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(-) Description

Title :  CRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE DECARBOXYLASE FROM PYROCOCCUS HORIKOSHII OT3 AT 1.6 A RESOLUTION
 
Authors :  R. Arai, K. Ito, T. Kamo-Uchikubo, M. Shirouzu, S. Yokoyama, Riken Str Genomics/Proteomics Initiative (Rsgi)
Date :  13 Jul 05  (Deposition) - 13 Jan 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pyrimidine Biosynthesis, Orotidine 5'-Phosphate Decarboxylase (Ompdecase), Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Arai, K. Ito, T. Kamo-Uchikubo, M. Shirouzu, S. Yokoyama
Crystal Structure Of Orotidine 5'-Phosphate Decarboxylase From Pyrococcus Horikoshii Ot3 At 1. 6 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
    ChainsA, B
    EC Number4.1.1.23
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET11A
    Expression System StrainBL21(DE3) CODONPLUS-RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GenePYRF, PH0731
    Organism ScientificPYROCOCCUS HORIKOSHII
    Organism Taxid70601
    StrainOT3
    SynonymOMP DECARBOXYLASE, OMPDCASE, OMPDECASE, PH0731

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
2GOL2Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:5 , ASP A:7 , LYS A:29 , ASN A:31 , HOH A:504 , HOH A:566 , HOH A:611 , HOH A:669 , ILE B:63 , THR B:66 , HOH B:249 , HOH B:275BINDING SITE FOR RESIDUE DTT A 501
2AC2SOFTWAREARG A:68 , ARG A:72 , LEU A:99BINDING SITE FOR RESIDUE GOL A 401
3AC3SOFTWAREHOH A:557 , HOH A:679BINDING SITE FOR RESIDUE GOL A 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OMPDECASEPS00156 Orotidine 5'-phosphate decarboxylase active site.PYRF_PYRHO54-67
 
  2A:54-67
B:54-67

(-) Exons   (0, 0)

(no "Exon" information available for 2CZD)

(-) 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:206
 aligned with PYRF_PYRHO | O58462 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      
           PYRF_PYRHO     1 MIVLALDVYEGERAIKIAKSVKDYISMIKVNWPLILGSGVDIIRRLKEETGVEIIADLKLADIPNTNRLIARKVFGAGADYVIVHTFVGRDSVMAVKELGEIIMVVEMSHPGALEFINPLTDRFIEVANEIEPFGVIAPGTRPERIGYIRDRLKEGIKILAPGIGAQGGKAKDAVKAGADYIIVGRAIYNAPNPREAAKAIYDEIR 206
               SCOP domains d2czda_ A: Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)                                                                                                                                        SCOP domains
               CATH domains 2czdA00 A:1-206 Aldolase class I                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....hhhhhhhhhhhhhhhh.eeeeehhhhhhhh.hhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhh..eeeee....hhhhhh.hhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhh....eeee.......hhhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------OMPDECASE     ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2czd A   1 MIVLALDVYEGERAIKIAKSVKDYISMIKVNWPLILGSGVDIIRRLKEETGVEIIADLKLADIPNTNRLIARKVFGAGADYVIVHTFVGRDSVMAVKELGEIIMVVEMSHPGALEFINPLTDRFIEVANEIEPFGVIAPGTRPERIGYIRDRLKEGIKILAPGIGAQGGKAKDAVKAGADYIIVGRAIYNAPNPREAAKAIYDEIR 206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      

Chain B from PDB  Type:PROTEIN  Length:207
 aligned with PYRF_PYRHO | O58462 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:207
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       
           PYRF_PYRHO     1 MIVLALDVYEGERAIKIAKSVKDYISMIKVNWPLILGSGVDIIRRLKEETGVEIIADLKLADIPNTNRLIARKVFGAGADYVIVHTFVGRDSVMAVKELGEIIMVVEMSHPGALEFINPLTDRFIEVANEIEPFGVIAPGTRPERIGYIRDRLKEGIKILAPGIGAQGGKAKDAVKAGADYIIVGRAIYNAPNPREAAKAIYDEIRG 207
               SCOP domains d2czdb_ B: Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)                                                                                                                                         SCOP domains
               CATH domains 2czdB00 B:1-207 Aldolase class I                                                                                                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....hhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhh..eeeee....hhhhhh.hhhhhhhhhhhhhhhh..eee.....hhhhhhhhh......eeee.......hhhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------OMPDECASE     -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2czd B   1 MIVLALDVYEGERAIKIAKSVKDYISMIKVNWPLILGSGVDIIRRLKEETGVEIIADLKLADIPNTNRLIARKVFGAGADYVIVHTFVGRDSVMAVKELGEIIMVVEMSHPGALEFINPLTDRFIEVANEIEPFGVIAPGTRPERIGYIRDRLKEGIKILAPGIGAQGGKAKDAVKAGADYIIVGRAIYNAPNPREAAKAIYDEIRG 207
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       

   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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PYRF_PYRHO | O58462)
molecular function
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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.
    GO:0004590    orotidine-5'-phosphate decarboxylase activity    Catalysis of the reaction: H(+) + orotidine 5'-phosphate = CO(2) + UMP.
biological process
    GO:0044205    'de novo' UMP biosynthetic process    The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD(+) or oxygen.
    GO:0006207    'de novo' pyrimidine nucleobase biosynthetic process    The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
    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:0006221    pyrimidine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PYRF_PYRHO | O584622cz5 2cze 2czf

(-) Related Entries Specified in the PDB File

2cz5 ORTHORHOMBIC FORM OF THE SAME PROTEIN (PH0731)
2cze THE SAME PROTEIN (PH0731) WITH UMP
2czf THE SAME PROTEIN (PH0731) WITH XMP RELATED ID: PHO001000731.1 RELATED DB: TARGETDB