Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  THE CRYSTAL STRUCTURE OF DTDP-D-GLUCOSE 4,6-DEHYDRATASE (RMLB) FROM SALMONELLA ENTERICA SEROVAR TYPHIMURIUM WITH DTDP-D-GLUCOSE 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) - 23 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
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  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1DAU2Ligand/Ion2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:84 , HIS A:85 , VAL A:86 , THR A:133 , ASP A:134 , GLU A:135 , TYR A:167 , 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 , NAD A:1400 , HOH A:2581 , HOH A:2582 , HOH A:2601 , HOH A:2645BINDING SITE FOR RESIDUE DAU A 2573
2AC2SOFTWARESER B:84 , HIS B:85 , VAL B:86 , THR B:133 , ASP B:134 , GLU B:135 , TYR B:167 , 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 , NAD B:1500 , HOH B:2576 , HOH B:2593 , HOH B:2594 , HOH B:2631BINDING SITE FOR RESIDUE DAU B 2574
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 , DAU A:2573 , HOH A:2589 , HOH A:2606 , HOH A:2617 , HOH A:2620 , HOH A:2622 , HOH A:2625 , HOH A:2644BINDING 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 , TYR B:167 , LYS B:171 , CYS B:194 , SER B:195 , ASN B:196 , ASN B:197 , DAU B:2574 , HOH B:2581 , HOH B:2583 , HOH B:2586 , HOH B:2589 , HOH B:2614 , HOH B:2617 , HOH B:2636 , HOH B:2637BINDING SITE FOR RESIDUE NAD B 1500

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1KEU)

(-) 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 d1keua_ A: dTDP-glucose 4,6-dehydratase (RmlB)                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1keuA01 A:1-203,A:231-264,A:303-324 NAD(P)-binding Rossmann-like Domain                                                                                                                                    1keuA02                    1keuA01                           1keuA02                      ---------1keuA01               1keuA02                     --------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         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
                 1keu 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 d1keub_ B: dTDP-glucose 4,6-dehydratase (RmlB)                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1keuB01 B:1-203,B:231-264,B:303-324 NAD(P)-binding Rossmann-like Domain                                                                                                                                    1keuB02                    1keuB01                           1keuB02                      ---------1keuB01               1keuB02                     --------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         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
                 1keu 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  (0, 0)

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

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    DAU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1keu)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1keu
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  RMLB_SALTY | P26391
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  4.2.1.46
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  RMLB_SALTY | P26391
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

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

(-) 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
1kew RMLB FROM SALMONELLA ENTERICA SEROVAR TYPHIMURIUM WITH NAD+ BOUND