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(-) Description

Title :  GLYCYL-TRNA SYNTHETASE MUTANT E71G IN COMPLEX WITH TRNA-GLY
 
Authors :  X. Qin, Z. Hao, Q. Tian, Z. Zhang, C. Zhou, W. Xie
Date :  16 May 13  (Deposition) - 21 May 14  (Release) - 13 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.23
Chains :  Asym. Unit :  A,C
Biol. Unit 1:  A,C  (2x)
Keywords :  Rossmann Fold, Aminoacylation, Trna-Gly, Ligase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Qin, Z. Hao, Q. Tian, Z. Zhang, C. Zhou, W. Xie
Cocrystal Structures Of Glycyl-Trna Synthetase In Complex With Trna Suggest Multiple Conformational States In Glycylation
J. Biol. Chem. V. 289 20359 2014
PubMed-ID: 24898252  |  Reference-DOI: 10.1074/JBC.M114.557249

(-) 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 114-739
    Gene: GARS
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DIADENOSINE TETRAPHOSPHATE SYNTHETASE, AP-4-A SYNTHETASE, GLYCYL-TRNA SYNTHETASE, GLYRS
 
Molecule 2 - GLY-TRNA-CCC
    Chains: C
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: RNA IS IN-VITRO TRANSCRIBED.
    Synonym: TRNA-GLY
    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  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2GLY1Mod. Amino AcidGLYCINE
3GTP1Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2GLY2Mod. Amino AcidGLYCINE
3GTP2Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:245 , GLU A:296 , ARG A:410 , GLU A:522 , SER A:524 , ANP A:702BINDING SITE FOR RESIDUE GLY A 701
2AC2SOFTWAREARG A:277 , GLU A:279 , LEU A:286 , ILE A:287 , ARG A:288 , VAL A:289 , PHE A:292 , HIS A:378 , ASP A:392 , GLU A:403 , ILE A:404 , SER A:524 , GLY A:526 , ARG A:529 , GLY A:701BINDING SITE FOR RESIDUE ANP A 702

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4KR3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:265 -Pro A:266

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KR3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KR3)

(-) Exons   (0, 0)

(no "Exon" information available for 4KR3)

(-) 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:467
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..eee.hhhhh.....eeehhhhhhhhhhhhhhhhhhhhhhhh........eeehhhhhhh............eee.......eeee...hhhhhhhhhhhhhhhh.....eeeeeeeeee..............eeeeeeeeeee........hhhhh...eeeeehhhhhhh....eeeehhhhhh.....hhhhhhhhhhhhhhhhhh......eeeee.......eeeeeeee..eeeeeeeeeee..hhhhhhhhhhh....eeeeeeeeeeee...eeeeeeeee..eeeeeeeehhhhhhhhhhhheee.......eee..hhhhh...eeeee...hhhhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhh...eeeeehhhhhh....eeeeee.....eeeee..hhhhhhhhhhh...hhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kr3 A  65 VDRAKMGDTLKRRFFYDQAFAIYGGVSGLYDFGPVGCALKNNIIQTWRQHFIQEEQILEIDCTMLTPEPVLKTSGHVDKFSFNLMFKTFIGPGGNMPGYLRPETAQGIFLNFKRLLEFNQGKLPFAAAQIGNSFRNEISPRSGLIRVREFTMAEIEHFVDPSEKDHPKFQNVADLHLYLYSAKAQVSGQSARKMRLGDAVEQGVINNTVLGYFIGRIYLYLTKVGISPDKLRFRQHMENACDCWDAESKTSYGWIEIVGCADRSCYDLSCHARATKVPLVAEKPLKEPKTVNVVFQKTLYVEEVVPNVIEPSFGLGRIMYTVFEHTFHVREGDEQRTFFSFPAVVAPFKCSVLPLSQNQEFMPFVKELSEALTRHGVSHKVDDSSGSIGRRYARTDEIGVAFGVTIDFDTVNKTPHTATLRDRDSMRQIRAEISELPSIVQDLANGNITWADVEARYPLFEGQETGG 701
                                    74        84        94       104       114       124       134       144|      232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       387       397       407       417       427       437   ||  512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672     ||
                                                                                                         144|                                                                                                                                                           381|                                                   441|                                                                                                                                                                        678|
                                                                                                          223                                                                                                                                                            387                                                    507                                                                                                                                                                         701


Chain C from PDB  Type:RNA  Length:70
                                                                                                      
                 4kr3 C   1 gCGCCGCUGGUGUAGUGGUAUCAUGCAAGAUUCCCAUUCUUGCGACCCGGGUUCGAUUCCCGGGCGGCGC  72
                            |       10     || 21        31        41    ||  52        62        72
                            |             16|                          46|                        
                            1-GTP          18                           48
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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 4KR3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KR3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KR3)

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)

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  4kr3
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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 4qei 5e6m

(-) Related Entries Specified in the PDB File

4kqe 4kr2