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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC ASPARTYL-TRNA SYNTHETASE, A COMPONENT OF MULTI-TRNA SYNTHETASE COMPLEX
 
Authors :  K. R. Kim, S. H. Park, H. S. Kim, B. -G. Kim, D. G. Kim, K. H. Rhee, M. S. Park, S. Kim, B. W. Han
Date :  01 Feb 13  (Deposition) - 15 May 13  (Release) - 16 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.24
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aspartyl-Trna Synthetase, Trna, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. R. Kim, S. H. Park, H. S. Kim, K. H. Rhee, B. -G. Kim, D. G. Kim, M. S. Park H. -J. Kim, S. Kim, B. W. Han
Crystal Structure Of Human Cytosolic Aspartyl-Trna Synthetase, A Component Of Multi-Trna Synthetase Complex
Proteins V. 81 1840 2013
PubMed-ID: 23609930  |  Reference-DOI: 10.1002/PROT.24306

(-) Compounds

Molecule 1 - ASPARTATE--TRNA LIGASE, CYTOPLASMIC
    ChainsA, B
    EC Number6.1.1.12
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneDARS
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymASPARTYL-TRNA SYNTHETASE, ASPRS, CELL PROLIFERATION-INDUCING GENE 40 PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:63 , ALA A:64 , GLN A:82 , HOH A:783 , HOH A:876 , ASP B:261 , GOL B:602 , HOH B:819BINDING SITE FOR RESIDUE GOL A 601
2AC2SOFTWARESER A:32 , VAL A:144 , ILE A:145 , SER A:146 , LEU A:147 , ASP B:434 , HOH B:852BINDING SITE FOR RESIDUE GOL A 602
3AC3SOFTWAREGLN A:199 , GLU A:474 , SER A:490 , MET A:491 , PHE A:492 , GLN B:219 , PRO B:221BINDING SITE FOR RESIDUE GOL A 603
4AC4SOFTWARELYS A:40 , GOL A:605 , HIS B:300 , ARG B:345BINDING SITE FOR RESIDUE GOL A 604
5AC5SOFTWAREGLN A:38 , GOL A:604 , HOH A:843 , ARG B:408BINDING SITE FOR RESIDUE GOL A 605
6AC6SOFTWAREHIS A:204 , ARG A:207 , GLU A:208 , ILE A:211 , HOH A:768 , HIS B:204 , ARG B:207 , HOH B:799BINDING SITE FOR RESIDUE GOL B 601
7AC7SOFTWAREARG A:63 , GLN A:82 , GOL A:601 , PHE B:295 , ASN B:296 , HOH B:841BINDING SITE FOR RESIDUE GOL B 602
8AC8SOFTWARETYR A:297 , ARG B:43 , ASP B:115BINDING SITE FOR RESIDUE GOL B 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J15)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Glu A:341 -Pro A:342
2Arg A:494 -Asp A:495
3Glu B:341 -Pro B:342

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J15)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J15)

(-) Exons   (0, 0)

(no "Exon" information available for 4J15)

(-) Sequences/Alignments

Asymmetric/Biological 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:431
                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d4j15a1 A:21-152 automated matches                                                                                                  d4j15a2 A:153-495 automated matches                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh.eee...............hhhhhhhhhh..eeeeeeeeeeeeee..eeeeeeee..eeeeeeee.....hhhhhhhhhhh....eeeeeeeeee............eeeeeeeeeeee........hhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..ee.......hhhhhhhhhhhh...eeeeeeee....eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeeehhhhhhhhhhh..........hhhhhhhhhhhhhhhhh..eeeee..hhhhh...............eeeeee..eeeeeeee...hhhhhhhhhhhh...hhhhhhhhhh.......eeeeeeehhhhhhhhhh..hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j15 A  21 AEDYAKERYGISSMIQSQEKPDRVLVRVRDLTIQKADEVVWVRARVHTSRAKGKQCFLVLRQQQFNVQALVAVGDHASKQMVKFAANINKESIVDVEGVVRKVNQKIGSCTQQDVELHVQKIYVISLAEPRLPLQLDDAVRPTVNQDTRLDNRVIDLRTSTSQAVFRLQSGICHLFRETLINKGFVEIQTPKIQSPQLYKQMCICADFEKVFSIGPVFLTEFVGLDIEMAFNYHYHEVMEEIADTMVQIFKGLQERFQTEIQTVNKQFPCEPFKFLEPTLRLEYCEALAMLREAGVEMGDEDDLSTPNEKLLGHLVKEKYDTDFYILDKYPLAVRPFYTMPDPRNPKQSNSYDMFMRGEEILSGAQRIHDPQLLTERALHHGIDLEKIKAYIDSFRFGAPPHAGGGIGLERVTMLFLGLHNVRQTSMFPRD 495
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160 ||    180       190       200       210       220  ||   254       264       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494 
                                                                                                                                                                       162|                                               223|                     272|                                                                                                                                                                                                                    
                                                                                                                                                                        173                                                248                      283                                                                                                                                                                                                                    

Chain B from PDB  Type:PROTEIN  Length:430
                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4j15b1 B:21-152 automated matches                                                                                                  d4j15b2 B:153-495 automated matches                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh.eee...............hhhhhhhhhh..eeeeeeeeeeeeee..eeeeeeee..eeeeeeee.....hhhhhhhhhhh....eeeeeeeeee............eeeeeeeeeeee........hhhhhh....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..ee.......hhhhhhhhhhh...eeeeeeee....eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeeehhhhhhhhhhh..........hhhhhhhhhhhhhhhhh..eeeee..hhhhh...............eeeeee..eeeeeeee...hhhhhhhhhhhh......hhhhhhh.......eeeeeeehhhhhhhhh...hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j15 B  21 AEDYAKERYGISSMIQSQEKPDRVLVRVRDLTIQKADEVVWVRARVHTSRAKGKQCFLVLRQQQFNVQALVAVGDHASKQMVKFAANINKESIVDVEGVVRKVNQKIGSCTQQDVELHVQKIYVISLAEPRLPLQLDDAVRPTVNQDTRLDNRVIDLRTSTSQAVFRLQSGICHLFRETLINKGFVEIQTPKISPQLYKQMCICADFEKVFSIGPVFLTEFVGLDIEMAFNYHYHEVMEEIADTMVQIFKGLQERFQTEIQTVNKQFPCEPFKFLEPTLRLEYCEALAMLREAGVEMGDEDDLSTPNEKLLGHLVKEKYDTDFYILDKYPLAVRPFYTMPDPRNPKQSNSYDMFMRGEEILSGAQRIHDPQLLTERALHHGIDLEKIKAYIDSFRFGAPPHAGGGIGLERVTMLFLGLHNVRQTSMFPRD 495
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160 ||    180       190       200       210       220  ||   255       265      |285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495
                                                                                                                                                                       162|                                               223|                    272|                                                                                                                                                                                                                    
                                                                                                                                                                        173                                                249                     283                                                                                                                                                                                                                    

   Legend:   → Mismatch (orange background)
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  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  (2, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J15)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J15)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg A:494 - Asp A:495   [ RasMol ]  
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