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(-) Description

Title :  CRYSTAL STRUCTURE OF GDP-4-KETO-6-DEOXY-D-MANNOSE EPIMERASE/REDUCTASE FROM ESCHERICHIA COLI A KEY ENZYME IN THE BIOSYNTHESIS OF GDP-L-FUCOSE
 
Authors :  M. Rizzi, M. Tonetti, A. D. Flora, M. Bolognesi
Date :  25 Sep 98  (Deposition) - 13 Jan 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (2x)
Keywords :  Epimerase/Reductase, Gdp-L-Fucose Biosynthesis, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Rizzi, M. Tonetti, P. Vigevani, L. Sturla, A. Bisso, A. D. Flora, D. Bordo, M. Bolognesi
Gdp-4-Keto-6-Deoxy-D-Mannose Epimerase/Reductase From Escherichia Coli, A Key Enzyme In The Biosynthesis Of Gdp-L-Fucose, Displays The Structural Characteristics Of Th Red Protein Homology Superfamily.
Structure V. 6 1453 1998
PubMed-ID: 9817848  |  Reference-DOI: 10.1016/S0969-2126(98)00144-0

(-) Compounds

Molecule 1 - PROTEIN (GDP-4-KETO-6-DEOXY-D-MANNOSE EPIMERASE/REDUCTASE)
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:12 , GLY A:13 , MET A:14 , VAL A:15 , LEU A:39 , ASN A:40 , LEU A:41 , ALA A:62 , ALA A:63 , ALA A:64 , VAL A:66 , ILE A:86 , LEU A:105 , GLY A:106 , TYR A:136 , LYS A:140 , HOH A:354 , HOH A:386 , HOH A:412 , HOH A:425 , HOH A:431BINDING SITE FOR RESIDUE NDP A 322
2CATAUTHORTYR A:136 , LYS A:140 , SER A:107CATALYTIC RESIDUES

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gln A:117 -Pro A:118

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 1BWS)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  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:314
 aligned with FCL_ECOLI | P32055 from UniProtKB/Swiss-Prot  Length:321

    Alignment length:314
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312    
            FCL_ECOLI     3 KQRVFIAGHRGMVGSAIRRQLEQRGDVELVLRTRDELNLLDSRAVHDFFASERIDQVYLAAAKVGGIVANNTYPADFIYQNMMIESNIIHAAHQNDVNKLLFLGSSCIYPKLAKQPMAESELLQGTLEPTNEPYAIAKIAGIKLCESYNRQYGRDYRSVMPTNLYGPHDNFHPSNSHVIPALLRRFHEATAQNAPDVVVWGSGTPMREFLHVDDMAAASIHVMELAHEVWLENTQPMLSHINVGTGVDCTIRELAQTIAKVVGYKGRVVFDASKPDGTPRKLLDVTRLHQLGWYHEISLEAGLASTYQWFLENQ 316
               SCOP domains d1bwsa_ A: GDP-4-keto-6-deoxy-d-mannose epimerase/reductase (GDP-fucose synthetase)                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1bwsA01 A:3-167,A:210-248,A:284-299 NAD(P)-binding Rossmann-like Domain                                                                                              1bwsA02 A:168-209,A:249-283,A:300-316     1bwsA01 A:3-167,A:210-248,A:284-299    1bwsA02                            1bwsA01         1bwsA02           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhh...eeee...........hhhhhhhhhhh...eeee.......hhhhhh.hhhhhhhhhhhhhhhhhhhhhh...eeeee..hhh..........hhh..........hhhhhhhhhhhhhhhhhhhhh..eeeeeee.eee............hhhhhhhhhhhhhh....eeeee........eeehhhhhhhhhhhhh..hhhhhh........eee.......hhhhhhhhhhhh....eeeee..............hhhhh........hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bws A   3 KQRVFIAGHRGMVGSAIRRQLEQRGDVELVLRTRDELNLLDSRAVHDFFASERIDQVYLAAAKVGGIVANNTYPADFIYQNMMIESNIIHAAHQNDVNKLLFLGSSCIYPKLAKQPMAESELLQGTLEPTNEPYAIAKIAGIKLCESYNRQYGRDYRSVMPTNLYGPHDNFHPSNSHVIPALLRRFHEATAQNAPDVVVWGSGTPMREFLHVDDMAAASIHVMELAHEVWLENTQPMLSHINVGTGVDCTIRDLAQTIAKVVGYKGRVVFDASKPDGTPRKLLDVTRLHQLGWYHEISLEAGLASTYQWFLENQ 316
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312    

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  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  (2, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (FCL_ECOLI | P32055)
molecular function
    GO:0050577    GDP-L-fucose synthase activity    Catalysis of the reaction: GDP-L-fucose + NAD+ = GDP-4-dehydro-6-deoxy-D-mannose + NADH + H+.
    GO:0070401    NADP+ binding    Interacting selectively and non-covalently with the oxidized form, NADP+, of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions.
    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:0050662    coenzyme binding    Interacting selectively and non-covalently with a coenzyme, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0042351    'de novo' GDP-L-fucose biosynthetic process    The chemical reactions and pathways resulting in the formation of GDP-L-fucose from GDP-D-mannose via GDP-4-dehydro-6-deoxy-D-mannose, requiring the functions of GDP-mannose 4,6-dehydratase (EC:4.2.1.47) and GDP-L-fucose synthase (EC:1.1.1.271).
    GO:0009242    colanic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of colanic acid, a capsular bacterial polysaccharide.
    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:0009226    nucleotide-sugar biosynthetic process    The chemical reactions and pathways resulting in the formation of nucleotide-sugars, any nucleotide-carbohydrate in which the distal phosphoric residue of a nucleoside 5'-diphosphate is in glycosidic linkage with a monosaccharide or monosaccharide derivative.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FCL_ECOLI | P320551bsv 1e6u 1e7q 1e7r 1e7s 1fxs 1gfs

(-) Related Entries Specified in the PDB File

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