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(-) Description

Title :  CRYSTAL STRUCTURE OF DTDP-6-DEOXY-D-XYLO-4-HEXULOASE 3,5-EPIMERASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM WITH BOUND LIGAND.
 
Authors :  D. Christendat, V. Saridakis, A. Bochkarev, E. F. Pai, C. Arrowsmith, A. M. Edwards
Date :  30 Mar 00  (Deposition) - 13 Dec 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Racemase, Dtdp-4-Dehydrorhamnose Epimerase, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Christendat, V. Saridakis, A. Dharamsi, A. Bochkarev, E. F. Pai, C. H. Arrowsmith, A. M. Edwards
Crystal Structure Of Dtdp-4-Keto-6-Deoxy-D-Hexulose 3, 5-Epimerase From Methanobacterium Thermoautotrophicum Complexed With Dtdp.
J. Biol. Chem. V. 275 24608 2000
PubMed-ID: 10827167  |  Reference-DOI: 10.1074/JBC.C000238200

(-) Compounds

Molecule 1 - DTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3,5-EPIMERASE
    Chains: A
    EC Number: 5.1.3.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Taxid: 562
    Organism Scientific: METHANOTHERMOBACTER THERMAUTOTROPHICUS
    Organism Taxid: 145262
    Synonym: DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1TYD1Ligand/IonTHYMIDINE-5'-DIPHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1TYD2Ligand/IonTHYMIDINE-5'-DIPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:22 , ARG A:26 , PHE A:29 , GLU A:31 , GLN A:49 , ASN A:51 , ARG A:61 , HIS A:64 , TYR A:139 , LYS A:171 , HOH A:1035 , HOH A:1036 , HOH A:1037 , HOH A:1040 , HOH A:1095BINDING SITE FOR RESIDUE TYD A 2187

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:62 -Leu A:63

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1EPZ)

(-) Sequences/Alignments

Asymmetric Unit
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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:183
 aligned with RMLC_METTH | O27818 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:183
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182   
           RMLC_METTH     3 EFRFIKTSLDGAIIIEPEVYTDERGYFMETFNEAIFQENGLEVRFVQDNESMSVRGVLRGLHFQREKPQGKLVRVIRGEIFDVAVDLRKNSDTYGEWTGVRLSDENRREFFIPEGFAHGFLALSDECIVNYKCTELYHPEYDSGIPWDDPDIGIDWPLEMVDDLIISEKDRNWKPLRENPVYL 185
               SCOP domains d1epza_ A: dTDP-4-dehydrorhamnose 3,5-epimerase RmlC                                                                                                                                    SCOP domains
               CATH domains 1epzA00 A:3-185 Jelly Rolls                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......eeeee.eeee..eeee...hhhhhhhh.......eeeeeeee...eeeeeee......eeeeeee.eeeeeeee..........eeeeeee.....eeee...eeeeeee...eeeeeeee....hhh.eee............hhhhh......hhhhh........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1epz A   3 EFRFIKTSLDGAIIIEPEVYTDERGYFMETFNEAIFQENGLEVRFVQDNESMSVRGVLRGLHFQREKPQGKLVRVIRGEIFDVAVDLRKNSDTYGEWTGVRLSDENRREFFIPEGFAHGFLALSDECIVNYKCTELYHPEYDSGIPWDDPDIGIDWPLEMVDDLIISEKDRNWKPLRENPVYL 185
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182
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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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (RMLC_METTH | O27818)
molecular function
    GO:0008830    dTDP-4-dehydrorhamnose 3,5-epimerase activity    Catalysis of the reaction: dTDP-4-dehydro-6-deoxy-alpha-D-glucose = dTDP-4-dehydro-6-deoxy-L-mannose.
    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.
biological process
    GO:0019305    dTDP-rhamnose biosynthetic process    The chemical reactions and pathways resulting in the formation of dTDP-rhamnose, a substance composed of rhamnose in glycosidic linkage with deoxyribosylthymine diphosphate.
    GO:0045226    extracellular polysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of polysaccharides used in extracellular structures.

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 Related Entries

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        RMLC_METTH | O27818: 1ep0

(-) Related Entries Specified in the PDB File

1epo 1EPO IS THE APO-FORM OF THIS ENZYME.