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(-) Description

Title :  CRYSTAL STRUCTURE OF E112Q MUTANT OF 3-KETO-L-GULONATE 6-PHOSPHATE DECARBOXYLASE WITH BOUND L-THREONOHYDROXAMATE 4-PHOSPHATE
 
Authors :  E. L. Wise, W. S. Yew, J. A. Gerlt, I. Rayment
Date :  12 Mar 04  (Deposition) - 08 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Tim Barrel; Beta Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. L. Wise, W. S. Yew, J. A. Gerlt, I. Rayment
Evolution Of Enzymatic Activities In The Orotidine 5'-Monophosphate Decarboxylase Suprafamily: Crystallographic Evidence For A Proton Relay System In The Active Site Of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase(, )
Biochemistry V. 43 6438 2004
PubMed-ID: 15157078  |  Reference-DOI: 10.1021/BI0497392
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 3-KETO-L-GULONATE 6-PHOSPHATE DECARBOXYLASE
    Chains: A, B
    EC Number: 4.1.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ULAD
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: HEXULOSE-6-PHOSPHATE SYNTHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2TX42Ligand/IonL-THREONOHYDROXAMATE 4-PHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2TX42Ligand/IonL-THREONOHYDROXAMATE 4-PHOSPHATE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2TX44Ligand/IonL-THREONOHYDROXAMATE 4-PHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:33 , ASP B:62 , TX4 B:1301 , HOH B:1480 , HOH B:1481BINDING SITE FOR RESIDUE MG B 1300
2AC2SOFTWAREGLU A:33 , ASP A:62 , TX4 A:2301 , HOH A:2472 , HOH A:2481BINDING SITE FOR RESIDUE MG A 2300
3AC3SOFTWAREASP A:67 , HOH A:2408 , ALA B:9 , ASP B:11 , GLU B:33 , ASP B:62 , LYS B:64 , HIS B:136 , THR B:169 , GLY B:171 , GLY B:191 , ARG B:192 , MG B:1300 , HOH B:1303 , HOH B:1314 , HOH B:1316 , HOH B:1387 , HOH B:1388 , HOH B:1480 , HOH B:1481BINDING SITE FOR RESIDUE TX4 B 1301
4AC4SOFTWAREALA A:9 , ASP A:11 , GLU A:33 , ASP A:62 , LYS A:64 , HIS A:136 , THR A:169 , GLY A:171 , GLY A:191 , ARG A:192 , MG A:2300 , HOH A:2303 , HOH A:2308 , HOH A:2313 , HOH A:2328 , HOH A:2376 , HOH A:2393 , HOH A:2472 , HOH A:2481 , ASP B:67BINDING SITE FOR RESIDUE TX4 A 2301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1SO5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1SO5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SO5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1SO5)

(-) Exons   (0, 0)

(no "Exon" information available for 1SO5)

(-) Sequences/Alignments

Asymmetric 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:213
 aligned with ULAD_ECOLI | P39304 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:213
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212   
           ULAD_ECOLI     3 LPMLQVALDNQTMDSAYETTRLIAEEVDIIEVGTILCVGEGVRAVRDLKALYPHKIVLADAKIADAGKILSRMCFEANADWVTVICCADINTAKGALDVAKEFNGDVQIELTGYWTWEQAQQWRDAGIGQVVYHRSRDAQAAGVAWGEADITAIKRLSDMGFKVTVTGGLALEDLPLFKGIPIHVFIAGRSIRDAASPVEAARQFKRSIAELW 215
               SCOP domains d1so5a_ A: 3-keto-L-gulonate 6-phosphate decarboxylase                                                                                                                                                                SCOP domains
               CATH domains 1so5A00 A:3-215 Aldolase class I                                                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhh..eeeee.hhhhhhh....hhhhhhhhhhhhhh..eeeee...hhhhhhhhh.....eeeehhhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1so5 A   3 LPMLQVALDNQTMDSAYETTRLIAEEVDIIEVGTILCVGEGVRAVRDLKALYPHKIVLADAKIADAGKILSRMCFEANADWVTVICCADINTAKGALDVAKEFNGDVQIQLTGYWTWEQAQQWRDAGIGQVVYHRSRDAQAAGVAWGEADITAIKRLSDMGFKVTVTGGLALEDLPLFKGIPIHVFIAGRSIRDAASPVEAARQFKRSIAELW 215
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212   


Chain B from PDB  Type:PROTEIN  Length:215
 aligned with ULAD_ECOLI | P39304 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:215
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     
           ULAD_ECOLI     2 SLPMLQVALDNQTMDSAYETTRLIAEEVDIIEVGTILCVGEGVRAVRDLKALYPHKIVLADAKIADAGKILSRMCFEANADWVTVICCADINTAKGALDVAKEFNGDVQIELTGYWTWEQAQQWRDAGIGQVVYHRSRDAQAAGVAWGEADITAIKRLSDMGFKVTVTGGLALEDLPLFKGIPIHVFIAGRSIRDAASPVEAARQFKRSIAELWG 216
               SCOP domains d1so5b_ B: 3-keto-L-gulonate 6-phosphate decarboxylase                                                                                                                                                                  SCOP domains
               CATH domains 1so5B00 B:2-216 Aldolase class I                                                                                                                                                                                        CATH domains
           Pfam domains (1) --OMPdecase-1so5B01 B:4-207                                                                                                                                                                                   --------- Pfam domains (1)
           Pfam domains (2) --OMPdecase-1so5B02 B:4-207                                                                                                                                                                                   --------- Pfam domains (2)
         Sec.struct. author ...eeeeee...hhhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhh..eeeee.hhhhhhh....hhhhhhhhhhhhhh..eeeee...hhhhhhhhh.....eeeehhhhhh..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1so5 B   2 SLPMLQVALDNQTMDSAYETTRLIAEEVDIIEVGTILCVGEGVRAVRDLKALYPHKIVLADAKIADAGKILSRMCFEANADWVTVICCADINTAKGALDVAKEFNGDVQIQLTGYWTWEQAQQWRDAGIGQVVYHRSRDAQAAGVAWGEADITAIKRLSDMGFKVTVTGGLALEDLPLFKGIPIHVFIAGRSIRDAASPVEAARQFKRSIAELWG 216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ULAD_ECOLI | P39304)
molecular function
    GO:0033982    3-dehydro-L-gulonate-6-phosphate decarboxylase activity    Catalysis of the reaction: 3-dehydro-L-gulonate 6-phosphate + H(+) = L-xylulose 5-phosphate + CO(2).
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0019854    L-ascorbic acid catabolic process    The chemical reactions and pathways resulting in the breakdown of L-ascorbic acid; L-ascorbic acid ionizes to give L-ascorbate, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate, which is required as a cofactor in the oxidation of prolyl residues to hydroxyprolyl, and other reactions.
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    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

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

UniProtKB/Swiss-Prot
        ULAD_ECOLI | P39304: 1kv8 1kw1 1q6l 1q6o 1q6q 1q6r 1so3 1so4 1so6 1xbv 1xbx 1xby 1xbz

(-) Related Entries Specified in the PDB File

1q6l 1q6o 1q6q 1q6r 1so3 1so4 1so6