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(-) Description

Title :  CRYSTAL STRUCTURE OF APO-DTDP-6-DEOXY-L-LYXO-4-HEXULOSE REDUCTASE (RMLD) FROM SALMONELLA ENTERICA SEROVAR TYPHIMURIUM
 
Authors :  W. Blankenfeldt, I. D. Kerr, M. F. Giraud, H. J. Mcmiken, G. A. Leonard, C. Whitfield, P. Messner, M. Graninger, J. H. Naismith
Date :  07 Nov 01  (Deposition) - 28 Jun 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Rossman-Fold, Sugar-Nucleotide-Binding Domain, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Blankenfeldt, I. D. Kerr, M. F. Giraud, H. J. Mcmiken, G. Leonard, C. Whitfield, P. Messner, M. Graninger, J. H. Naismith
Variation On A Theme Of Sdr. Dtdp-6-Deoxy-L- Lyxo-4-Hexulos Reductase (Rmld) Shows A New Mg2+-Dependent Dimerization Mode.
Structure V. 10 773 2002
PubMed-ID: 12057193  |  Reference-DOI: 10.1016/S0969-2126(02)00770-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DTDP-GLUCOSE OXIDOREDUCTASE
    Chains: A
    EC Number: 1.1.1.133
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30
    Expression System Strain: BL21(LAMBDA DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RFBA
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 602
    Synonym: DTDP-6-DEOXY-L-LYXO-4-HEXULOSE REDUCTASE

 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
1MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:506 , HOH A:508 , HOH A:555BINDING SITE FOR RESIDUE MG A 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1KBZ)

(-) Sequences/Alignments

Asymmetric 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:298
 aligned with RMLD_SALTY | P26392 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:298
                                    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        
           RMLD_SALTY     1 MNILLFGKTGQVGWELQRSLAPVGNLIALDVHSKEFCGDFSNPKGVAETVRKLRPDVIVNAAAHTAVDKAESEPELAQLLNATSVEAIAKAANETGAWVVHYSTDYVFPGTGDIPWQETDATSPLNVYGKTKLAGEKALQDNCPKHLIFRTSWVYAGKGNNFAKTMLRLAKERQTLSVINDQYGAPTGAELLADCTAHAIRVALNKPEVAGLYHLVAGGTTTWHDYAALVFDEARKAGITLALTELNAVPTSAYPTPASRPGNSRLNTEKFQRNFDLILPQWELGVKRMLTEMFTTTT 298
               SCOP domains d1kbza_ A: dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD)                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1kbzA01 A:1-161,A:185-220,A:265-280 NAD(P)-binding Rossmann-like Domain                                                                                          1kbzA02                1kbzA01 A:1-161,A:185-220,A:265-280 1kbzA02 A:162-184,A:221-264,A:281-298       1kbzA01         1kbzA02            CATH domains
               Pfam domains RmlD_sub_bind-1kbzA01 A:1-295                                                                                                                                                                                                                                                                          --- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhh....eeee.............hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.hhh.................hhhhhhhhhhhhhhhhhh..eeeeee..ee.....hhhhhhhhhhhhh.eeeee...ee..eehhhhhhhhhhhhhhhhhhhhhheeee......eehhhhhhhhhhhhhhh.......eeeee..................hhhhhhhhh....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kbz A   1 MNILLFGKTGQVGWELQRSLAPVGNLIALDVHSKEFCGDFSNPKGVAETVRKLRPDVIVNAAAHTAVDKAESEPELAQLLNATSVEAIAKAANETGAWVVHYSTDYVFPGTGDIPWQETDATSPLNVYGKTKLAGEKALQDNCPKHLIFRTSWVYAGKGNNFAKTMLRLAKERQTLSVINDQYGAPTGAELLADCTAHAIRVALNKPEVAGLYHLVAGGTTTWHDYAALVFDEARKAGITLALTELNAVPTSAYPTPASRPGNSRLNTEKFQRNFDLILPQWELGVKRMLTEMFTTTT 298
                                    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
   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, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (RMLD_SALTY | P26392)
molecular function
    GO:0008831    dTDP-4-dehydrorhamnose reductase activity    Catalysis of the reaction: dTDP-6-deoxy-L-mannose + NADP(+) = dTDP-4-dehydro-6-deoxy-L-mannose + H(+) + NADPH.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
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:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RMLD_SALTY | P26392: 1kc1 1kc3 1n2s

(-) Related Entries Specified in the PDB File

1kc0 NADH COMPLEX
1kc1 NADPH COMPLEX
1kc3 NADPH/DTDP-L-RHAMNOSE COMPLEX