Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
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 STREPTOCOCCUS SUIS 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 :  2.20
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: PET21
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RMLB
    Organism Scientific: STREPTOCOCCUS SUIS
    Organism Taxid: 1307
    Synonym: RMLB
    Variant: SEROTYPE 2

 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
1DAU2Ligand/Ion2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3SO43Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:53 , ASP A:54 , ARG A:55 , HOH A:2574 , HOH A:2689 , HOH A:2868 , HOH A:2880 , HOH A:2884BINDING SITE FOR RESIDUE SO4 A 2001
2AC2SOFTWARELYS A:258 , THR A:309 , ASP A:310 , PHE A:311 , SER A:312 , HOH A:2723 , HOH A:2897BINDING SITE FOR RESIDUE SO4 A 2002
3AC3SOFTWARELYS B:258 , THR B:309 , ASP B:310 , PHE B:311 , SER B:312 , HOH B:2787 , HOH B:2883 , HOH B:2894BINDING SITE FOR RESIDUE SO4 B 2003
4AC4SOFTWARESER A:86 , HIS A:87 , ASN A:88 , THR A:125 , ASP A:126 , GLU A:127 , TYR A:161 , ASN A:190 , GLU A:199 , LYS A:200 , PHE A:201 , ARG A:204 , GLN A:205 , LYS A:216 , LEU A:217 , TYR A:218 , ASN A:223 , ARG A:225 , ASN A:260 , ARG A:284 , HIS A:287 , TYR A:340 , NAD A:1400 , HOH A:2586 , HOH A:2591 , HOH A:2606 , HOH A:2666BINDING SITE FOR RESIDUE DAU A 2573
5AC5SOFTWARESER B:86 , HIS B:87 , ASN B:88 , THR B:125 , ASP B:126 , GLU B:127 , TYR B:161 , ASN B:190 , GLU B:199 , LYS B:200 , PHE B:201 , ARG B:204 , GLN B:205 , LYS B:216 , LEU B:217 , TYR B:218 , ARG B:225 , ASN B:260 , ARG B:284 , HIS B:287 , TYR B:340 , NAD B:1500 , HOH B:2597 , HOH B:2612 , HOH B:2614 , HOH B:2637BINDING SITE FOR RESIDUE DAU B 2574
6AC6SOFTWAREGLY A:11 , ALA A:13 , GLY A:14 , PHE A:15 , ILE A:16 , ASP A:37 , LYS A:38 , LEU A:39 , THR A:40 , ALA A:42 , GLY A:43 , GLY A:61 , ASP A:62 , ILE A:63 , TYR A:82 , ALA A:83 , ALA A:84 , SER A:86 , THR A:101 , VAL A:123 , SER A:124 , TYR A:161 , LYS A:165 , CYS A:188 , SER A:189 , ASN A:190 , ASN A:191 , DAU A:2573 , HOH A:2580 , HOH A:2582 , HOH A:2600 , HOH A:2607 , HOH A:2608 , HOH A:2613 , HOH A:2626 , HOH A:2637 , HOH A:2654BINDING SITE FOR RESIDUE NAD A 1400
7AC7SOFTWAREGLY B:11 , ALA B:13 , GLY B:14 , PHE B:15 , ILE B:16 , ASP B:37 , LYS B:38 , LEU B:39 , THR B:40 , ALA B:42 , GLY B:43 , GLY B:61 , ASP B:62 , ILE B:63 , TYR B:82 , ALA B:83 , ALA B:84 , SER B:86 , THR B:101 , VAL B:123 , SER B:124 , TYR B:161 , LYS B:165 , CYS B:188 , SER B:189 , ASN B:191 , DAU B:2574 , HOH B:2580 , HOH B:2582 , HOH B:2587 , HOH B:2598 , HOH B:2599 , HOH B:2600 , HOH B:2622 , HOH B:2627 , HOH B:2631 , HOH B:2658BINDING SITE FOR RESIDUE NAD B 1500

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1KER)

(-) 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:346
 aligned with Q8GIP9_STRSU | Q8GIP9 from UniProtKB/TrEMBL  Length:348

    Alignment length:346
                                    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       322       332       342      
         Q8GIP9_STRSU     3 QFKNIIVTGGAGFIGSNFVHYVYNNHPDVHVTVLDKLTYAGNKANLEAILGDRVELVVGDIADAELVDKLAAKADAIVHYAAESHNDNSLNDPSPFIHTNFIGTYTLLEAARKYDIRFHHVSTDEVYGDLPLREDLPGHGEGPGEKFTAETNYNPSSPYSSTKAASDLIVKAWVRSFGVKATISNCSNNYGPYQHIEKFIPRQITNILAGIKPKLYGEGKNVRDWIHTNDHSTGVWAILTKGRMGETYLIGADGEKNNKEVLELILEKMGQPKDAYDHVTDRAGHDLRYAIDASKLRDELGWTPQFTDFSQGLEETIQWYTDNQDWWKAEKEAVEANYAKTQEVIK 348
               SCOP domains d1kera_ A: dTDP-glucose 4,6-dehydratase (RmlB)                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -1kerA01 A:4-197,A:225-258,A:290-312 NAD(P)-binding Rossmann-like Domain                                                                                                                           1kerA02                    1kerA01                           1kerA02               ---------1kerA01                1kerA02                     -------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhhh...eeeeee......hhhhhhhhh...eeeee....hhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.hhhh...hhhhh....................hhhhhhhhhhhhhhhhhhhhhh..eeeeee.eee.......hhhhhhhhhhhh....eee.....eeeeeehhhhhhhhhhhhhhh....eeee....eeehhhhhhhhhhhh.......eee.............hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ker A   3 QFKNIIVTGGAGFIGSNFVHYVYNNHPDVHVTVLDKLTYAGNKANLEAILGDRVELVVGDIADAELVDKLAAKADAIVHYAAESHNDNSLNDPSPFIHTNFIGTYTLLEAARKYDIRFHHVSTDEVYGDLPLREDLPGHGEGPGEKFTAETNYNPSSPYSSTKAASDLIVKAWVRSFGVKATISNCSNNYGPYQHIEKFIPRQITNILAGIKPKLYGEGKNVRDWIHTNDHSTGVWAILTKGRMGETYLIGADGEKNNKEVLELILEKMGQPKDAYDHVTDRAGHDLRYAIDASKLRDELGWTPQFTDFSEGLEETIQWYTDNQDWWKAEKEAVEANYAKTQEVIK 348
                                    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       322       332       342      


Chain A from PDB  Type:PROTEIN  Length:346
 aligned with RMLB_STRMU | P95780 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:346
                                    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       322       332       342      
           RMLB_STRMU     3 EYKNIIVTGGAGFIGSNFVHYVYNNHPDVHVTVLDKLTYAGNRANLEEILGDRVELVVGDIADSELVDKLAAKADAIVHYAAESHNDNSLKDPSPFIYTNFVGTYILLEAARKYDIRFHHVSTDEVYGDLPLREDLPGHGEGPGEKFTAETKYNPSSPYSSTKAASDLIVKAWVRSFGVKATISNCSNNYGPYQHIEKFIPRQITNILSGIKPKLYGEGKNVRDWIHTNDHSTGVWAILTKGRIGETYLIGADGEKNNKEVLELILEKMSQPKNAYDHVTDRAGHDLRYAIDSTKLREELGWKPQFTNFEEGLEDTIKWYTEHEDWWKAEKEAVEANYAKTQKILN 348
               SCOP domains d1kera_ A: dTDP-glucose 4,6-dehydratase (RmlB)                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -1kerA01 A:4-197,A:225-258,A:290-312 NAD(P)-binding Rossmann-like Domain                                                                                                                           1kerA02                    1kerA01                           1kerA02               ---------1kerA01                1kerA02                     -------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhhh...eeeeee......hhhhhhhhh...eeeee....hhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.hhhh...hhhhh....................hhhhhhhhhhhhhhhhhhhhhh..eeeeee.eee.......hhhhhhhhhhhh....eee.....eeeeeehhhhhhhhhhhhhhh....eeee....eeehhhhhhhhhhhh.......eee.............hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ker A   3 QFKNIIVTGGAGFIGSNFVHYVYNNHPDVHVTVLDKLTYAGNKANLEAILGDRVELVVGDIADAELVDKLAAKADAIVHYAAESHNDNSLNDPSPFIHTNFIGTYTLLEAARKYDIRFHHVSTDEVYGDLPLREDLPGHGEGPGEKFTAETNYNPSSPYSSTKAASDLIVKAWVRSFGVKATISNCSNNYGPYQHIEKFIPRQITNILAGIKPKLYGEGKNVRDWIHTNDHSTGVWAILTKGRMGETYLIGADGEKNNKEVLELILEKMGQPKDAYDHVTDRAGHDLRYAIDASKLRDELGWTPQFTDFSEGLEETIQWYTDNQDWWKAEKEAVEANYAKTQEVIK 348
                                    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       322       332       342      


Chain B from PDB  Type:PROTEIN  Length:347
 aligned with Q8GIP9_STRSU | Q8GIP9 from UniProtKB/TrEMBL  Length:348

    Alignment length:347
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       
         Q8GIP9_STRSU     2 SQFKNIIVTGGAGFIGSNFVHYVYNNHPDVHVTVLDKLTYAGNKANLEAILGDRVELVVGDIADAELVDKLAAKADAIVHYAAESHNDNSLNDPSPFIHTNFIGTYTLLEAARKYDIRFHHVSTDEVYGDLPLREDLPGHGEGPGEKFTAETNYNPSSPYSSTKAASDLIVKAWVRSFGVKATISNCSNNYGPYQHIEKFIPRQITNILAGIKPKLYGEGKNVRDWIHTNDHSTGVWAILTKGRMGETYLIGADGEKNNKEVLELILEKMGQPKDAYDHVTDRAGHDLRYAIDASKLRDELGWTPQFTDFSQGLEETIQWYTDNQDWWKAEKEAVEANYAKTQEVIK 348
               SCOP domains d1kerb_ B: dTDP-glucose 4,6-dehydratase (RmlB)                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --1kerB01 B:4-197,B:225-258,B:290-312 NAD(P)-binding Rossmann-like Domain                                                                                                                           1kerB02                    1kerB01                           1kerB02               ---------1kerB01                1kerB02                     -------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...hhhhhhhhhhhhhhh...eeeeee......hhhhhhhhh...eeeee....hhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.hhhh...hhhhh....................hhhhhhhhhhhhhhhhhhhhhh..eeeeee.eee.......hhhhhhhhhhhh....eee.....eeeeeehhhhhhhhhhhhhhh....eeee....eeehhhhhhhhhhhh.......eee.............hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ker B   2 SQFKNIIVTGGAGFIGSNFVHYVYNNHPDVHVTVLDKLTYAGNKANLEAILGDRVELVVGDIADAELVDKLAAKADAIVHYAAESHNDNSLNDPSPFIHTNFIGTYTLLEAARKYDIRFHHVSTDEVYGDLPLREDLPGHGEGPGEKFTAETNYNPSSPYSSTKAASDLIVKAWVRSFGVKATISNCSNNYGPYQHIEKFIPRQITNILAGIKPKLYGEGKNVRDWIHTNDHSTGVWAILTKGRMGETYLIGADGEKNNKEVLELILEKMGQPKDAYDHVTDRAGHDLRYAIDASKLRDELGWTPQFTDFSEGLEETIQWYTDNQDWWKAEKEAVEANYAKTQEVIK 348
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       


Chain B from PDB  Type:PROTEIN  Length:347
 aligned with RMLB_STRMU | P95780 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:347
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       
           RMLB_STRMU     2 TEYKNIIVTGGAGFIGSNFVHYVYNNHPDVHVTVLDKLTYAGNRANLEEILGDRVELVVGDIADSELVDKLAAKADAIVHYAAESHNDNSLKDPSPFIYTNFVGTYILLEAARKYDIRFHHVSTDEVYGDLPLREDLPGHGEGPGEKFTAETKYNPSSPYSSTKAASDLIVKAWVRSFGVKATISNCSNNYGPYQHIEKFIPRQITNILSGIKPKLYGEGKNVRDWIHTNDHSTGVWAILTKGRIGETYLIGADGEKNNKEVLELILEKMSQPKNAYDHVTDRAGHDLRYAIDSTKLREELGWKPQFTNFEEGLEDTIKWYTEHEDWWKAEKEAVEANYAKTQKILN 348
               SCOP domains d1kerb_ B: dTDP-glucose 4,6-dehydratase (RmlB)                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --1kerB01 B:4-197,B:225-258,B:290-312 NAD(P)-binding Rossmann-like Domain                                                                                                                           1kerB02                    1kerB01                           1kerB02               ---------1kerB01                1kerB02                     -------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...hhhhhhhhhhhhhhh...eeeeee......hhhhhhhhh...eeeee....hhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.hhhh...hhhhh....................hhhhhhhhhhhhhhhhhhhhhh..eeeeee.eee.......hhhhhhhhhhhh....eee.....eeeeeehhhhhhhhhhhhhhh....eeee....eeehhhhhhhhhhhh.......eee.............hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ker B   2 SQFKNIIVTGGAGFIGSNFVHYVYNNHPDVHVTVLDKLTYAGNKANLEAILGDRVELVVGDIADAELVDKLAAKADAIVHYAAESHNDNSLNDPSPFIHTNFIGTYTLLEAARKYDIRFHHVSTDEVYGDLPLREDLPGHGEGPGEKFTAETNYNPSSPYSSTKAASDLIVKAWVRSFGVKATISNCSNNYGPYQHIEKFIPRQITNILAGIKPKLYGEGKNVRDWIHTNDHSTGVWAILTKGRMGETYLIGADGEKNNKEVLELILEKMGQPKDAYDHVTDRAGHDLRYAIDASKLRDELGWTPQFTDFSEGLEETIQWYTDNQDWWKAEKEAVEANYAKTQEVIK 348
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341
   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 1KER)

(-) Gene Ontology  (7, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8GIP9_STRSU | Q8GIP9)
molecular function
    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.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    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.

Chain A,B   (RMLB_STRMU | P95780)
molecular function
    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: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 ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ker)
 

(-) 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
  1ker
    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
  Q8GIP9_STRSU | Q8GIP9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  RMLB_STRMU | P95780
    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
  Q8GIP9_STRSU | Q8GIP9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  RMLB_STRMU | P95780
    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_STRMU | P95780: 1kep 1ket
UniProtKB/TrEMBL
        Q8GIP9_STRSU | Q8GIP9: 1kep 1oc2

(-) 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
1ket RMLB FROM STREPTOCOCCUS SUIS WITH THYMIDINE DIPHOSPHATE BOUND
1keu RMLB FROM SALMONELLA ENTERICA SEROVAR TYPHIMURIUM WITH DTDP -D-GLUCOSE BOUND
1kew RMLB FROM SALMONELLA ENTERICA SEROVAR TYPHIMURIUM WITH NAD+ BOUND