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(-) Description

Title :  CRYSTAL STRUCTURE OF RESVERATROL BOUND HUMAN TYROSYL TRNA SYNTHETASE
 
Authors :  S. Mathew, P. Schimmel
Date :  28 Apr 14  (Deposition) - 17 Dec 14  (Release) - 25 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Resveratrol, Aminoacyl Trna Synthetases, Amino Acid Activation, Active Site, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Sajish, P. Schimmel
A Human Trna Synthetase Is A Potent Parp1-Activating Effector Target For Resveratrol.
Nature V. 519 370 2014
PubMed-ID: 25533949  |  Reference-DOI: 10.1038/NATURE14028

(-) Compounds

Molecule 1 - TYROSINE--TRNA LIGASE, CYTOPLASMIC
    Chains: A
    EC Number: 6.1.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: MINI TYRRS (UNP RESIDUES 1-364)
    Gene: YARS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TYROSYL-TRNA SYNTHETASE, TYRRS

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 12)

Asymmetric Unit (5, 12)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3PO42Ligand/IonPHOSPHATE ION
4SO46Ligand/IonSULFATE ION
5STL1Ligand/IonRESVERATROL
Biological Unit 1 (4, 22)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL4Ligand/IonGLYCEROL
3PO44Ligand/IonPHOSPHATE ION
4SO412Ligand/IonSULFATE ION
5STL2Ligand/IonRESVERATROL

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:39 , GLY A:41 , LEU A:72 , HIS A:77 , TYR A:166 , GLN A:170 , ASP A:173 , GLN A:182 , HOH A:583 , HOH A:654 , HOH A:711BINDING SITE FOR RESIDUE STL A 401
02AC2SOFTWARELYS A:282 , TRP A:283 , HOH A:555 , HOH A:595BINDING SITE FOR RESIDUE SO4 A 402
03AC3SOFTWARELYS A:26 , ARG A:34BINDING SITE FOR RESIDUE SO4 A 403
04AC4SOFTWAREHIS A:305 , PRO A:306 , GLY A:307 , HOH A:567 , HOH A:570BINDING SITE FOR RESIDUE SO4 A 404
05AC5SOFTWAREHIS A:12 , ARG A:16BINDING SITE FOR RESIDUE SO4 A 405
06AC6SOFTWARELYS A:114 , ASP A:280 , GLU A:281 , HOH A:687 , HOH A:690 , HOH A:694 , HOH A:709BINDING SITE FOR RESIDUE SO4 A 406
07AC7SOFTWAREALA A:51 , GLY A:217 , LEU A:218 , THR A:219 , LYS A:231 , HOH A:556 , HOH A:607 , HOH A:638 , HOH A:718BINDING SITE FOR RESIDUE SO4 A 407
08AC8SOFTWARELYS A:265 , HIS A:266 , HOH A:725 , HOH A:726BINDING SITE FOR RESIDUE CL A 408
09AC9SOFTWARESER A:126 , LYS A:127 , GLU A:128 , HIS A:143 , LYS A:146BINDING SITE FOR RESIDUE GOL A 409
10BC1SOFTWAREHOH A:729BINDING SITE FOR RESIDUE GOL A 410
11BC2SOFTWAREARG A:189BINDING SITE FOR RESIDUE PO4 A 411
12BC3SOFTWARELYS A:265BINDING SITE FOR RESIDUE PO4 A 412

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q93)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:4 -Pro A:5

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q93)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q93)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q93)

(-) 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:330
                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhh...eeehhhhhhhhhhhh..eeeeeee.....hhhhhhhhhhhhhhhhhh.eeeeeeehhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhh..hhhhhhhhhhhhh..hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhh....eeeee...............hhhhhhhhhhh..........hhhhhhhhhhhhhhhh.eee..hhhhh..eee.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4q93 A   4 APSPEEKLHLITRNLQEVLGEEKLKEILKERELKIYWGTATTGKPHVAYFVPMSKIADFLKAGCEVTILFADLHAYLDNMKAPWELLELRVSYYENVIKAMLESIGVPLEKLKFIKGTDYQLSKEYTLDVYRLSSVVTQHDSKKAGAEVVKQVEHPLLSGLLYPGLQALDEEYLKVDAQFGGIDQRKIFTFAEKYLPALGYSKRVHLMNPMVPGLTGSKIDLLDRKEDVKKKLKKAFCEPGNVENNGVLSFIKHVLFPLKSEFVILRDEKWGGNKTYTAYVDLEKDFAAEVVHPGDLKNSVEVALNKLLDPIREKFNTPALKKLASAAYP 342
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213      |232       242       252       262       272       282       292       302       312       322       332       342
                                                                                                                                                                                                                                                  220|                                                                                                                
                                                                                                                                                                                                                                                   230
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  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 4Q93)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q93)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q93)

(-) Gene Ontology  (21, 21)

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  4q93
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  6.1.1.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        SYYC_HUMAN | P54577: 1n3l 1ntg 1q11 4qbt 5thh 5thl

(-) Related Entries Specified in the PDB File

1n3l 1q11 4qbt