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(-) Description

Title :  CRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE DECARBOXYLASE FROM LACTOBACILLUS ACIDOPHILUS
 
Authors :  L. Satyanarayana, S. Chamala, B. Evans, R. Foti, A. Gizzi, B. Hillerich J. Lafleur, R. Seidel, G. Villigas, W. Zencheck, S. C. Almo, S. Swamina York Structural Genomics Research Consortium (Nysgrc)
Date :  16 Aug 11  (Deposition) - 28 Sep 11  (Release) - 28 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.19
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Psi-Biology, Nysgrc, 000529, Structural Genomics, New York Structural Genomics Research Consortium, Tim Barrel Fold, Pyrimidine Metabolism; Ump Biosynthesis Via De Novo Pathway; Ump From Orotate, Decarboxylase Lyase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Satyanarayana, S. C. Almo, S. Swaminathan
Crystal Structure Of Orotidine 5'-Phosphate Decarboxylase From Lactobacillus Acidophilus
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: PET3A
    Expression System Strain: BL21 CODON + RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LBA1386, PYRF, PYRF/LBA1386
    Organism Scientific: LACTOBACILLUS ACIDOPHILUS
    Organism Taxid: 1579
    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, 12)

Asymmetric/Biological Unit (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3TFX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OMPDECASEPS00156 Orotidine 5'-phosphate decarboxylase active site.PYRF_LACAC57-70
 		  2A:57-70
B:57-70

(-) Exons   (0, 0)

(no "Exon" information available for 3TFX)

(-) 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_LACAC | Q5FJB3 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:242
                                                                                                                                                                                                                                                                   235        
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231   |     -  
           PYRF_LACAC     2 DRPVIVALDLDNEEQLNKILSKLGDPHDVFVKVGMELFYNAGIDVIKKLTQQGYKIFLDLKMHDIPNTVYNGAKALAKLGITFTTVHALGGSQMIKSAKDGLIAGTPAGHSVPKLLAVTELTSISDDVLRNEQNCRLPMAEQVLSLAKMAKHSGADGVICSPLEVKKLHENIGDDFLYVTPGIRPAGNAKDDQSRVATPKMAKEWGSSAIVVGRPITLASDPKAAYEAIKKEFN--------   -
               SCOP domains d3tfxa_ A: automated matches                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhh..hhhh.eeeehhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhh.......eeeee......hhhhhhhh.....hhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhh...eeee.....-----------.hhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------OMPDECASE     ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tfx A   2 DRPVIVALDLDNEEQLNKILSKLGDPHDVFVKVGmELFYNAGIDVIKKLTQQGYKIFLDLKmHDIPNTVYNGAKALAKLGITFTTVHALGGSQmIKSAKDGLIAGTPAGHSVPKLLAVTELTSISDDVLRNEQNCRLPmAEQVLSLAKmAKHSGADGVICSPLEVKKLHENIGDDFLYVTPGIRP-----------ATPKmAKEWGSSAIVVGRPITLASDPKAAYEAIKKEFNAENLYFQS 243
                                    11        21        31    |   41        51        61 |      71        81        91   |   101       111       121       131       141       151       161       171       181    |    -      |201|      211       221       231       241  
                                                             36-MSE                     63-MSE                          95-MSE                                      140-MSE   150-MSE                             186         198   |                                         
                                                                                                                                                                                                                                  202-MSE                                     


Chain B from PDB  Type:PROTEIN  Length:224
 aligned with PYRF_LACAC | Q5FJB3 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:235
                                                                                                                                                                                                                                                                   235 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231   | 
           PYRF_LACAC     2 DRPVIVALDLDNEEQLNKILSKLGDPHDVFVKVGMELFYNAGIDVIKKLTQQGYKIFLDLKMHDIPNTVYNGAKALAKLGITFTTVHALGGSQMIKSAKDGLIAGTPAGHSVPKLLAVTELTSISDDVLRNEQNCRLPMAEQVLSLAKMAKHSGADGVICSPLEVKKLHENIGDDFLYVTPGIRPAGNAKDDQSRVATPKMAKEWGSSAIVVGRPITLASDPKAAYEAIKKEFN-   -
               SCOP domains d3tfxb_ B: automated matches                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhh..hhhh.eeeeehhhhh...hhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhh.......eeeee......hhhhhhhh.....hhhhhhhhhhhhhhhh...eee....hhhhhhhhhh...eeee.....-----------.hhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------OMPDECASE     ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tfx B   2 DRPVIVALDLDNEEQLNKILSKLGDPHDVFVKVGmELFYNAGIDVIKKLTQQGYKIFLDLKmHDIPNTVYNGAKALAKLGITFTTVHALGGSQmIKSAKDGLIAGTPAGHSVPKLLAVTELTSISDDVLRNEQNCRLPmAEQVLSLAKmAKHSGADGVICSPLEVKKLHENIGDDFLYVTPGIRP-----------ATPKmAKEWGSSAIVVGRPITLASDPKAAYEAIKKEFNA 236
                                    11        21        31    |   41        51        61 |      71        81        91   |   101       111       121       131       141       151       161       171       181    |    -      |201|      211       221       231     
                                                             36-MSE                     63-MSE                          95-MSE                                      140-MSE   150-MSE                             186         198   |                                  
                                                                                                                                                                                                                                  202-MSE
   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 3TFX)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PYRF_LACAC | Q5FJB3)
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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