Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM METALLOSPHAERA SEDULA
 
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 :  1.45
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Metallosphaera Sedula, Tim Barrel Fold, Orotidine 5'-Monophosphate Decarboxylase, Lyase (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
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
    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  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:28 , ASP A:56 , LYS A:58 , VAL A:133 , PRO A:157 , ILE A:178 , HOH A:408BINDING SITE FOR RESIDUE GOL A 301
2AC2SOFTWARELEU A:34 , HOH A:521 , LEU B:34 , GLY B:38 , LYS B:39BINDING SITE FOR RESIDUE PEG A 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VE9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3VE9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VE9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VE9)

(-) Exons   (0, 0)

(no "Exon" information available for 3VE9)

(-) 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:204
 aligned with A4YI54_METS5 | A4YI54 from UniProtKB/TrEMBL  Length:215

    Alignment length:204
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    
         A4YI54_METS5     1 MNRVILSLDSPIPEETLRKLNGKVAGIKVGWPLLLNLGKEKVKELVGLVDGIKILDLKLADIDNTMILIVDELKDITNSFIAHAFVGVEGSLASLSQRVDLFLVLSMSHPGWNDAFYPYLREVARRVNPKGFVAPATRPSMISRVKGDFPDKLVISPGVGTQGAKPGIALCHGADYEIVGRSVYQSADPVRKLEEIVRSQEEVL 204
               SCOP domains d3ve9a_ A: automated matches                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee....hhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhh....eeeeeeee..hhhhhhhhhhhhh....eeeee.hhh...hhhhhhhhheeeee........hhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhh...eeee..........hhhhhh...eeeehhhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ve9 A   1 MNRVILSLDSPIPEETLRKLNGKVAGIKVGWPLLLNLGKEKVKELVGLVDGIKILDLKLADIDNTMILIVDELKDITNSFIAHAFVGVEGSLASLSQRVDLFLVLSMSHPGWNDAFYPYLREVARRVNPKGFVAPATRPSMISRVKGDFPDKLVISPGVGTQGAKPGIALCHGADYEIVGRSVYQSADPVRKLEEIVRSQEEVL 204
                                    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:204
 aligned with A4YI54_METS5 | A4YI54 from UniProtKB/TrEMBL  Length:215

    Alignment length:204
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    
         A4YI54_METS5     1 MNRVILSLDSPIPEETLRKLNGKVAGIKVGWPLLLNLGKEKVKELVGLVDGIKILDLKLADIDNTMILIVDELKDITNSFIAHAFVGVEGSLASLSQRVDLFLVLSMSHPGWNDAFYPYLREVARRVNPKGFVAPATRPSMISRVKGDFPDKLVISPGVGTQGAKPGIALCHGADYEIVGRSVYQSADPVRKLEEIVRSQEEVL 204
               SCOP domains d3ve9b_ B: automated matches                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee....hhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhh....eeeee.hhh....hhhhhh..eeeee........hhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhh...eeee..........hhhhhh...eeeehhhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ve9 B   1 MNRVILSLDSPIPEETLRKLNGKVAGIKVGWPLLLNLGKEKVKELVGLVDGIKILDLKLADIDNTMILIVDELKDITNSFIAHAFVGVEGSLASLSQRVDLFLVLSMSHPGWNDAFYPYLREVARRVNPKGFVAPATRPSMISRVKGDFPDKLVISPGVGTQGAKPGIALCHGADYEIVGRSVYQSADPVRKLEEIVRSQEEVL 204
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VE9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VE9)

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ve9)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3ve9
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  A4YI54_METS5 | A4YI54
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  4.1.1.23
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  A4YI54_METS5 | A4YI54
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A4YI54_METS5 | A4YI54: 3ve7

(-) Related Entries Specified in the PDB File

3ve7 4dbd 4dbe