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(-) Description

Title :  THE STRUCTURE OF NADH IN THE DTDP-D-GLUCOSE DEHYDRATASE (RMLB) ENZYME
 
Authors :  K. Beis, J. H. Naismith
Date :  04 Feb 03  (Deposition) - 02 Oct 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lyase, Dehydratase, Nadh, Rhamnose (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Beis, S. T. Allard, A. D. Hegeman, G. Murshudov, D. Philp, J. H. Naismith
The Structure Of Nadh In The Enzyme Dtdp-D-Glucose Dehydratase (Rmlb)
J. Am. Chem. Soc. V. 125 11872 2003
PubMed-ID: 14505409  |  Reference-DOI: 10.1021/JA035796R

(-) Compounds

Molecule 1 - DTDP-GLUCOSE 4,6-DEHYDRATASE
    Cell Line: BL21DE3
    Chains: A, B
    EC Number: 4.2.1.46
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: BL21DE3
    Expression System Plasmid: PET21(+)
    Expression System Taxid: 562
    Expression System Variant: BACTERIA
    Expression System Vector Type: PLASMID
    Organism Scientific: STREPTOCOCCUS SUIS
    Organism Taxid: 1307
    Strain: 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
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2SO43Ligand/IonSULFATE ION
3TDX2Ligand/IonTHYMIDINE-5'-DIPHOSPHO-BETA-D-XYLOSE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:258 , THR A:309 , ASP A:310 , PHE A:311 , SER A:312 , HOH A:2394 , HOH A:2395BINDING SITE FOR RESIDUE SO4 A1351
2AC2SOFTWARELEU A:52 , GLY A:53 , ASP A:255 , ARG A:299 , SO4 A:1353 , HOH A:2320 , HOH A:2396 , HOH A:2397 , HOH A:2398 , HOH A:2399 , HOH A:2400 , HOH A:2401BINDING SITE FOR RESIDUE SO4 A1352
3AC3SOFTWAREGLY A:53 , ASP A:54 , ARG A:55 , SO4 A:1352 , HOH A:2062 , HOH A:2400 , HOH A:2401 , HOH A:2402 , HOH A:2403 , HOH A:2404BINDING SITE FOR RESIDUE SO4 A1353
4AC4SOFTWARESER A:86 , HIS A:87 , ASN A:88 , THR A:125 , 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:1350 , HOH A:2211 , HOH A:2212 , HOH A:2310 , HOH A:2387 , HOH A:2388BINDING SITE FOR RESIDUE TDX A1349
5AC5SOFTWAREALA 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 , TDX A:1349 , HOH A:2051 , HOH A:2113 , HOH A:2211 , HOH A:2214 , HOH A:2220 , HOH A:2389 , HOH A:2390 , HOH A:2391 , HOH A:2392 , HOH A:2393BINDING SITE FOR RESIDUE NAD A1350
6AC6SOFTWAREALA 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 , TDX B:1349 , HOH B:2050 , HOH B:2115 , HOH B:2218 , HOH B:2227 , HOH B:2345 , HOH B:2346 , HOH B:2347 , HOH B:2348 , HOH B:2349 , HOH B:2350BINDING SITE FOR RESIDUE NAD B1348
7AC7SOFTWARESER B:86 , HIS B:87 , ASN B:88 , THR B:125 , 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:1348 , HOH B:2219 , HOH B:2351 , HOH B:2352 , HOH B:2353BINDING SITE FOR RESIDUE TDX B1349

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OC2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1OC2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OC2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OC2)

(-) Exons   (0, 0)

(no "Exon" information available for 1OC2)

(-) 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 d1oc2a_ A: dTDP-glucose 4,6-dehydratase (RmlB)                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -1oc2A01 A:4-197,A:225-258,A:290-312 NAD(P)-binding Rossmann-like Domain                                                                                                                           1oc2A02                    1oc2A01                           1oc2A02               ---------1oc2A01                1oc2A02                     -------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhhh...eeeeee......hhhhhhhhh...eeeee....hhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.hhhh...hhhhh....................hhhhhhhhhhhhhhhhhhhhhh.eeeeeee..ee.......hhhhhhhhhhhhh...eee.....eee.eehhhhhhhhhhhhhhh....eeee....eeehhhhhhhhhhhh.......eee.............hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oc2 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 d1oc2b_ B: dTDP-glucose 4,6-dehydratase (RmlB)                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --1oc2B01 B:4-197,B:225-258,B:290-312 NAD(P)-binding Rossmann-like Domain                                                                                                                           1oc2B02                    1oc2B01                           1oc2B02               ---------1oc2B01                1oc2B02                     -------- CATH domains
           Pfam domains (1) -----Epimerase-1oc2B01 B:7-253                                                                                                                                                                                                                              ----------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----Epimerase-1oc2B02 B:7-253                                                                                                                                                                                                                              ----------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....eeeee...hhhhhhhhhhhhhhh...eeeeee......hhhhhhhhh...eeeee....hhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.hhhh...hhhhh....................hhhhhhhhhhhhhhhhhhhhhh.eeeeeee..ee.......hhhhhhhhhhhhh...eee.....eee.eehhhhhhhhhhhhhhh....eeee....eeehhhhhhhhhhhh.......eee.............hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oc2 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  (1, 2)

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

(-) Gene Ontology  (4, 4)

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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q8GIP9_STRSU | Q8GIP9: 1kep 1ker

(-) Related Entries Specified in the PDB File

1kep THE CRYSTAL STRUCTURE OF DTDP-D-GLUCOSE 4 ,6-DEHYDRATASE(RMLB) FROM STREPTOCOCCUS SUIS WITH DTDP-XYLOSE BOUND
1ker THE CRYSTAL STRUCTURE OF DTDP-D-GLUCOSE 4 ,6-DEHYDRATASE(RMLB) FROM STREPTOCOCCUS SUIS WITH DTDP-D-GLUCOSE BOUND
1ket THE CRYSTAL STRUCTURE OF DTDP-D-GLUCOSE 4 ,6-DEHYDRATASE(RMLB) FROM STREPTOCOCCUS SUIS WITH THYMIDINE DIPHOSPHATEBOUND