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(-) Description

Title :  THE 1.65A CRYSTAL STRUCTURE OF 3-HEXULOSE-6-PHOSPHATE SYNTHASE FROM SALMONELLA TYPHIMURIUM
 
Authors :  J. Vijayalakshmi, R. W. Woodard
Date :  03 Nov 08  (Deposition) - 25 Nov 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Synthase, Humps, Malonate, Salmonella Typhimurium, Crystal Structure, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Vijayalakshmi, T. C. Meredith, R. W. Woodard
The 1. 65A Crystal Structure Of 3-Hexulose-6-Phosphate Synthase From Salmonella Typhimurium
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE HEXULOSE 6 PHOSPHATE SYNTHASE
    Chains: A, B
    EC Number: 4.1.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PT7-7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: HUMPS, STM2755
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 602
    Strain: STM2755

 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
1MLI2Ligand/IonMALONATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:134 , GLN A:140 , GLY A:166 , GLY A:167 , GLY A:187 , SER A:188BINDING SITE FOR RESIDUE MLI A 300
2AC2SOFTWAREHIS B:134 , THR B:137 , GLN B:140 , GLY B:166 , GLY B:167 , GLY B:187 , SER B:188BINDING SITE FOR RESIDUE MLI B 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3F4W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3F4W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3F4W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3F4W)

(-) Exons   (0, 0)

(no "Exon" information available for 3F4W)

(-) 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:211
 aligned with Q8ZMP9_SALTY | Q8ZMP9 from UniProtKB/TrEMBL  Length:211

    Alignment length:211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 
         Q8ZMP9_SALTY     1 MKLQLALDELTLPEAMVFMDKVVDDVDIIEVGTPFLIREGVNAIKAIKEKYPHKEVLADAKIMDGGHFESQLLFDAGADYVTVLGVTDVLTIQSCIRAAKEAGKQVVVDMICVDDLPARVRLLEEAGADMLAVHTGTDQQAAGRKPIDDLITMLKVRRKARIAVAGGISSQTVKDYALLGPDVVIVGSAITHAADPAGEARKISQVLLQHH 211
               SCOP domains d3f4wa_ A: automated matches                                                                                                                                                                                        SCOP domains
               CATH domains 3f4wA00 A:1-211 Aldolase class I                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhh..eeeee.hhhhhhh...hhhhhhhhhhhh...eeeee......hhhhhhh....eeeehhhhhh..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f4w A   1 MKLQLALDELTLPEAMVFMDKVVDDVDIIEVGTPFLIREGVNAIKAIKEKYPHKEVLADAKIMDGGHFESQLLFDAGADYVTVLGVTDVLTIQSCIRAAKEAGKQVVVDMICVDDLPARVRLLEEAGADMLAVHTGTDQQAAGRKPIDDLITMLKVRRKARIAVAGGISSQTVKDYALLGPDVVIVGSAITHAADPAGEARKISQVLLQHH 211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 


Chain B from PDB  Type:PROTEIN  Length:211
 aligned with Q8ZMP9_SALTY | Q8ZMP9 from UniProtKB/TrEMBL  Length:211

    Alignment length:211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 
         Q8ZMP9_SALTY     1 MKLQLALDELTLPEAMVFMDKVVDDVDIIEVGTPFLIREGVNAIKAIKEKYPHKEVLADAKIMDGGHFESQLLFDAGADYVTVLGVTDVLTIQSCIRAAKEAGKQVVVDMICVDDLPARVRLLEEAGADMLAVHTGTDQQAAGRKPIDDLITMLKVRRKARIAVAGGISSQTVKDYALLGPDVVIVGSAITHAADPAGEARKISQVLLQHH 211
               SCOP domains d3f4wb_ B: automated matches                                                                                                                                                                                        SCOP domains
               CATH domains 3f4wB00 B:1-211 Aldolase class I                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhh..eeeee.hhhhhhh...hhhhhhhhhhhh...eeeee......hhhhhhh....eeeehhhhhh..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f4w B   1 MKLQLALDELTLPEAMVFMDKVVDDVDIIEVGTPFLIREGVNAIKAIKEKYPHKEVLADAKIMDGGHFESQLLFDAGADYVTVLGVTDVLTIQSCIRAAKEAGKQVVVDMICVDDLPARVRLLEEAGADMLAVHTGTDQQAAGRKPIDDLITMLKVRRKARIAVAGGISSQTVKDYALLGPDVVIVGSAITHAADPAGEARKISQVLLQHH 211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "Pfam Domain" information available for 3F4W)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8ZMP9_SALTY | Q8ZMP9)
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:0043801    hexulose-6-phosphate synthase activity    Catalysis of the reaction: D-ribulose 5-phosphate + formaldehyde = D-arabino-3-hexulose 6-phosphate.
    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: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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