1E6U - JenaLib

Title :   GDP 4-KETO-6-DEOXY-D-MANNOSE EPIMERASE REDUCTASE

Authors :   C. Rosano, G. Izzo, M. Bolognesi

Date :   23 Aug 00 (Deposition) - 22 Oct 00 (Release) - 21 Apr 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.45

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Epimerase/Reductase, Sdr, Red (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Rosano, A. Bisso, G. Izzo, M. Tonetti, L. Sturla, A. De Flora, M. Bolognesi
Probing The Catalytic Mechanism Of Gdp-4-Keto-6- Deoxy-D-Mannose Epimerase/Reductase By Kinetic And Crystallographic Characterization Of Site-Specific Mutants
J. Mol. Biol. V. 303 77 2000
PubMed-ID: 11021971 | Reference-DOI: 10.1006/JMBI.2000.4106
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (7, 7)

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:152 , PRO A:238 , ARG A:254 , VAL A:270 , VAL A:271 , PHE A:272 , HOH A:2287 , HOH A:2367 , HOH A:2368	BINDING SITE FOR RESIDUE SO4 A1319
2	AC2	SOFTWARE	HIS A:11 , ARG A:12 , ARG A:20	BINDING SITE FOR RESIDUE SO4 A1320
3	AC3	SOFTWARE	ARG A:5 , VAL A:32 , ARG A:34 , GLU A:54 , HOH A:2369	BINDING SITE FOR RESIDUE SO4 A1321
4	AC4	SOFTWARE	ARG A:34 , PHE A:50 , SER A:53 , GLU A:54	BINDING SITE FOR RESIDUE SO4 A1322
5	AC5	SOFTWARE	GLY A:13 , MET A:14 , VAL A:15 , ARG A:36 , LEU A:39 , ASN A:40 , LEU A:41 , LEU A:42 , ALA A:63 , ALA A:64 , VAL A:66 , ILE A:86 , LEU A:105 , GLY A:106 , TYR A:136 , LYS A:140 , PRO A:163 , THR A:164 , HOH A:2083 , HOH A:2203 , HOH A:2355 , HOH A:2356 , HOH A:2357 , HOH A:2358 , HOH A:2359 , HOH A:2360 , HOH A:2361 , HOH A:2362 , HOH A:2363 , HOH A:2364	BINDING SITE FOR RESIDUE NAP A1317
6	AC6	SOFTWARE	GLY A:68 , ILE A:69 , VAL A:70 , ALA A:71 , SER A:178 , LYS A:262 , HOH A:2092 , HOH A:2214 , HOH A:2365 , HOH A:2366	BINDING SITE FOR RESIDUE UVW A1318
7	AC7	SOFTWARE	ARG A:20 , ARG A:21 , HIS A:170 , TRP A:311 , HOH A:2351 , HOH A:2370 , HOH A:2371 , HOH A:2372	BINDING SITE FOR RESIDUE TRS A1323

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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:315
 aligned with FCL_ECOLI | P32055 from UniProtKB/Swiss-Prot  Length:321

    Alignment length:315
                                    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     
            FCL_ECOLI     2 SKQRVFIAGHRGMVGSAIRRQLEQRGDVELVLRTRDELNLLDSRAVHDFFASERIDQVYLAAAKVGGIVANNTYPADFIYQNMMIESNIIHAAHQNDVNKLLFLGSSCIYPKLAKQPMAESELLQGTLEPTNEPYAIAKIAGIKLCESYNRQYGRDYRSVMPTNLYGPHDNFHPSNSHVIPALLRRFHEATAQNAPDVVVWGSGTPMREFLHVDDMAAASIHVMELAHEVWLENTQPMLSHINVGTGVDCTIRELAQTIAKVVGYKGRVVFDASKPDGTPRKLLDVTRLHQLGWYHEISLEAGLASTYQWFLENQ 316
               SCOP domains d1e6ua_ A: GDP-4-keto-6-deoxy-d-mannose epimerase/reductase (GDP-fucose synthetase)                                                                                                                                                                                                                                         SCOP domains
               CATH domains -1e6uA01 A:3-167,A:210-248,A:284-299 NAD(P)-binding Rossmann-like Domain                                                                                              1e6uA02 A:168-209,A:249-283,A:300-316     1e6uA01 A:3-167,A:210-248,A:284-299    1e6uA02                            1e6uA01         1e6uA02           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhh....eeee..........hhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh........hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.eee...........hhhhhhhhhhhhhhhhh..eeeee........eeehhhhhhhhhhhhhhhhhhhhhh.......eee.......hhhhhhhhhhhhh...eeeee.............hhhhhhh......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e6u A   2 AKQRVFIAGHRGMVGSAIRRQLEQRGDVELVLRTRDELNLLDSRAVHDFFASERIDQVYLAAAKVGGIVANNTYPADFIYQNMMIESNIIHAAHQNDVNKLLFLGSSCIYPKLAKQPMAESELLQGTLEPTNEPYAIAKIAGIKLCESYNRQYGRDYRSVMPTNLYGPHDNFHPSNSHVIPALLRRFHEATAQKAPDVVVWGSGTPMREFLHVDDMAAASIHVMELAHEVWLENTQPMLSHINVGTGVDCTIRELAQTIAKVVGYKGRVVFDASKPDGTPRKLLDVTRLHQLGWYHEISLEAGLASTYQWFLENQ 316
                                    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

Legend:		→ Mismatch	(orange background)
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		→ 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 (0, 0)

Gene Ontology (12, 12)

Asymmetric Unit(hide GO term definitions)

Chain A (FCL_ECOLI | P32055)

molecular function
	GO:0050577	GDP-L-fucose synthase activity	Catalysis of the reaction: GDP-L-fucose + NAD+ = GDP-4-dehydro-6-deoxy-D-mannose + NADH + H+.
	GO:0070401	NADP+ binding	Interacting selectively and non-covalently with the oxidized form, NADP+, of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0050662	coenzyme binding	Interacting selectively and non-covalently with a coenzyme, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	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:0042351	'de novo' GDP-L-fucose biosynthetic process	The chemical reactions and pathways resulting in the formation of GDP-L-fucose from GDP-D-mannose via GDP-4-dehydro-6-deoxy-D-mannose, requiring the functions of GDP-mannose 4,6-dehydratase (EC:4.2.1.47) and GDP-L-fucose synthase (EC:1.1.1.271).
	GO:0009242	colanic acid biosynthetic process	The chemical reactions and pathways resulting in the formation of colanic acid, a capsular bacterial polysaccharide.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0009226	nucleotide-sugar biosynthetic process	The chemical reactions and pathways resulting in the formation of 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.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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