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(-) Description

Title :  1.77 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE DECARBOXYLASE FROM VIBRIO CHOLERAE O1 BIOVAR ELTOR STR. N16961
 
Authors :  A. S. Halavaty, L. Shuvalova, G. Minasov, I. Dubrovska, J. Winsor, E. M. Glass, S. N. Peterson, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
Date :  13 Jan 10  (Deposition) - 26 Jan 10  (Release) - 26 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Orotidine 5'-Phosphate Decarboxylase, Structural Genomics, Infectious Diseases, Center For Structural Genomics Of Infectious Diseases, Decarboxylase, Lyase, Pyrimidine Biosynthesis, Csgid (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. S. Halavaty, L. Shuvalova, G. Minasov, I. Dubrovska, J. Winsor, E. M. Glass, S. N. Peterson, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
1. 77 Angstrom Resolution Crystal Structure Of Orotidine 5'-Phosphate Decarboxylase From Vibrio Cholerae O1 Biovar Eltor Str. N16961
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
    ChainsA, B
    EC Number4.1.1.23
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMCSG7
    Expression System StrainBL21(DE3)CODONPLUS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentOROTIDINE 5'-PHOSPHATE DECARBOXYLASE
    GenePYRF, VC_1911
    Organism ScientificVIBRIO CHOLERAE O1 BIOVAR EL TOR
    Organism Taxid243277
    StrainN16961
    SynonymOMP DECARBOXYLASE, OMPDCASE, OMPDECASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:26 , HOH A:330 , HOH A:487 , HOH A:516BINDING SITE FOR RESIDUE MG A 232
2AC2SOFTWAREPRO A:67 , ASN A:68BINDING SITE FOR RESIDUE CL A 233
3AC3SOFTWAREILE A:25 , ASP A:26 , THR A:29 , GLU A:220BINDING SITE FOR RESIDUE CL A 234
4AC4SOFTWAREPRO B:67 , ASN B:68BINDING SITE FOR RESIDUE CL B 232
5AC5SOFTWAREGLY B:107 , LYS B:108 , GLN B:128 , HOH B:328BINDING SITE FOR RESIDUE CL B 233

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LDV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LDV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LDV)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OMPDECASEPS00156 Orotidine 5'-phosphate decarboxylase active site.PYRF_VIBCH57-70
 
  2A:57-70
B:57-70

(-) Exons   (0, 0)

(no "Exon" information available for 3LDV)

(-) 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:231
 aligned with PYRF_VIBCH | Q9KQT7 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:231
                             1                                                                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229 
           PYRF_VIBCH     - -MNDPKVIVALDYDNLADALAFVDKIDPSTCRLKVGKEMFTLFGPDFVRELHKRGFSVFLDLKFHDIPNTCSKAVKAAAELGVWMVNVHASGGERMMAASREILEPYGKERPLLIGVTVLTSMESADLQGIGILSAPQDHVLRLATLTKNAGLDGVVCSAQEASLLKQHLGREFKLVTPGIRPAGSEQGDQRRIMTPAQAIASGSDYLVIGRPITQAAHPEVVLEEINSSL 230
               SCOP domains d3ldva_ A: automated matches                                                                                                                                                                                                            SCOP domains
               CATH domains 3ldvA00 A:0-230 Aldolase class I                                                                                                                                                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhhhhheeeeehhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhhh.eeeee......hhhhhhhh....hhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhh...eeeee................hhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------OMPDECASE     ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ldv A   0 AMNDPKVIVALDYDNLADALAFVDKIDPSTCRLKVGKEMFTLFGPDFVRELHKRGFSVFLDLKFHDIPNTCSKAVKAAAELGVWMVNVHASGGERMMAASREILEPYGKERPLLIGVTVLTSMESADLQGIGILSAPQDHVLRLATLTKNAGLDGVVCSAQEASLLKQHLGREFKLVTPGIRPAGSEQGDQRRIMTPAQAIASGSDYLVIGRPITQAAHPEVVLEEINSSL 230
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229 

Chain B from PDB  Type:PROTEIN  Length:224
 aligned with PYRF_VIBCH | Q9KQT7 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:230
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231
           PYRF_VIBCH     2 NDPKVIVALDYDNLADALAFVDKIDPSTCRLKVGKEMFTLFGPDFVRELHKRGFSVFLDLKFHDIPNTCSKAVKAAAELGVWMVNVHASGGERMMAASREILEPYGKERPLLIGVTVLTSMESADLQGIGILSAPQDHVLRLATLTKNAGLDGVVCSAQEASLLKQHLGREFKLVTPGIRPAGSEQGDQRRIMTPAQAIASGSDYLVIGRPITQAAHPEVVLEEINSSLV 231
               SCOP domains d3ldvb_ B: automated matches                                                                                                                                                                                                           SCOP domains
               CATH domains 3ldvB00 B:2-231 Aldolase class I                                                                                                                                                                                                       CATH domains
           Pfam domains (1) --OMPdecase-3ldvB01 B:4-226                                                                                                                                                                                                      ----- Pfam domains (1)
           Pfam domains (2) --OMPdecase-3ldvB02 B:4-226                                                                                                                                                                                                      ----- Pfam domains (2)
         Sec.struct. author ....eeeee...hhhhhhhhhh.......eeeeehhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhhh.eeeee......hhhhhhhh....hhhhhhhhhhhhhhhh...eee....hhhhhhhhhh...eeeee.....------.....hhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------OMPDECASE     ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ldv B   2 NDPKVIVALDYDNLADALAFVDKIDPSTCRLKVGKEMFTLFGPDFVRELHKRGFSVFLDLKFHDIPNTCSKAVKAAAELGVWMVNVHASGGERMMAASREILEPYGKERPLLIGVTVLTSMESADLQGIGILSAPQDHVLRLATLTKNAGLDGVVCSAQEASLLKQHLGREFKLVTPGIRPA------QRRIMTPAQAIASGSDYLVIGRPITQAAHPEVVLEEINSSLV 231
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181 |     191       201       211       221       231
                                                                                                                                                                                                               183    190                                         

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PYRF_VIBCH | Q9KQT7)
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.
    GO:0009220    pyrimidine ribonucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyrimidine ribonucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a 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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