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(-) Description

Title :  EDITING DOMAIN OF THREONYL-TRNA SYNTHETASE FROM METHANOCOCCUS JANNASCHII WITH L-THR3AA
 
Authors :  S. Ahmad, A. S. K. Yerabham, V. Kamarthapu, R. Sankaranarayanan
Date :  06 Nov 14  (Deposition) - 15 Jul 15  (Release) - 15 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Dtd-Like Fold, Proofreading, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ahmad, S. Muthukumar, S. K. Kuncha, S. B. Routh, A. S. Yerabham, T. Hussain, V. Kamarthapu, S. P. Kruparani, R. Sankaranarayanan
Specificity And Catalysis Hardwired At The Rna-Protein Interface In A Translational Proofreading Enzyme.
Nat Commun V. 6 7552 2015
PubMed-ID: 26113036  |  Reference-DOI: 10.1038/NCOMMS8552

(-) Compounds

Molecule 1 - THREONINE--TRNA LIGASE
    Chains: A, B, C, D
    EC Number: 6.1.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-141
    Gene: THRS, MJ1197
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 243232
    Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
    Synonym: THREONYL-TRNA SYNTHETASE, THRRS

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1A3T3Ligand/Ion3'-DEOXY-3'-(L-THREONYLAMINO)ADENOSINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1A3T2Ligand/Ion3'-DEOXY-3'-(L-THREONYLAMINO)ADENOSINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1A3T1Ligand/Ion3'-DEOXY-3'-(L-THREONYLAMINO)ADENOSINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:25 , ILE A:44 , VAL A:46 , PRO A:81 , TYR A:82 , ALA A:83 , HIS A:84 , SER A:90 , ALA A:95 , PHE A:118 , GLY A:119 , HOH A:601 , GLU B:135BINDING SITE FOR RESIDUE A3T A 501
2AC2SOFTWAREGLU A:135 , ILE B:25 , ILE B:44 , VAL B:46 , TYR B:82 , ALA B:83 , HIS B:84 , LEU B:89 , SER B:90 , ALA B:95 , PHE B:118 , GLY B:119 , TYR B:121 , HOH B:302 , HOH B:344BINDING SITE FOR RESIDUE A3T B 201
3AC3SOFTWAREILE C:25 , ILE C:44 , VAL C:46 , TYR C:82 , ALA C:83 , HIS C:84 , LEU C:89 , SER C:90 , ALA C:95 , PHE C:118 , GLY C:119 , HOH C:302 , GLU D:135BINDING SITE FOR RESIDUE A3T C 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4RRG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RRG)

(-) 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:138
                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeeeee..........eeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhh....hhhhhhhhhhhhhhhhhhh..eeee....eeeeeeeee......eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4rrg A   5 MKMLLIHSDYLEFEAKEKTKIAEETENLKGKLDECLACFIAVEREDENNPEGTAIGAVEEIEKVANQLKVNNIVVYPYAHLSSDLSSPETAVKVLKDIESILKERGYNVLRAPFGWYKAFKISCKGHPLSELSRKIVA 142
                                    14        24        34        44        54        64        74        84        94       104       114       124       134        


Chain B from PDB  Type:PROTEIN  Length:138
                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeeeee..........eeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhh....hhhhhhhhhhhhhhhhhhh..eeee....eeeeeeeee......eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4rrg B   5 MKMLLIHSDYLEFEAKEKTKIAEETENLKGKLDECLACFIAVEREDENNPEGTAIGAVEEIEKVANQLKVNNIVVYPYAHLSSDLSSPETAVKVLKDIESILKERGYNVLRAPFGWYKAFKISCKGHPLSELSRKIVA 142
                                    14        24        34        44        54        64        74        84        94       104       114       124       134        


Chain C from PDB  Type:PROTEIN  Length:137
                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeeeee..........eeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhh....hhhhhhhhhhhhhhhhhhh..eeee....eeeeeeeee......eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rrg C   5 MKMLLIHSDYLEFEAKEKTKIAEETENLKGKLDECLACFIAVEREDENNPEGTAIGAVEEIEKVANQLKVNNIVVYPYAHLSSDLSSPETAVKVLKDIESILKERGYNVLRAPFGWYKAFKISCKGHPLSELSRKIV 141
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       


Chain D from PDB  Type:PROTEIN  Length:138
                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeeeee..........eeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhh....hhhhhhhhhhhhhhhhhhh..eeee....eeeeeeeee......eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4rrg D   5 MKMLLIHSDYLEFEAKEKTKIAEETENLKGKLDECLACFIAVEREDENNPEGTAIGAVEEIEKVANQLKVNNIVVYPYAHLSSDLSSPETAVKVLKDIESILKERGYNVLRAPFGWYKAFKISCKGHPLSELSRKIVA 142
                                    14        24        34        44        54        64        74        84        94       104       114       124       134
   Legend:   → Mismatch (orange background)
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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 4RRG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        SYT_METJA | Q58597: 4rrf

(-) Related Entries Specified in the PDB File

4rr6 4rr7 4rr8 4rr9 4rra 4rrb 4rrc 4rrd 4rrf 4rrh 4rri 4rrj 4rrk 4rrl 4rrm 4rrq 4rrr