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(-) Description

Title :  TWO DISTINCT CONFORMATIONAL STATES OF GLYRS CAPTURED IN CRYSTAL LATTICE
 
Authors :  W. Xie, X. Qin, X. Deng, Q. Zhang, Q. Li
Date :  16 May 14  (Deposition) - 20 May 15  (Release) - 13 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.88
Chains :  Asym. Unit :  A,C
Biol. Unit 1:  A,C  (2x)
Keywords :  Aminoacyl-Trna Synthetase, Glycylation, Glycyl-Trna Synthetase, Trna Ligase, Ligase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Deng, X. Qin, L. Chen, Q. Jia, Y. Zhang, Z. Zhang, D. Lei, G. Ren, Z. Zhou, Z. Wang, Q. Li, W. Xie
Large Conformational Changes Of Insertion 3 In Human Glycyl-Trna Synthetase (Hglyrs) During Catalysis
J. Biol. Chem. V. 291 5740 2016
PubMed-ID: 26797133  |  Reference-DOI: 10.1074/JBC.M115.679126

(-) Compounds

Molecule 1 - GLYCINE--TRNA LIGASE
    Chains: A
    EC Number: 6.1.1.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 118-739
    Gene: GARS
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Strain: 293T
    Synonym: DIADENOSINE TETRAPHOSPHATE SYNTHETASE, AP-4-A SYNTHETASE, GLYCYL-TRNA SYNTHETASE, GLYRS
 
Molecule 2 - TRNA-GLY-CCC-2-2
    Chains: C
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: THE RNA IS OBTAINED FROM IN VITRO TRANSCRIPTION
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AC
Biological Unit 1 (2x): AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2GTP1Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2GTP2Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:277 , GLU A:279 , ILE A:287 , VAL A:289 , PHE A:292 , MET A:294 , GLU A:403 , ILE A:404 , GLY A:406 , SER A:524 , GLY A:526 , ARG A:529 , HOH A:805 , HOH A:823BINDING SITE FOR RESIDUE AMP A 701

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:265 -Pro A:266
2Lys A:483 -Gly A:484

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QEI)

(-) 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:562
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..eee.hhhhh.....eeehhhhhhhhhhhhhhhhhhhhhhh..ee.....eeehhhhhhhhhhhhh...ee.......eehhhhhhhh......hhhhhhhh......eeee.....eeeee...hhhhhhhhhhhhhhhh.....eeeeeeeeee.......hhhhh..eeeeeeeeeee........hhhhh...eeeeehhhhhhh....eeeehhhhhhh....hhhhhhhhhhhhhhhhhh..hhh.eeeee.....eeeeeee..eeeeeeeeee...hhhhhhhhhhh....eeeeeeeeeeeeeeeeeehhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhhhh....ee....ee...eeeeeeeeeeeeeee..eeeeeeeehhhhhhhhhhhheee.......eee..........eeeee...hhhhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhh...eeeeehhhhhhh...eeeeee.....eeeee..hhhhhhhhhhh...hhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qei A  64 IVDRAKMGDTLKRRFFYDQAFAIYGGVSGLYDFGPVGCALKNNIIQTWRQHFIQEEQILEIDCTMLTPEPVLKTSGHVDKFADFMVKDVKNGERFRADHLLKAHLQKLQQELADLFVNFNLMFKTFIGPGGNMPGYLRPETAQGIFLNFKRLLEFNQGKLPFAAAQIGNSFRNEISPRSGLIRVREFTMAEIEHFVDPSEKDHPKFQNVADLHLYLYSAKAQVSGQSARKMRLGDAVEQGVINNTVLGYFIGRIYLYLTKVGISPDKLRFRQHMEDCWDAESKTSYGWIEIVGCADRSCYDLSCHARATKVPLVAEKPLKEPKTVNVVQFEPSKGAIGKAYKKDAKLVMEYLAICDECYITEMEMLLNEKGEFTIETQLTKDMINVKRFQKTLYVEEVVPNVIEPSFGLGRIMYTVFEHTFHVREGDEQRTFFSFPAVVAPFKCSVLPLSQNQEFMPFVKELSEALTRHGVSHKVDDSSGSIGRRYARTDEIGVAFGVTIDFDTVNKTPHTATLRDRDSMRQIRAEISELPSIVQDLANGNITWADVEARYPLFEGQETGKK 680
                                    73        83        93       103       113       123       133       143       153       163       198       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375    || 393       403       413       423       433       443       453       463       473       483      |498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678  
                                                                                                                                     171|      206|                                                                                                                                                         380|                                                                                                  490|                                                                                                                                                                                        
                                                                                                                                      197       224                                                                                                                                                          389                                                                                                   496                                                                                                                                                                                        


Chain C from PDB  Type:RNA  Length:69
                                                                                                     
                 4qei C   1 gCGCCGCUGGUGUAGUGGUAUCAUGCAAGAUUCCCAUUCUUGCGACCCGGGUUCGAUUCCCGGGCGGCG  71
                            |       10     || 21        31        41    ||  52        62         
                            1-GTP         16|                          46|                       
                                           18                           48
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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  (0, 0)

(no "SCOP Domain" information available for 4QEI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)

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    Leu A:265 - Pro A:266   [ RasMol ]  
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  4qei
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  GARS_HUMAN | P41250
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  6.1.1.14
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 Related Entries

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

UniProtKB/Swiss-Prot
        GARS_HUMAN | P41250: 2pme 2pmf 2q5h 2q5i 2zt5 2zt6 2zt7 2zt8 2zxf 4kqe 4kr2 4kr3 5e6m

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4QEI)