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(-) Description

Title :  THE CRYSTAL STRUCTURE OF DTDP-D-GLUCOSE 4,6-DEHYDRATASE (RMLB) FROM SALMONELLA ENTERICA SEROVAR TYPHIMURIUM WITH THYMIDINE DIPHOSPHATE BOUND
 
Authors :  S. T. M. Allard, K. Beis, M. -F. Giraud, A. D. Hegeman, J. W. Gross, C. Whit M. Graninger, P. Messner, A. G. Allen, J. H. Naismith
Date :  17 Nov 01  (Deposition) - 25 Jan 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. T. Allard, K. Beis, M. F. Giraud, A. D. Hegeman, J. W. Gross, R. C. Wilmouth, C. Whitfield, M. Graninger, P. Messner, A. G. Allen, D. J. Maskell, J. H. Naismith
Toward A Structural Understanding Of The Dehydratase Mechanism.
Structure V. 10 81 2002
PubMed-ID: 11796113  |  Reference-DOI: 10.1016/S0969-2126(01)00694-3

(-) Compounds

Molecule 1 - DTDP-D-GLUCOSE 4,6-DEHYDRATASE
    Chains: A, B
    EC Number: 4.2.1.46
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RMLB
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
    Organism Taxid: 90371
    Strain: SUBSP. ENTERICA SEROVAR TYPHIMURIUM
    Synonym: DTDP-GLUCOSE 4,6-DEHYDRATASE;
RMLB

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3TYD2Ligand/IonTHYMIDINE-5'-DIPHOSPHATE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:85 , VAL A:86 , GLU A:135 , ASN A:196 , GLU A:205 , LYS A:206 , LEU A:207 , LEU A:210 , PRO A:222 , TYR A:224 , ARG A:231 , ASN A:266 , ARG A:297 , HIS A:300 , TYR A:357 , HOH A:2604 , HOH A:2615 , HOH A:2624 , HOH A:2636 , HOH A:2741BINDING SITE FOR RESIDUE TYD A 2600
2AC2SOFTWAREHIS B:85 , VAL B:86 , GLU B:135 , ASN B:196 , GLU B:205 , LYS B:206 , LEU B:207 , LEU B:210 , PRO B:222 , TYR B:224 , ARG B:231 , ASN B:266 , ARG B:297 , HIS B:300 , TYR B:357 , HOH B:2708 , HOH B:2712 , HOH B:2723 , HOH B:2726 , HOH B:2826BINDING SITE FOR RESIDUE TYD B 2700
3AC3SOFTWAREALA A:9 , GLY A:10 , PHE A:11 , ILE A:12 , ASP A:32 , LYS A:33 , LEU A:34 , THR A:35 , ALA A:37 , GLY A:38 , ALA A:57 , ASP A:58 , ILE A:59 , LEU A:80 , ALA A:81 , ALA A:82 , SER A:84 , THR A:99 , ILE A:131 , SER A:132 , THR A:133 , TYR A:167 , LYS A:171 , CYS A:194 , SER A:195 , ASN A:196 , ASN A:197 , HOH A:2601 , HOH A:2611 , HOH A:2613 , HOH A:2627 , HOH A:2628 , HOH A:2633 , HOH A:2639 , HOH A:2645 , HOH A:2674BINDING SITE FOR RESIDUE NAD A 1400
4AC4SOFTWAREALA B:9 , GLY B:10 , PHE B:11 , ILE B:12 , ASP B:32 , LYS B:33 , LEU B:34 , THR B:35 , ALA B:37 , GLY B:38 , ALA B:57 , ASP B:58 , ILE B:59 , LEU B:80 , ALA B:81 , ALA B:82 , SER B:84 , THR B:99 , ILE B:131 , SER B:132 , THR B:133 , TYR B:167 , LYS B:171 , CYS B:194 , SER B:195 , ASN B:196 , ASN B:197 , HOH B:2702 , HOH B:2714 , HOH B:2715 , HOH B:2720 , HOH B:2728 , HOH B:2736 , HOH B:2747 , HOH B:2750 , HOH B:2761BINDING SITE FOR RESIDUE NAD B 1500
5AC5SOFTWAREHOH A:2811 , ARG B:288BINDING SITE FOR RESIDUE GOL A 1473
6AC6SOFTWAREARG A:179 , GLY A:253 , GLU A:254 , THR A:255 , LYS A:310 , HOH A:2714 , HOH A:2732BINDING SITE FOR RESIDUE GOL A 1474
7AC7SOFTWAREASN A:262 , LYS A:264 , THR A:322 , PHE A:323 , HOH A:2900BINDING SITE FOR RESIDUE GOL A 1475

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1KEW)

(-) 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:361
 aligned with RMLB_SALTY | P26391 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:361
                                    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       290       300       310       320       330       340       350       360 
           RMLB_SALTY     1 MKILITGGAGFIGSAVVRHIIKNTQDTVVNIDKLTYAGNLESLSDISESNRYNFEHADICDSAEITRIFEQYQPDAVMHLAAESHVDRSITGPAAFIETNIVGTYALLEVARKYWSALGEDKKNNFRFHHISTDEVYGDLPHPDEVENSVTLPLFTETTAYAPSSPYSASKASSDHLVRAWRRTYGLPTIVTNCSNNYGPYHFPEKLIPLVILNALEGKPLPIYGKGDQIRDWLYVEDHARALHMVVTEGKAGETYNIGGHNEKKNLDVVFTICDLLDEIVPKATSYREQITYVADRPGHDRRYAIDAGKISRELGWKPLETFESGIRKTVEWYLANTQWVNNVKSGAYQSWIEQNYEGRQ 361
               SCOP domains d1kewa_ A: dTDP-glucose 4,6-dehydratase (RmlB)                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1kewA01 A:1-203,A:231-264,A:303-324 NAD(P)-binding Rossmann-like Domain                                                                                                                                    1kewA02                    1kewA01                           1kewA02                      ---------1kewA01               1kewA02                     --------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhhh..eeeeee......hhhhhh.......eeeee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhheeeeeee.hhhh...hhhhh..................hhhhhhhhhhhhhhhhhhhhhh..eeeeee.eee.......hhhhhhhhhhhhh..eeee.....eeeeeehhhhhhhhhhhhhhh....eeee....eeehhhhhhhhhhhhhhhh....hhhh.eeee.............hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kew A   1 MKILITGGAGFIGSAVVRHIIKNTQDTVVNIDKLTYAGNLESLSDISESNRYNFEHADICDSAEITRIFEQYQPDAVMHLAAESHVDRSITGPAAFIETNIVGTYALLEVARKYWSALGEDKKNNFRFHHISTDEVYGDLPHPDEVENSVTLPLFTETTAYAPSSPYSASKASSDHLVRAWRRTYGLPTIVTNCSNNYGPYHFPEKLIPLVILNALEGKPLPIYGKGDQIRDWLYVEDHARALHMVVTEGKAGETYNIGGHNEKKNLDVVFTICDLLDEIVPKATSYREQITYVADRPGHDRRYAIDAGKISRELGWKPLETFESGIRKTVEWYLANTQWVNNVKSGAYQSWIEQNYEGRQ 361
                                    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       290       300       310       320       330       340       350       360 


Chain B from PDB  Type:PROTEIN  Length:361
 aligned with RMLB_SALTY | P26391 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:361
                                    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       290       300       310       320       330       340       350       360 
           RMLB_SALTY     1 MKILITGGAGFIGSAVVRHIIKNTQDTVVNIDKLTYAGNLESLSDISESNRYNFEHADICDSAEITRIFEQYQPDAVMHLAAESHVDRSITGPAAFIETNIVGTYALLEVARKYWSALGEDKKNNFRFHHISTDEVYGDLPHPDEVENSVTLPLFTETTAYAPSSPYSASKASSDHLVRAWRRTYGLPTIVTNCSNNYGPYHFPEKLIPLVILNALEGKPLPIYGKGDQIRDWLYVEDHARALHMVVTEGKAGETYNIGGHNEKKNLDVVFTICDLLDEIVPKATSYREQITYVADRPGHDRRYAIDAGKISRELGWKPLETFESGIRKTVEWYLANTQWVNNVKSGAYQSWIEQNYEGRQ 361
               SCOP domains d1kewb_ B: dTDP-glucose 4,6-dehydratase (RmlB)                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1kewB01 B:1-203,B:231-264,B:303-324 NAD(P)-binding Rossmann-like Domain                                                                                                                                    1kewB02                    1kewB01                           1kewB02                      ---------1kewB01               1kewB02                     --------- CATH domains
           Pfam domains (1) --Epimerase-1kewB01 B:3-259                                                                                                                                                                                                                                        ------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) --Epimerase-1kewB02 B:3-259                                                                                                                                                                                                                                        ------------------------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author .eeeee...hhhhhhhhhhhhhhh..eeeeee......hhhhhh.......eeeee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhheeeeeee.hhhh...hhhhh..................hhhhhhhhhhhhhhhhhhhhhh..eeeeee.eee.......hhhhhhhhhhhh...eeee.....eeeeeehhhhhhhhhhhhhhh....eeee....eeehhhhhhhhhhhhhhhh....hhhh.eeee.............hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kew B   1 MKILITGGAGFIGSAVVRHIIKNTQDTVVNIDKLTYAGNLESLSDISESNRYNFEHADICDSAEITRIFEQYQPDAVMHLAAESHVDRSITGPAAFIETNIVGTYALLEVARKYWSALGEDKKNNFRFHHISTDEVYGDLPHPDEVENSVTLPLFTETTAYAPSSPYSASKASSDHLVRAWRRTYGLPTIVTNCSNNYGPYHFPEKLIPLVILNALEGKPLPIYGKGDQIRDWLYVEDHARALHMVVTEGKAGETYNIGGHNEKKNLDVVFTICDLLDEIVPKATSYREQITYVADRPGHDRRYAIDAGKISRELGWKPLETFESGIRKTVEWYLANTQWVNNVKSGAYQSWIEQNYEGRQ 361
                                    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       290       300       310       320       330       340       350       360
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RMLB_SALTY | P26391)
molecular function
    GO:0070404    NADH binding    Interacting selectively and non-covalently with the reduced form, NADH, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions.
    GO:0008460    dTDP-glucose 4,6-dehydratase activity    Catalysis of the reaction: dTDP-glucose = dTDP-4-dehydro-6-deoxy-alpha-D-glucose + H(2)O.
    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.
biological process
    GO:0009243    O antigen biosynthetic process    The chemical reactions and pathways resulting in the formation of the O side chain of a lipopolysaccharide, which determines the antigenic specificity of the organism. It is made up of about 50 repeating units of a branched tetrasaccharide.
    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.
    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:0009225    nucleotide-sugar metabolic process    The cellular chemical reactions and pathways involving 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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RMLB_SALTY | P26391: 1g1a 1keu

(-) Related Entries Specified in the PDB File

1g1a RMLB FROM SALMONELLA ENTERICA SEROVAR TYPHIMURIUM WITH NAD+ BOUND
1kep RMLB FROM STREPTOCOCCUS SUIS WITH DTDP-XYLOSE BOUND
1ker RMLB FROM STREPTOCOCCUS SUIS WITH DTDP-D-GLUCOSE BOUND
1ket RMLB FROM STREPTOCOCCUS SUIS WITH THYMIDINE DIPHOSPHATE BOUND
1keu RMLB FROM SALMONELLA ENTERICA SEROVAR TYPHIMURIUM WITH DTDP -D-GLUCOSE BOUND