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(-) Description

Title :  CRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE DECARBOXYLASE (TM0332) FROM THERMOTOGA MARITIMA AT 2.00 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  04 Jan 05  (Deposition) - 18 Jan 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Tm0332, Orotidine 5'-Phosphate Decarboxylase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Orotidine 5'-Phosphate Decarboxylase (Tm0332) From Thermotoga Maritima At 2. 00 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
    ChainsA
    EC Number4.1.1.23
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GenePYRF, TM0332
    Organism ScientificTHERMOTOGA MARITIMA
    Organism Taxid2336
    SynonymOMP DECARBOXYLASE, OMPDCASE, OMPDECASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric Unit (1, 9)
No.NameCountTypeFull Name
1EDO9Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 18)
No.NameCountTypeFull Name
1EDO18Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:36 , LYS A:37 , ASP A:40BINDING SITE FOR RESIDUE EDO A 202
2AC2SOFTWAREVAL A:164 , HOH A:248BINDING SITE FOR RESIDUE EDO A 203
3AC3SOFTWAREASP A:52 , LYS A:54 , LEU A:148 , PRO A:150 , EDO A:209BINDING SITE FOR RESIDUE EDO A 204
4AC4SOFTWARELEU A:47 , ALA A:73 , HOH A:269BINDING SITE FOR RESIDUE EDO A 205
5AC5SOFTWAREHIS A:-1 , HIS A:0BINDING SITE FOR RESIDUE EDO A 206
6AC6SOFTWARETHR A:166 , GLU A:168BINDING SITE FOR RESIDUE EDO A 207
7AC7SOFTWARESER A:60 , THR A:61 , ARG A:64 , ARG A:181 , EDO A:210BINDING SITE FOR RESIDUE EDO A 208
8AC8SOFTWARESER A:6 , ASP A:8 , LYS A:26 , EDO A:204 , HOH A:246BINDING SITE FOR RESIDUE EDO A 209
9AC9SOFTWAREASP A:8 , ARG A:64 , EDO A:208BINDING SITE FOR RESIDUE EDO A 210

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:82 -A:82

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OMPDECASEPS00156 Orotidine 5'-phosphate decarboxylase active site.PYRF_THEMA49-62  1A:49-62
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OMPDECASEPS00156 Orotidine 5'-phosphate decarboxylase active site.PYRF_THEMA49-62  2A:49-62

(-) Exons   (0, 0)

(no "Exon" information available for 1VQT)

(-) Sequences/Alignments

Asymmetric 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:191
 aligned with PYRF_THEMA | Q9WYG7 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:200
                              1                                                                                                                                                                                                     
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198
           PYRF_THEMA     - --MTPVLSLDMEDPIRFIDENGSFEVVKVGHNLAIHGKKIFDELAKRNLKIILDLKFCDIPSTVERSIKSWDHPAIIGFTVHSCAGYESVERALSATDKHVFVVVKLTSMEGSLEDYMDRIEKLNKLGCDFVLPGPWAKALREKIKGKILVPGIRMEVKADDQKDVVTLEEMKGIANFAVLGREIYLSENPREKIKRIKE 198
               SCOP domains --d1vqta1 A:1-198 Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --OMPdecase-1vqtA01 A:1-196                                                                                                                                                                           -- Pfam domains
         Sec.struct. author ...eeeee....hhhhhhhhhh...eeeehhhhhh..hhhhhhhhh...eeeeeeee..hhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhh..eeeee........hhhhhhhhhhhhhhh..eee.hhhhhhhhh......eee..ee---------..eehhhhh....eeeehhhhhh..hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------OMPDECASE     ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vqt A  -1 HHMTPVLSLDMEDPIRFIDENGSFEVVKVGHNLAIHGKKIFDELAKRNLKIILDLKFCDIPSTVERSIKSWDHPAIIGFTVHSCAGYESVERALSATDKHVFVVVKLTSMEGSLEDYMDRIEKLNKLGCDFVLPGPWAKALREKIKGKILVPGIR---------DVVTLEEMKGIANFAVLGREIYLSENPREKIKRIKE 198
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148    |    -    |  168       178       188       198
                                                                                                                                                                                    153       163                                   

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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 Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (PYRF_THEMA | Q9WYG7)
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.
cellular component
    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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