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(-) Description

Title :  ALANYL-TRNA SYNTHETASE EDITING DOMAIN HOMOLOGUE PROTEIN FROM PYROCOCCUS HORIKOSHII
 
Authors :  A. Okada, M. Yao, M. Sokabe, I. Tanaka
Date :  18 Dec 03  (Deposition) - 13 Jan 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.62
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase (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
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PH0574
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1V7O)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V7O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V7O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V7O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V7O)

(-) Exons   (0, 0)

(no "Exon" information available for 1V7O)

(-) Sequences/Alignments

Asymmetric/Biological 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: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 d1v7oa_ A: Hypothetical protein PH0574                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhh...........eeeeee...eeee.......hhhhh..eeeeeeeee....eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v7o A   1 mYSIEVRTHSALHVVKGAVVKVLGSEAKWTYSTYVKGNKGVLIVKFDRKPSDEEIREIERLANEKVKENAPIKIYELPREEAEKmFGEDmYDLFPVPEDVRILKVVVIEDWNVNACNKEHTKTTGEIGPIKIRKVRFRKSKGLLEIHFELLELEN 155
                            |       10        20        30        40        50        60        70        80    |   90       100       110       120       130       140       150     
                            |                                                                                  85-MSE|                                                                 
                            1-MSE                                                                                   90-MSE                                                             


Chain B from PDB  Type:PROTEIN  Length:153
 aligned with ALAXS_PYRHO | O58307 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150   
          ALAXS_PYRHO     1 MYSIEVRTHSALHVVKGAVVKVLGSEAKWTYSTYVKGNKGVLIVKFDRKPSDEEIREIERLANEKVKENAPIKIYELPREEAEKMFGEDMYDLFPVPEDVRILKVVVIEDWNVNACNKEHTKTTGEIGPIKIRKVRFRKSKGLLEIHFELLEL 153
               SCOP domains d1v7ob_ B: Hypothetical protein PH0574                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------tRNA_SAD-1v7oB01 B:103-143               ---------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------tRNA_SAD-1v7oB02 B:103-143               ---------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhh..........eeeeeee...eeee.......hhhhh..eeeeeeeee....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v7o B   1 mYSIEVRTHSALHVVKGAVVKVLGSEAKWTYSTYVKGNKGVLIVKFDRKPSDEEIREIERLANEKVKENAPIKIYELPREEAEKmFGEDmYDLFPVPEDVRILKVVVIEDWNVNACNKEHTKTTGEIGPIKIRKVRFRKSKGLLEIHFELLEL 153
                            |       10        20        30        40        50        60        70        80    |   90       100       110       120       130       140       150   
                            1-MSE                                                                              85-MSE|                                                               
                                                                                                                    90-MSE
   Legend:   → Mismatch (orange background)
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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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1V7O)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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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  1v7o
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 Related Entries

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

UniProtKB/Swiss-Prot
        ALAXS_PYRHO | O58307: 1v4p 1wnu 1wxo 3rfn 3rhu

(-) Related Entries Specified in the PDB File

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