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(-) Description

Title :  CRYSTAL STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM METALLOSPHAERA SEDULA COMPLEXED WITH INHIBITOR BMP
 
Authors :  A. A. Fedorov, E. V. Fedorov, B. Desai, J. A. Gerlt, S. C. Almo
Date :  07 Jan 12  (Deposition) - 09 Jan 13  (Release) - 09 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.54
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tim Barrel Fold, Orotidine 5'-Monophosphate Decarboxylase, Inhibitor Bmp, Lyase-Lyase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Fedorov, E. V. Fedorov, B. Desai, J. A. Gerlt, S. C. Almo
Crystal Structure Of Orotidine 5'-Monophosphate Decarboxylase From Metallosphaera Sedula Complexed With Inhibitor Bmp
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - OROTIDINE-5'-PHOSPHATE DECARBOXYLASE
    Chains: A, B
    EC Number: 4.1.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MSED_1966
    Organism Scientific: METALLOSPHAERA SEDULA DSM 5348
    Organism Taxid: 399549
    Strain: ATCC 51363 / DSM 5348

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1ACY3Ligand/IonACETIC ACID
2BMP2Ligand/Ion6-HYDROXYURIDINE-5'-PHOSPHATE
3SO43Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:7 , ASP A:9 , LYS A:28 , ASP A:56 , LYS A:58 , MET A:107 , SER A:108 , PRO A:157 , GLN A:162 , GLY A:180 , ARG A:181 , HOH A:402 , HOH A:405 , HOH A:413 , HOH A:416 , HOH A:417 , HOH A:421 , ASP B:61 , ILE B:62 , THR B:65BINDING SITE FOR RESIDUE BMP A 301
2AC2SOFTWAREARG A:138 , PRO A:139 , SER A:140BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWAREASP A:61 , ILE A:62 , THR A:65 , SER B:7 , ASP B:9 , LYS B:28 , ASP B:56 , LYS B:58 , MET B:107 , SER B:108 , PRO B:157 , GLN B:162 , GLY B:180 , ARG B:181 , HOH B:403 , HOH B:406 , HOH B:409 , HOH B:410 , HOH B:415 , HOH B:419BINDING SITE FOR RESIDUE BMP B 301
4AC4SOFTWAREPRO B:110 , ARG B:138 , HOH B:471BINDING SITE FOR RESIDUE ACY B 302
5AC5SOFTWAREHOH A:434 , HOH A:513 , GLY B:38 , LYS B:39 , GLU B:40 , HOH B:570BINDING SITE FOR RESIDUE ACY B 303
6AC6SOFTWARELEU B:35 , HOH B:446 , HOH B:456BINDING SITE FOR RESIDUE ACY B 304
7AC7SOFTWARESER B:186 , ARG B:191 , LYS B:192 , HOH B:575BINDING SITE FOR RESIDUE SO4 B 305
8AC8SOFTWAREARG B:138 , PRO B:139 , SER B:140BINDING SITE FOR RESIDUE SO4 B 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VE7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3VE7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VE7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VE7)

(-) Exons   (0, 0)

(no "Exon" information available for 3VE7)

(-) 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 A4YI54_METS5 | A4YI54 from UniProtKB/TrEMBL  Length:215

    Alignment length:206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      
         A4YI54_METS5     1 MNRVILSLDSPIPEETLRKLNGKVAGIKVGWPLLLNLGKEKVKELVGLVDGIKILDLKLADIDNTMILIVDELKDITNSFIAHAFVGVEGSLASLSQRVDLFLVLSMSHPGWNDAFYPYLREVARRVNPKGFVAPATRPSMISRVKGDFPDKLVISPGVGTQGAKPGIALCHGADYEIVGRSVYQSADPVRKLEEIVRSQEEVLSS 206
               SCOP domains d3ve7a_ A: automated matches                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....hhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhh....eeeee.hhh....hhhhhh..eeeee........hhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhh...eeee..........hhhhhh...eeeehhhhhh..hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ve7 A   1 MNRVILSLDSPIPEETLRKLNGKVAGIKVGWPLLLNLGKEKVKELVGLVDGIKILDLKLADIDNTMILIVDELKDITNSFIAHAFVGVEGSLASLSQRVDLFLVLSMSHPGWNDAFYPYLREVARRVNPKGFVAPATRPSMISRVKGDFPDKLVISPGVGTQGAKPGIALCHGADYEIVGRSVYQSADPVRKLEEIVRSQEEVLSS 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:205
 aligned with A4YI54_METS5 | A4YI54 from UniProtKB/TrEMBL  Length:215

    Alignment length:205
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200     
         A4YI54_METS5     1 MNRVILSLDSPIPEETLRKLNGKVAGIKVGWPLLLNLGKEKVKELVGLVDGIKILDLKLADIDNTMILIVDELKDITNSFIAHAFVGVEGSLASLSQRVDLFLVLSMSHPGWNDAFYPYLREVARRVNPKGFVAPATRPSMISRVKGDFPDKLVISPGVGTQGAKPGIALCHGADYEIVGRSVYQSADPVRKLEEIVRSQEEVLS 205
               SCOP domains d3ve7b_ B: automated matches                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....hhhhhhhhh....eeeeehhhhhhhhhhhhhhhhh....eeeeeeee..hhhhhhhhhh.......eeeee.hhh...hhhhhhh..eeeee........hhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhh...eeee..........hhhhhh...eeeehhhhhh..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ve7 B   1 MNRVILSLDSPIPEETLRKLNGKVAGIKVGWPLLLNLGKEKVKELVGLVDGIKILDLKLADIDNTMILIVDELKDITNSFIAHAFVGVEGSLASLSQRVDLFLVLSMSHPGWNDAFYPYLREVARRVNPKGFVAPATRPSMISRVKGDFPDKLVISPGVGTQGAKPGIALCHGADYEIVGRSVYQSADPVRKLEEIVRSQEEVLS 205
                                    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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  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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VE7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VE7)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A4YI54_METS5 | A4YI54)
molecular function
    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: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.

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 Related Entries

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        A4YI54_METS5 | A4YI54: 3ve9

(-) Related Entries Specified in the PDB File

3ve9 4dbd 4dbe