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(-) Description

Title :  CRYSTAL STRUCTURE OF ALANYL-TRNA SYNTHETASE FROM PYROCOCCUS HORIKOSHII OT3
 
Authors :  J. Ishijima, K. Yutani, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  14 Nov 03  (Deposition) - 23 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  A,C  (1x)
Keywords :  Alanyl-Trna Synthetase, Alanine-Trna Ligase, Pyrococcus Horikoshii, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Ishijima, Y. Uchida, C. Kuroishi, C. Tuzuki, N. Takahashi, N. Okazaki, K. Yutani, M. Miyano
Crystal Structure Of Alanyl-Trna Synthetase Editing-Domain Homolog (Ph0574) From A Hyperthermophile, Pyrococcus Horikoshii Ot3 At 1. 45 A Resolution
Proteins V. 62 1133 2006
PubMed-ID: 16374837  |  Reference-DOI: 10.1002/PROT.20760
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALANYL-TRNA SYNTHETASE
    Chains: A, B, C
    EC Number: 6.1.1.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C
Biological Unit 4 (1x): A 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
Biological Unit 4 (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 1V4P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V4P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V4P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V4P)

(-) Exons   (0, 0)

(no "Exon" information available for 1V4P)

(-) 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:151
 aligned with ALAXS_PYRHO | O58307 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 
          ALAXS_PYRHO     1 MYSIEVRTHSALHVVKGAVVKVLGSEAKWTYSTYVKGNKGVLIVKFDRKPSDEEIREIERLANEKVKENAPIKIYELPREEAEKMFGEDMYDLFPVPEDVRILKVVVIEDWNVNACNKEHTKTTGEIGPIKIRKVRFRKSKGLLEIHFELL 151
               SCOP domains d1v4pa_ A: Hypothetical protein PH0574                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhh..........eeeeeee...eeee.......hhhhh..eeeeeeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v4p A   1 MYSIEVRTHSALHVVKGAVVKVLGSEAKWTYSTYVKGNKGVLIVKFDRKPSDEEIREIERLANEKVKENAPIKIYELPREEAEKMFGEDMYDLFPVPEDVRILKVVVIEDWNVNACNKEHTKTTGEIGPIKIRKVRFRKSKGLLEIHFELL 151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 


Chain B from PDB  Type:PROTEIN  Length:151
 aligned with ALAXS_PYRHO | O58307 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 
          ALAXS_PYRHO     1 MYSIEVRTHSALHVVKGAVVKVLGSEAKWTYSTYVKGNKGVLIVKFDRKPSDEEIREIERLANEKVKENAPIKIYELPREEAEKMFGEDMYDLFPVPEDVRILKVVVIEDWNVNACNKEHTKTTGEIGPIKIRKVRFRKSKGLLEIHFELL 151
               SCOP domains d1v4pb_ B: Hypothetical protein PH0574                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhh..........eeeeeee...eeee.......hhhhh..eeeeeeee.....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v4p B   1 MYSIEVRTHSALHVVKGAVVKVLGSEAKWTYSTYVKGNKGVLIVKFDRKPSDEEIREIERLANEKVKENAPIKIYELPREEAEKMFGEDMYDLFPVPEDVRILKVVVIEDWNVNACNKEHTKTTGEIGPIKIRKVRFRKSKGLLEIHFELL 151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 


Chain C from PDB  Type:PROTEIN  Length:155
 aligned with ALAXS_PYRHO | O58307 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150     
          ALAXS_PYRHO     1 MYSIEVRTHSALHVVKGAVVKVLGSEAKWTYSTYVKGNKGVLIVKFDRKPSDEEIREIERLANEKVKENAPIKIYELPREEAEKMFGEDMYDLFPVPEDVRILKVVVIEDWNVNACNKEHTKTTGEIGPIKIRKVRFRKSKGLLEIHFELLELEN 155
               SCOP domains d1v4pc_ C: Hypothetical protein PH0574                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------tRNA_SAD-1v4pC01 C:103-143               ------------ Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------tRNA_SAD-1v4pC02 C:103-143               ------------ Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------tRNA_SAD-1v4pC03 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
                 1v4p C   1 MYSIEVRTHSALHVVKGAVVKVLGSEAKWTYSTYVKGNKGVLIVKFDRKPSDEEIREIERLANEKVKENAPIKIYELPREEAEKMFGEDMYDLFPVPEDVRILKVVVIEDWNVNACNKEHTKTTGEIGPIKIRKVRFRKSKGLLEIHFELLELEN 155
                                    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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1V4P)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: tRNA_SAD] (15)

(-) 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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        ALAXS_PYRHO | O58307: 1v7o 1wnu 1wxo 3rfn 3rhu

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