVEKKSEMESVLAQLDNYGQQELADLFVNYNVKSPITGNDLSPPVSFNLMFKTFIGPGGNMPGYLRPETAQGIFLNFKRLLEFNQGKLPFAAAQIGNSFRNEISPRSGLIRVREFTMAEIEHFVDPSEKDHPKFQNVADLHLYLYSAKAQVSGQSARKMRLGDAVEQGVINNTVLGYFIGRIYLYLTKVGISPDKLRFRQHMENEMAHYACDCWDAESKTSYGWIEIVGCADRSCYDLSCHARATKVPLVAEKPLKEPKTVNVVQFEPSKGAIGKAYKKDAKLVMEYLAICDECYITEMEMLLNEKGEFTIETEGKTFQLTKDMINVKRFQKTLYVEEVVPNVIEPSFGLGRIMYTVFEHTFHVREGDEQRTFFSFPAVVAPFKCSVLPLSQNQEFMPFVKELSEALTRHGVSHKVDDSSGSIGRRYARTDEIGVAFGVTIDFDTVNKTPHTATLRDRDSMRQIRAEISELPSIVQDLANGNITWADVEARYPLFE 727
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2zt5A01 A:64-142,A:227-552 Bira Bifunctional Protein; Domain 2                 ------------------------------------------------------------------------------------2zt5A01 A:64-142,A:227-552 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                                                                        2zt5A03 A:553-673  [code=3.40.50.800, no name defined]                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..eee.hhhhh.....eeehhhhhhhhhhhhhhhhhhhhhhhh.ee.....eeehhhhhhhhhhhhheeeeee......eeehhhhhhhhhhhhhhh...hhhhhhhhhhhhh.....hhhhhhhhhhhh..............eeee...eee.......eeee...hhhhhhhhhhhhhhhh.....eeeeeeeeee.......hhhhh..eeeeeeeeeee........hhhhh...eeeeehhhhhhh....eeeehhhhhhh....hhhhhhhhhhhhhhhhhhh.hhh.eeeee.hhhhh......eeeeeeee..eeeeeeeee...hhhhhhhhhhhh....eee.--------------------------------------------------------------------------------..eee..eeeeeeeehhhhhhhhhhhheee.......eee..........eeeee......hhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhh...eeeeehhhhhh....eeeeee.....eeeee..hhhhhhhhhhh...hhhhhhhhh.... Sec.struct. author
             SAPs(SNPs) (1) -------G---------------------------------------------------------P----------------N----------------------------------------------------------------F--I-----------------------R-R---L-----------------------------------F-----------------------------------------------------Q-----------------------------------------------------------------------------------R-----------------------------------------------------------------------------------------------------------R------------------------------------------------------L----------------A--------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------Y----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4  PDB: A:64-89    ----------------------------------------------Exon 1.6b  PDB: A:136-166      -------------------------Exon 1.8  PDB: A:192-240 UniProt: 246-294        -------------------------------------------------Exon 1.11  PDB: A:290-344 UniProt: 344-398             Exon 1.12  PDB: A:345-399 UniProt: 399-453             Exon 1.13a  PDB: A:400-431          Exon 1.14b  PDB: - UniProt: 490-538              ----------------------------Exon 1.17c  PDB: A:513-549           Exon 1.18b  PDB: A:550-581      ---------------------------------------------------------------Exon 1.20b  PDB: A:645-673    Transcript 1 (1)
           Transcript 1 (2) -------------------------Exon 1.5  PDB: A:89-136 UniProt: 143-190        -----------------------------Exon 1.7  PDB: A:166-191  ------------------------------------------------Exon 1.9  PDB: A:240-290 UniProt: 294-344          -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.15  PDB: A:512-513     -------------------------------------------------------------------Exon 1.19d  PDB: A:581-644 UniProt: 635-698                     ----------------------------- Transcript 1 (2)
                 2zt5 A  64 IVDRAKMEDTLKRRFFYDQAFAIYGGVSGLYDFGPVGCALKNNIIQTWRQHFIQEEQILEIDCTMLTPEPVLKTSGHVDKFADFMVKDVKNGECFRADHLLKAHLQKLMSDKKCSVEKKSEMESVLAQLDNYGQQELADLFVNYNVKSPITGNDLSPPVSFNLMFKTFIGPGGNMPGYLRPETAQGIFLNFKRLLEFNQGKLPFAAAQIGNSFRNEISPRSGLIRVREFTMAEIEHFVDPSEKDHPKFQNVADLHLYLYSAKAQVSGQSARKMRLGDAVEQGVINNTVLGYFIGRIYLYLTKVGISPDKLRFRQHMENEMAHYACDCWDAESKTSYGWIEIVGCADRSCYDLSCHARATKVPLVAEKP--------------------------------------------------------------------------------YVEEVVPNVIEPSFGLGRIMYTVFEHTFHVREGDEQRTFFSFPAVVAPFKCSVLPLSQNQEFMPFVKELSEALTRHGVSHKVDDSSGSIGRRYARTDEIGVAFGVTIDFDTVNKTPHTATLRDRDSMRQIRAEISELPSIVQDLANGNITWADVEARYPLFE 673
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       | -         -         -         -         -         -         -         -       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673
                                                                                                                                                                                                                                                                                                                                                                                                         431                                                                              512                                                                                                                                                                 

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2ZT5)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2ZT5)

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)
Chain A   (GARS_HUMAN | P41250)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004812    aminoacyl-tRNA ligase activity    Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
    GO:0004820    glycine-tRNA ligase activity    Catalysis of the reaction: ATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-tRNA(Gly).
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
biological process
    GO:0015966    diadenosine tetraphosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of diadenosine tetraphosphate, a derivative of the nucleoside adenosine with four phosphate groups attached.
    GO:0006426    glycyl-tRNA aminoacylation    The process of coupling glycine to glycyl-tRNA, catalyzed by glycyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA.
    GO:0006418    tRNA aminoacylation for protein translation    The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, to be used in ribosome-mediated polypeptide synthesis.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0030141    secretory granule    A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        GARS_HUMAN | P412502pme 2pmf 2q5h 2q5i 2zt6 2zt7 2zt8 2zxf 4kqe 4kr2 4kr3 4qei 5e6m

(-) Related Entries Specified in the PDB File

2pme THE SAMPLE PROTEIN (APO FORM)
2pmf G526R MUTANT
2zt6
2zt7
2zt8