1KC3 - JenaLib

Title :   CRYSTAL STRUCTURE OF DTDP-6-DEOXY-L-LYXO-4-HEXULOSE REDUCTASE (RMLD) IN COMPLEX WITH NADPH AND DTDP-L-RHAMNOSE

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 :   2.70

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

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:908 , HOH A:909 , HOH A:910	BINDING SITE FOR RESIDUE MG A 501
2	AC2	SOFTWARE	GLY A:10 , GLN A:11 , VAL A:12 , VAL A:31 , GLY A:38 , ASP A:39 , PHE A:40 , SER A:41 , ALA A:61 , ALA A:62 , ALA A:63 , THR A:65 , LEU A:80 , TYR A:102 , SER A:103 , THR A:104 , TYR A:128 , LYS A:132 , THR A:151 , VAL A:154 , GLN A:174 , TRH A:601 , HOH A:904 , HOH A:907 , HOH A:978 , HOH A:994	BINDING SITE FOR RESIDUE NDP A 901
3	AC3	SOFTWARE	VAL A:67 , THR A:104 , ASP A:105 , TYR A:106 , TYR A:128 , SER A:152 , TRP A:153 , PHE A:162 , SER A:177 , VAL A:178 , ILE A:179 , GLN A:182 , TRP A:223 , ARG A:260 , NDP A:901 , HOH A:951 , HOH A:952 , HOH A:988	BINDING SITE FOR RESIDUE TRH A 601

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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 d1kc3a_ A: dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD)                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1kc3A01 A:1-163,A:185-220,A:265-282 NAD(P)-binding Rossmann-like Domain                                                                                            1kc3A02              1kc3A01 A:1-163,A:185-220,A:265-282 1kc3A02 A:164-184,A:221-264,A:283-298       1kc3A01           1kc3A02          CATH domains
               Pfam domains RmlD_sub_bind-1kc3A01 A:1-295                                                                                                                                                                                                                                                                          --- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhh...eeeee............hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.hhh.................hhhhhhhhhhhhhhhhhh..eeeeee..ee.....hhhhhhhhhhhhh.eeeee...ee..eehhhhhhhhhhhhhhhhhhhhhheeee......eehhhhhhhhhhhhhhh.......eeeeehhhhh........ee...hhhhhhhhh....hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kc3 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)

CATH Domains (2, 2)

Pfam Domains (1, 1)

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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