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(-) Description

Title :  CRYSTAL STRUCTURES OF KDO8P SYNTHASE IN ITS BINARY COMPLEX WITH SUBSTRATE PHOSPHOENOL PYRUVATE
 
Authors :  O. A. Asojo, J. M. Friedman, V. Belakhov, Y. Shoham, N. Adir, T. Baasov
Date :  14 Nov 00  (Deposition) - 16 May 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (4x)
Keywords :  Beta-Alpha-Barrels, Lyase, Lipopolysaccharide (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  O. Asojo, J. Friedman, N. Adir, V. Belakhov, Y. Shoham, T. Baasov
Crystal Structures Of Kdop Synthase In Its Binary Complexes With The Substrate Phosphoenolpyruvate And With A Mechanism-Based Inhibitor.
Biochemistry V. 40 6326 2001
PubMed-ID: 11371194  |  Reference-DOI: 10.1021/BI010339D

(-) Compounds

Molecule 1 - 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE
    ChainsA
    EC Number4.1.2.16
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymKDO 8-P SYNTHASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (4x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1PEP1Ligand/IonPHOSPHOENOLPYRUVATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PEP1Ligand/IonPHOSPHOENOLPYRUVATE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1PEP4Ligand/IonPHOSPHOENOLPYRUVATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:117 , ARG A:168 , HIS A:202 , PRO A:252BINDING SITE FOR RESIDUE PEP A 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1G7U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1G7U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1G7U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1G7U)

(-) Exons   (0, 0)

(no "Exon" information available for 1G7U)

(-) 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:284
 aligned with KDSA_ECOLI | P0A715 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:284
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280    
           KDSA_ECOLI     1 MKQKVVSIGDINVANDLPFVLFGGMNVLESRDLAMRICEHYVTVTQKLGIPYVFKASFDKANRSSIHSYRGPGLEEGMKIFQELKQTFGVKIITDVHEPSQAQPVADVVDVIQLPAFLARQTDLVEAMAKTGAVINVKKPQFVSPGQMGNIVDKFKEGGNEKVILCDRGANFGYDNLVVDMLGFSIMKKVSGNSPVIFDVTHALQCRDPFGAASGGRRAQVAELARAGMAVGLAGLFIEAHPDPEHAKCDGPSALPLAKLEPFLKQMKAIDDLVKGFEELDTSK 284
               SCOP domains d1g7ua_ A: 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8P synthase)                                                                                                                                                                                                                SCOP domains
               CATH domains 1g7uA00 A:1-284 Aldolase class I                                                                                                                                                                                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee..ee.......eeeee.......hhhhhhhhhhhhhhhhhh..eeee.................hhhhhhhhhhhhhhhh.........hhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh....eeeee..ee.....ee...hhhhhhhhhh....eeeehhhhhhhhh...........hhhhhhhhhhh....eee..ee.............ee...hhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g7u A   1 MKQKVVSIGDINVANDLPFVLFGGMNVLESRDLAMRICEHYVTVTQKLGIPYVFKASFDKANRSSIHSYRGPGLEEGMKIFQELKQTFGVKIITDVHEPSQAQPVADVVDVIQLPAFLARQTDLVEAMAKTGAVINVKKPQFVSPGQMGNIVDKFKEGGNEKVILCDRGANFGYDNLVVDMLGFSIMKKVSGNSPVIFDVTHALQCRDPFVAASGGRRAQVAELARAGMAVGLAGLFIEAHPDPEHAKCDGPSALPLAKLEPFLKQMKAIDDLVKGFEELDTSK 284
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280    

   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, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1G7U)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (KDSA_ECOLI | P0A715)
molecular function
    GO:0008676    3-deoxy-8-phosphooctulonate synthase activity    Catalysis of the reaction: D-arabinose 5-phosphate + H(2)O + phosphoenolpyruvate = 8-phospho-3-deoxy-D-manno-oct-2-ulosonate + 2 H(+) + phosphate.
    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:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0019294    keto-3-deoxy-D-manno-octulosonic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of keto-3-deoxy-D-manno-octulosonic acid, an acidic sugar present in lipopolysaccharides of the outer membranes of some Gram-negative bacteria.
    GO:0009103    lipopolysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.
    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:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KDSA_ECOLI | P0A7151d9e 1g7v 1gg0 1phq 1phw 1pl9 1q3n 1x6u 1x8f

(-) Related Entries Specified in the PDB File

1g7v CRYSTAL STRUCTURES OF KDO8P SYNTHASE IN ITS BINARY COMPLEXES WITH THE MECHANISM-BASED INHIBITOR