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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF ASPARTATE RACEMASE FROM PYROCOCCUS HORIKOSHII OT3
 
Authors :  L. Liu, K. Iwata, M. Yohda, K. Miki
Date :  28 Feb 02  (Deposition) - 09 Sep 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
Chains :  Asym./Biol. Unit :  A
Keywords :  Aspartate Racemase, C-Terminal Domain, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Liu, K. Iwata, M. Yohda, K. Miki
Structural Insight Into Gene Duplication, Gene Fusion And Domain Swapping In The Evolution Of Plp-Independent Amino Acid Racemases
Febs Lett. V. 528 114 2002
PubMed-ID: 12297289  |  Reference-DOI: 10.1016/S0014-5793(02)03264-7

(-) Compounds

Molecule 1 - ASPARTATE RACEMASE
    Chains: A
    EC Number: 5.1.1.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET23C
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN
    Gene: PPH0670E
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:115 , ASP A:204 , HOH A:243 , HOH A:244 , HOH A:245 , HOH A:256BINDING SITE FOR RESIDUE CA A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IU9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1IU9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IU9)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ASP_GLU_RACEMASE_2PS00924 Aspartate and glutamate racemases signature 2.RACD_PYRHO190-200  1A:190-200

(-) Exons   (0, 0)

(no "Exon" information available for 1IU9)

(-) 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:111
 aligned with RACD_PYRHO | O58403 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:111
                                   112       122       132       142       152       162       172       182       192       202       212 
           RACD_PYRHO   103 MIEETAKKVKELGFKKAGLLATTGTIVSGVYEKEFSKYGVEIMTPTEDEQKDVMRGIYEGVKAGNLKLGRELLLKTAKILEERGAECIIAGCTEVSVVLKQDDLKVPLIDP 213
               SCOP domains d1iu9a_ A: Aspartate racemase                                                                                   SCOP domains
               CATH domains 1iu9A00 A:103-213  [code=3.40.50.1860, no name defined]                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhh...ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------ASP_GLU_RAC------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 1iu9 A 103 MIEETAKKVKELGFKKAGLLATTGTIVSGVYEKEFSKYGVEIMTPTEDEQKDVMRGIYEGVKAGNLKLGRELLLKTAKILEERGAECIIAGCTEVSVVLKQDDLKVPLIDP 213
                                   112       122       132       142       152       162       172       182       192       202       212
   Legend:   → Mismatch (orange background)
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  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) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IU9)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RACD_PYRHO | O58403)
molecular function
    GO:0047689    aspartate racemase activity    Catalysis of the reaction: L-aspartate = D-aspartate.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0036361    racemase activity, acting on amino acids and derivatives    Catalysis of the interconversion of the two enantiomers of a chiral amino acid or amino acid derivative.
    GO:0016855    racemase and epimerase activity, acting on amino acids and derivatives    Catalysis of a reaction that alters the configuration of one or more chiral centers in an amino acid.
biological process
    GO:0006520    cellular amino acid metabolic process    The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0006807    nitrogen compound metabolic process    The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RACD_PYRHO | O58403: 1jfl 2dx7

(-) Related Entries Specified in the PDB File

1jfl IJFL CONTAINS ENTIRE PROTEIN.