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Title :  CRYSTAL STRUCTURE OF THE K93R MUTANT OF THE OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM SACCHAROMYCES CEREVISIAE
 
Authors :  A. A. Fedorov, E. V. Fedorov, B. M. Wood, J. A. Gerlt, S. C. Almo
Date :  24 Feb 09  (Deposition) - 09 Feb 10  (Release) - 09 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Orotidine 5'-Monophosphate Decarboxylase, Saccharomyces Cerevisiae, K93R Mutant, Decarboxylase, Lyase, Phosphoprotein, Pyrimidine Biosynthesis, Ubl Conjugation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. A. Fedorov, E. V. Fedorov, B. M. Wood, J. A. Gerlt, S. C. Almo
Crystal Structure Of The K93R Mutant Of The Orotidine 5'-Monophosphate Decarboxylase From Saccharomyces Cerevisiae.
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 Taxid562
    GeneURA3, YEL021W
    MutationYES
    Organism CommonYEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymOMP DECARBOXYLASE, OMPDECASE, OMPDCASE, URIDINE 5'-MONOPHOSPHATE SYNTHASE, UMP SYNTHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3GDM)

(-) Sites  (0, 0)

(no "Site" information available for 3GDM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_PYRF_YEAST_001 *A160SPYRF_YEAST  ---  ---A/BA160S
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OMPDECASEPS00156 Orotidine 5'-phosphate decarboxylase active site.PYRF_YEAST88-101
 
  2A:88-101
B:88-101

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YEL021W1YEL021W.1V:116167-116970804PYRF_YEAST1-2672672A:3-263
B:3-262 (gaps)
261
260

(-) 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:261
 aligned with PYRF_YEAST | P03962 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:261
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262 
           PYRF_YEAST     3 KATYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEALGPKICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFEDRKFADIGNTVKLQYSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLMLAELSCKGSLATGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIMTPGVGLDDKGDALGQQYRTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGERYRKAGWEAYLRRC 263
               SCOP domains d3gdma_ A: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains 3gdmA00 A:3-263 Aldolase class I                                                                                                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh.hhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhh.eeeehhhhh.......hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhh...hhhhhh.eeeee.hhhhhhhhhhhhhhhhhh....eeeee..........hhhhhhhhhhhhh.....eeeee......hhhhh...eeee..ee.......hhhhheehhhhhhh...eeeehhhhh....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------OMPDECASE     ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:3-263 UniProt: 1-267 [INCOMPLETE]                                                                                                                                                                                                                    Transcript 1
                 3gdm A   3 KATYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEALGPKICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFEDRRFADIGNTVKLQYSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLMLAELSCKGSLATGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIMTPGVGLDDKGDALGQQYRTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGERYRKAGWEAYLRRC 263
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262 

Chain B from PDB  Type:PROTEIN  Length:249
 aligned with PYRF_YEAST | P03962 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:260
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262
           PYRF_YEAST     3 KATYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEALGPKICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFEDRKFADIGNTVKLQYSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLMLAELSCKGSLATGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIMTPGVGLDDKGDALGQQYRTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGERYRKAGWEAYLRR 262
               SCOP domains d3gdmb_ B: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains 3gdmB00 B:3-262 Aldolase class I                                                                                                                                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh.hhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhh.eeeehhhhh.......hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhh...hhhhhh.eeeee.hhhhhhhhhhhhhhhhhh....eeeee..........hhhhhhhhhhhhhh....eeeee......hhhhh...eeee.....-----------.hhhhhhhhh..eeeehhhhh....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------OMPDECASE     ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:3-262 (gaps) UniProt: 1-267 [INCOMPLETE]                                                                                                                                                                                                            Transcript 1
                 3gdm B   3 KATYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEALGPKICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFEDRRFADIGNTVKLQYSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLMLAELSCKGSLATGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIMTPGVGL-----------RTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGERYRKAGWEAYLRR 262
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202   |     -     | 222       232       242       252       262
                                                                                                                                                                                                                                     206         218                                            

   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, 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 3GDM)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PYRF_YEAST | P03962)
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:0006222    UMP biosynthetic process    The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        PYRF_YEAST | P039621dqw 1dqx 3gdk 3gdl 3gdr 3gdt

(-) Related Entries Specified in the PDB File

1dqw CRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE DECARBOXYLASE (THE SAME PROTEIN WITH DIFFERENT UNIT CELL PARAMETERS)
3gdk CRYSTAL STRUCTURE OF THE OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM SACCHAROMYCES CEREVISIAE (THE SAME PROTEIN IN WT FORM)
3gdl CRYSTAL STRUCTURE OF THE OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH 6-AZAURIDINE 5'-MONOPHOSPHATE
3gdr CRYSTAL STRUCTURE OF THE D91N MUTANT OF THE OROTIDINE 5'- MONOPHOSPHATE DECARBOXYLASE FROM SACCHAROMYCES CEREVISIAE
3gdt CRYSTAL STRUCTURE OF THE D91N MUTANT OF THE OROTIDINE 5'- MONOPHOSPHATE DECARBOXYLASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH 6-AZAURIDINE 5'-MONOPHOSPHATE