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(-) Description

Title :  CRYSTAL STRUCTURE OF TRANS EDITING ENZYME PROX FROM E.COLI
 
Authors :  M. Kato-Murayama, K. Murayama, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  25 Aug 06  (Deposition) - 25 Feb 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.58
Chains :  Asym./Biol. Unit :  A
Keywords :  Trans-Editing Domain, Prolyl-Trna Synthetase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kato-Murayama, K. Murayama, T. Terada, M. Shirouzu, S. Yokoyama
Crystal Structure Of Trans Editing Enzyme Prox From E. Coli
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN YBAK
    Chains: A
    Engineered: YES
    Expression System Plasmid: PX060110-16
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: CELL-FREE PROTEIN SYNTHESIS
    Synonym: PUTATIVE TRANS-EDITING ENZYME FOR PROLYL-TRNA SYNTHETASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:70 , LEU A:72 , HOH A:1397BINDING SITE FOR RESIDUE CL A 1201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DXA)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DXA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DXA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DXA)

(-) Exons   (0, 0)

(no "Exon" information available for 2DXA)

(-) 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:158
 aligned with YBAK_ECOLI | P0AAR3 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        
           YBAK_ECOLI     1 MTPAVKLLEKNKISFQIHTYEHDPAETNFGDEVVKKLGLNPDQVYKTLLVAVNGDMKHLAVAVTPVAGQLDLKKVAKALGAKKVEMADPMVAQRSTGYLVGGISPLGQKKRLPTIIDAPAQEFATIYVSGGKRGLDIELAAGDLAKILDAKFADIARR 158
               SCOP domains d2dxaa_ A: automated matches                                                                                                                                   SCOP domains
               CATH domains -2dxaA00 A:2-158  [code=3.90.960.10, no name defined]                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh....eeee...........hhhhhhhh.....eeeeeeeee..eeeeeeeeeee...eehhhhhhhhhh...eee.hhhhhhhhhh................eeee.hhhhh..eeeeeee..eeeeehhhhhhhhhh.eee..ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dxa A   1 mTPAVKLLEKNKISFQIHTYEHDPAETNFGDEVVKKLGLNPDQVYKTLLVAVNGDmKHLAVAVTPVAGQLDLKKVAKALGAKKVEmADPmVAQRSTGYLVGGISPLGQKKRLPTIIDAPAQEFATIYVSGGKRGLDIELAAGDLAKILDAKFADIARR 158
                            |       10        20        30        40        50     |  60        70        80     |  90       100       110       120       130       140       150        
                            |                                                     56-MSE                        86-MSE                                                                    
                            1-MSE                                                                                   90-MSE
   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, 1)

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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DXA)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (YBAK_ECOLI | P0AAR3)
molecular function
    GO:0043906    Ala-tRNA(Pro) hydrolase activity    Catalysis of the hydrolysis of misacylated Ala-tRNA(Pro).
    GO:0043907    Cys-tRNA(Pro) hydrolase activity    Catalysis of the hydrolysis of misacylated Cys-tRNA(Pro).
    GO:0002161    aminoacyl-tRNA editing activity    The hydrolysis of an incorrectly aminoacylated tRNA.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
    GO:0006450    regulation of translational fidelity    Any process that modulates the ability of the translational apparatus to interpret the genetic code.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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