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(-) Description

Title :  STRUCTURE OF ARCHAEAL TRANS-EDITING PROTEIN ALAX IN COMPLEX WITH L-SERINE
 
Authors :  M. Sokabe, A. Okada, T. Nakashima, M. Yao, I. Tanaka
Date :  09 Aug 04  (Deposition) - 26 Jul 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
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: BL21-CODONPLUS-(DE3)-RIL-X
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PH0574
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3
    Synonym: ALAX

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2SER2Mod. Amino AcidSERINE
3ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:9 , HIS A:13 , CYS A:116 , HIS A:120 , SER A:1002BINDING 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 A:9 , HIS A:13 , THR A:30 , THR A:33 , ASP A:92 , ASN A:114 , CYS A:116 , ZN A:1001 , HOH A:1026BINDING SITE FOR RESIDUE SER A 1002
4AC4SOFTWAREHIS B:13 , THR B:30 , ASP B:92 , ASN B:114 , HOH B:2008BINDING SITE FOR RESIDUE SER B 2001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WNU)

(-) 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: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 d1wnua_ A: Hypothetical protein PH0574                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhh..........eeeeeee...eeee.......hhhhh..eeeeeeeee....eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wnu A   1 mYSIEVRTHSALHVVKGAVVKVLGSEAKWTYSTYVKGNKGVLIVKFDRKPSDEEIREIERLANEKVKENAPIKIYELPREEAEKmFGEDmYDLFPVPEDVRILKVVVIEDWNVNACNKEHTKTTGEIGPIKIRKVRFRKSKGLLEIHFELLELE 154
                            |       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: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 d1wnub_ B: Hypothetical protein PH0574                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------tRNA_SAD-1wnuB01 B:103-143               --------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------tRNA_SAD-1wnuB02 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
                 1wnu B   1 mYSIEVRTHSALHVVKGAVVKVLGSEAKWTYSTYVKGNKGVLIVKFDRKPSDEEIREIERLANEKVKENAPIKIYELPREEAEKmFGEDmYDLFPVPEDVRILKVVVIEDWNVNACNKEHTKTTGEIGPIKIRKVRFRKSKGLLEIHFELLE 152
                            |       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)
  - → 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  (1, 2)

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

(-) CATH Domains  (0, 0)

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

(-) 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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  1wnu
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 Related Entries

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

UniProtKB/Swiss-Prot
        ALAXS_PYRHO | O58307: 1v4p 1v7o 1wxo 3rfn 3rhu

(-) Related Entries Specified in the PDB File

1v7o STRUCTURE ANALYSIS OF ALANYL-TRNA SYNTHETASE EDITING DOMAIN HOMOLOGUE PROTEIN FROM PYROCOCCUS HORIKOSHII