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(-) Description

Title :  STRUCTURE OF ARCHAEAL TRANS-EDITING PROTEIN ALAX IN COMPLEX WITH ZINC
 
Authors :  M. Sokabe, A. Okada, T. Nakashima, M. Yao, I. Tanaka
Date :  27 Jan 05  (Deposition) - 26 Jul 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Hydrolase, Trans-Editing (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Sokabe, A. Okada, M. Yao, T. Nakashima, I. Tanaka
Molecular Basis Of Alanine Discrimination In Editing Site
Proc. Natl. Acad. Sci. Usa V. 102 11669 2005
PubMed-ID: 16087889  |  Reference-DOI: 10.1073/PNAS.0502119102

(-) Compounds

Molecule 1 - ALANYL-TRNA SYNTHETASE
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET26B
    Expression System StrainBL21-CODONPLUS-(DE3)-RIL-X
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GenePH0574
    Organism ScientificPYROCOCCUS HORIKOSHII
    Organism Taxid70601
    StrainOT3
    SynonymTRANS-EDITING PROTEIN ALAX

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1ZN3Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:9 , HIS A:13 , CYS A:116 , HIS A:120BINDING SITE FOR RESIDUE ZN A 1001
2AC2SOFTWAREHIS B:9 , HIS B:13 , CYS B:116 , HIS B:120BINDING SITE FOR RESIDUE ZN B 1002
3AC3SOFTWAREHIS C:9 , HIS C:13 , CYS C:116 , HIS C:120BINDING SITE FOR RESIDUE ZN C 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WXO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WXO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WXO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WXO)

(-) Exons   (0, 0)

(no "Exon" information available for 1WXO)

(-) 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:152
 aligned with ALAXS_PYRHO | O58307 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  
          ALAXS_PYRHO     1 MYSIEVRTHSALHVVKGAVVKVLGSEAKWTYSTYVKGNKGVLIVKFDRKPSDEEIREIERLANEKVKENAPIKIYELPREEAEKMFGEDMYDLFPVPEDVRILKVVVIEDWNVNACNKEHTKTTGEIGPIKIRKVRFRKSKGLLEIHFELLE 152
               SCOP domains d1wxoa_ A: Hypothetical protein PH0574                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhh..........eeeeeee...eeee.......hhhhhh.eeeeeeee.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wxo A   1 MYSIEVRTHSALHVVKGAVVKVLGSEAKWTYSTYVKGNKGVLIVKFDRKPSDEEIREIERLANEKVKENAPIKIYELPREEAEKMFGEDMYDLFPVPEDVRILKVVVIEDWNVNACNKEHTKTTGEIGPIKIRKVRFRKSKGLLEIHFELLE 152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  

Chain B from PDB  Type:PROTEIN  Length:154
 aligned with ALAXS_PYRHO | O58307 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    
          ALAXS_PYRHO     1 MYSIEVRTHSALHVVKGAVVKVLGSEAKWTYSTYVKGNKGVLIVKFDRKPSDEEIREIERLANEKVKENAPIKIYELPREEAEKMFGEDMYDLFPVPEDVRILKVVVIEDWNVNACNKEHTKTTGEIGPIKIRKVRFRKSKGLLEIHFELLELE 154
               SCOP domains d1wxob_ B: Hypothetical protein PH0574                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhh..........eeeeeee...eeee.......hhhhhh.eeeeeeeee....eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wxo B   1 MYSIEVRTHSALHVVKGAVVKVLGSEAKWTYSTYVKGNKGVLIVKFDRKPSDEEIREIERLANEKVKENAPIKIYELPREEAEKMFGEDMYDLFPVPEDVRILKVVVIEDWNVNACNKEHTKTTGEIGPIKIRKVRFRKSKGLLEIHFELLELE 154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    

Chain C from PDB  Type:PROTEIN  Length:152
 aligned with ALAXS_PYRHO | O58307 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  
          ALAXS_PYRHO     1 MYSIEVRTHSALHVVKGAVVKVLGSEAKWTYSTYVKGNKGVLIVKFDRKPSDEEIREIERLANEKVKENAPIKIYELPREEAEKMFGEDMYDLFPVPEDVRILKVVVIEDWNVNACNKEHTKTTGEIGPIKIRKVRFRKSKGLLEIHFELLE 152
               SCOP domains d1wxoc_ C: Hypothetical protein PH0574                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------tRNA_SAD-1wxoC01 C:103-143               --------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------tRNA_SAD-1wxoC02 C:103-143               --------- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------tRNA_SAD-1wxoC03 C:103-143               --------- Pfam domains (3)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhh..........eeeeeee...eeee.......hhhhhh.eeeeeeeee....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wxo C   1 MYSIEVRTHSALHVVKGAVVKVLGSEAKWTYSTYVKGNKGVLIVKFDRKPSDEEIREIERLANEKVKENAPIKIYELPREEAEKMFGEDMYDLFPVPEDVRILKVVVIEDWNVNACNKEHTKTTGEIGPIKIRKVRFRKSKGLLEIHFELLE 152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 3)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1WXO)

(-) Pfam Domains  (1, 3)

Asymmetric Unit

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (ALAXS_PYRHO | O58307)
molecular function
    GO:0002161    aminoacyl-tRNA editing activity    The hydrolysis of an incorrectly aminoacylated tRNA.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0006450    regulation of translational fidelity    Any process that modulates the ability of the translational apparatus to interpret the genetic code.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ALAXS_PYRHO | O583071v4p 1v7o 1wnu 3rfn 3rhu

(-) Related Entries Specified in the PDB File

1v7o THE SAME PROTEIN IN APO-FORM
1wnu THE SAME PROTEIN IN COMPLEX WITH L-SERINE AND ZINC