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(-) Description

Title :  CRYSTAL STRUCTURE OF A MUTANT M. JANNASHII TYROSYL-TRNA SYNTHETASE
 
Authors :  X. Luo, G. Fu, X. Zhu, I. A. Wilson, F. Wang
Date :  01 Dec 16  (Deposition) - 07 Jun 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.03
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A (1x),B (1x)
Keywords :  Tyrosine Phosphorylation, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Luo, G. Fu, R. E. Wang, X. Zhu, C. Zambaldo, R. Liu, T. Liu, X. Lyu, J. Du W. Xuan, A. Yao, S. A. Reed, M. Kang, Y. Zhang, H. Guo, C. Huang, P. Y. Yang I. A. Wilson, P. G. Schultz, F. Wang
Genetically Encoding Phosphotyrosine And Its Nonhydrolyzabl Analog In Bacteria.
Nat. Chem. Biol. 2017
PubMed-ID: 28604693  |  Reference-DOI: 10.1038/NCHEMBIO.2405

(-) Compounds

Molecule 1 - TYROSINE--TRNA LIGASE
    Chains: A, B
    EC Number: 6.1.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: TYRS, MJ0389
    Mutation: YES
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII (STRAIN ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
    Organism Taxid: 243232
    Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
    Synonym: TYROSYL-TRNA SYNTHETASE,TYRRS

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5U36)

(-) Sites  (0, 0)

(no "Site" information available for 5U36)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5U36)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:251 -Pro A:252
2Tyr B:251 -Pro B:252

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5U36)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5U36)

(-) Exons   (0, 0)

(no "Exon" information available for 5U36)

(-) 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:294
                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhh...ee.hhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhhhhh.eeeeeee.......hhhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhh....eeeee........................hhhhhhhhhhh..........hhhhhhhhhhh...eee..hhhhh..eee.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5u36 A   2 DEFEMIKRNTSEIISEEELREVLKKDEKSASIGFEPSGKIHLGHYLQIKKMIDLQNAGFDIIIALADLHAYELDEIRKIGDYNKKVFEAMGLKAKYVYGSLDKDYTLNVYRLALKTTLKRARRSMELIARPKVAEVIYPIMQVNGIHYKGVDVAVGGMEQRKIHMLARELLPKKVVCIHNPVLTGLDGEGKMSSSKGNFIAVDDSPEEIRAKIKKAYCPAGVVEGNPIMEIAKYFLEYPLTIKRPEKFGGDLTVNSYEELESLFKNKELHPMDLKNAVAEELIKILEPIRKRLL 307
                                    11        21        31        41        51        61        71||      86        96       106|      119       129       139|      153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303    
                                                                                                 72|                         106|                          139|                                                                                                                                                                   
                                                                                                  78                          110                           144                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:294
                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhh...ee.hhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhh..hhhhhhhh.......hhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhh....eeeee........................hhhhhhhhhhhh.........hhhhhhhhhhh...eee..hhhhh..eee.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5u36 B   2 DEFEMIKRNTSEIISEEELREVLKKDEKSASIGFEPSGKIHLGHYLQIKKMIDLQNAGFDIIIALADLHAYELDEIRKIGDYNKKVFEAMGLKAKYVYGSLDKDYTLNVYRLALKTTLKRARRSMELIARPKVAEVIYPIMQVNGIHYKGVDVAVGGMEQRKIHMLARELLPKKVVCIHNPVLTGLDGEGKMSSSKGNFIAVDDSPEEIRAKIKKAYCPAGVVEGNPIMEIAKYFLEYPLTIKRPEKFGGDLTVNSYEELESLFKNKELHPMDLKNAVAEELIKILEPIRKRLL 307
                                    11        21        31        41        51        61        71||      86        96       106|      119       129       139|      153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303    
                                                                                                 72|                         106|                          139|                                                                                                                                                                   
                                                                                                  78                          110                           144
   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 5U36)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5U36)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5U36)

(-) Gene Ontology  (12, 12)

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  Ligands, Modified Residues, Ions
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  Sites
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  Cis Peptide Bonds
    Tyr A:251 - Pro A:252   [ RasMol ]  
    Tyr B:251 - Pro B:252   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        SYY_METJA | Q57834: 1j1u 1u7d 1u7x 1zh0 1zh6 2ag6 2hgz 2pxh 2zp1 3d6u 3d6v 3n2y 3qe4 4hjr 4hjx 4hk4 4hpw 4nd6 4nd7 4nda 4nx2 4pbr 4pbs 4pbt

(-) Related Entries Specified in the PDB File

1j1u CRYSTAL STRUCTURE OF ARCHAEAL TYROSYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(TYR) AND L-TYROSINE
1u7d CRYSTAL STRUCTURE OF APO M. JANNASHII TYROSYL-TRNA SYNTHETASE