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(-) Description

Title :  CRYSTAL STRUCTURE OF UNCHARACTERIZED CONSERVED PROTEIN FROM GEOBACILLUS KAUSTOPHILUS
 
Authors :  M. Kanagawa, S. Baba, Y. Nakamura, Y. Bessho, S. Kuramitsu, S. Yokoyama G. Sampei, Riken Structural Genomics/Proteomics Initiative (R
Date :  02 May 07  (Deposition) - 06 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tim Barrel, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kanagawa, S. Baba, Y. Nakamura, Y. Bessho, S. Kuramitsu, S. Yokoyama, G. Kawai, G. Sampei
Crystal Structure Of Uncharacterized Conserved Protein From Geobacillus Kaustophilus
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 Plasmid: PET-HISTEV
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL-X
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: GEOBACILLUS KAUSTOPHILUS
    Organism Taxid: 235909
    Strain: HTA426
    Synonym: OMP DECARBOXYLASE, OMPDCASE, OMPDECASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1C5P2Ligand/IonCYTIDINE-5'-MONOPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:12 , LYS A:34 , THR A:124 , ARG A:186 , GLY A:215 , ARG A:216 , HOH A:1307 , HOH A:1320 , HOH A:1349 , HOH B:2321BINDING SITE FOR RESIDUE C5P A 1301
2AC2SOFTWAREHOH A:1315 , ALA B:10 , ASP B:12 , LYS B:34 , THR B:124 , PRO B:183 , ARG B:186 , GLY B:215 , ARG B:216 , HOH B:2304 , HOH B:2324BINDING SITE FOR RESIDUE C5P B 2301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YYU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2YYU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YYU)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OMPDECASEPS00156 Orotidine 5'-phosphate decarboxylase active site.PYRF_GEOKA56-69
 		  2A:58-71
B:58-71

(-) Exons   (0, 0)

(no "Exon" information available for 2YYU)

(-) 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:225
 aligned with PYRF_GEOKA | Q5L0U0 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:232
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232  
           PYRF_GEOKA     3 TPFIVALDFPSKQEVERFLRPFAGTPLFVKVGMELYYQEGPAIVAFLKEQGHAVFLDLKLHDIPNTVKQAMKGLARVGADLVNVHAAGGRRMMEAAIEGLDAGTPSGRMRPRCIAVTQLTSTDERMLHEELWISRPLVETVAHYAALAKESGLDGVVCSANEAAFIKERCGASFLAVTPGIRFADDAAHDQVRVVTPRKARALGSDYIVIGRSLTRAADPLRTYARLQHEWN 234
               SCOP domains d2yyua_ A: automated matches                                                                                                                                                                                                             SCOP domains
               CATH domains 2yyuA00 A:5-236 Aldolase class I                                                                                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh.......eeeee......hhhhhhhh.....hhhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhh...eeee.......-------...hhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------OMPDECASE     --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yyu A   5 TPFIVALDFPSKQEVERFLRPFAGTPLFVKVGMELYYQEGPAIVAFLKEQGHAVFLDLKLHDIPNTVKQAMKGLARVGADLVNVHAAGGRRMMEAAIEGLDAGTPSGRMRPRCIAVTQLTSTDERMLHEELWISRPLVETVAHYAALAKESGLDGVVCSANEAAFIKERCGASFLAVTPGIRFAD-------RVVTPRKARALGSDYIVIGRSLTRAADPLRTYARLQHEWN 236
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184    |    -  |    204       214       224       234  
                                                                                                                                                                                                                  189     197                                       


Chain B from PDB  Type:PROTEIN  Length:229
 aligned with PYRF_GEOKA | Q5L0U0 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:233
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231   
           PYRF_GEOKA     2 HTPFIVALDFPSKQEVERFLRPFAGTPLFVKVGMELYYQEGPAIVAFLKEQGHAVFLDLKLHDIPNTVKQAMKGLARVGADLVNVHAAGGRRMMEAAIEGLDAGTPSGRMRPRCIAVTQLTSTDERMLHEELWISRPLVETVAHYAALAKESGLDGVVCSANEAAFIKERCGASFLAVTPGIRFADDAAHDQVRVVTPRKARALGSDYIVIGRSLTRAADPLRTYARLQHEWN 234
               SCOP domains d2yyub_ B: automated matches                                                                                                                                                                                                              SCOP domains
               CATH domains 2yyuB00 B:4-236 Aldolase class I                                                                                                                                                                                                          CATH domains
           Pfam domains (1) -OMPdecase-2yyuB01 B:5-231                                                                                                                                                                                                          ----- Pfam domains (1)
           Pfam domains (2) -OMPdecase-2yyuB02 B:5-231                                                                                                                                                                                                          ----- Pfam domains (2)
         Sec.struct. author ...eeee....hhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhh........eeeee......hhhhhhhh.....hhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhh...eeee..........----...hhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------OMPDECASE     --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yyu B   4 HTPFIVALDFPSKQEVERFLRPFAGTPLFVKVGMELYYQEGPAIVAFLKEQGHAVFLDLKLHDIPNTVKQAMKGLARVGADLVNVHAAGGRRMMEAAIEGLDAGTPSGRMRPRCIAVTQLTSTDERMLHEELWISRPLVETVAHYAALAKESGLDGVVCSANEAAFIKERCGASFLAVTPGIRFADDAA----RVVTPRKARALGSDYIVIGRSLTRAADPLRTYARLQHEWN 236
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183        |-   |   203       213       223       233   
                                                                                                                                                                                                                      192  197
   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  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PYRF_GEOKA | Q5L0U0)
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.

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  2yyu
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 Related Entries

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

UniProtKB/Swiss-Prot
        PYRF_GEOKA | Q5L0U0: 2yyt

(-) Related Entries Specified in the PDB File

2yyt THE SAME PROTEIN WITHOUT LINGADS RELATED ID: GKA001001155.2 RELATED DB: TARGETDB