1E7R - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   GDP 4-KETO-6-DEOXY-D-MANNOSE EPIMERASE REDUCTASE Y136E

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

Date :   07 Sep 00 (Deposition) - 18 Oct 00 (Release) - 01 Sep 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Epimerase, Reductase, Sdr, Red, Isomerase (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

Molecule 1 - GDP-FUCOSE SYNTHETASE
	Chains	:	A
	EC Number	:	5.1.3.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	UNKNOWN MOLECULE LABELED AS ACETYLPHOSPHATE
	Synonym	:	GDP-4-KETO 6-DEOXY-MANNOSE 3,5-EPIMERASE 4-REDUCTASE, GMER

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 6)

No.	Name	Count	Type	Full Name
1	NAP	1	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2	SO4	2	Ligand/Ion	SULFATE ION
3	TRS	2	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
4	UVW	1	Ligand/Ion	ACETYLPHOSPHATE

Biological Unit 1 (4, 12)

No.	Name	Count	Type	Full Name
1	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2	SO4	4	Ligand/Ion	SULFATE ION
3	TRS	4	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
4	UVW	2	Ligand/Ion	ACETYLPHOSPHATE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:11 , ARG A:12 , ARG A:20 , THR A:35	BINDING SITE FOR RESIDUE SO4 A1320
2	AC2	SOFTWARE	ARG A:152 , PRO A:238 , ARG A:254 , VAL A:270 , VAL A:271 , PHE A:272 , HOH A:2343 , HOH A:2344 , HOH A:2345	BINDING SITE FOR RESIDUE SO4 A1321
3	AC3	SOFTWARE	GLY A:10 , 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:62 , ALA A:63 , ALA A:64 , VAL A:66 , ILE A:86 , LEU A:105 , GLY A:106 , SER A:107 , LYS A:140 , PRO A:163 , THR A:164 , LEU A:166 , HOH A:2101 , HOH A:2323 , HOH A:2324 , HOH A:2325 , HOH A:2326 , HOH A:2327 , HOH A:2328 , HOH A:2329 , HOH A:2330 , HOH A:2331 , HOH A:2332 , HOH A:2333	BINDING SITE FOR RESIDUE NAP A1317
4	AC4	SOFTWARE	GLY A:67 , GLY A:68 , ILE A:69 , VAL A:70 , ALA A:71 , SER A:178 , LYS A:262 , HOH A:2335 , HOH A:2336	BINDING SITE FOR RESIDUE UVW A1318
5	AC5	SOFTWARE	ASP A:78 , TYR A:81 , GLN A:82 , HIS A:92 , HIS A:95 , TYR A:150 , GLN A:153 , TYR A:154 , HOH A:2337 , HOH A:2338 , HOH A:2339 , HOH A:2341 , HOH A:2342	BINDING SITE FOR RESIDUE TRS A1319
6	AC6	SOFTWARE	ARG A:20 , ARG A:21 , HIS A:170 , TRP A:311 , HOH A:2346 , HOH A:2347	BINDING SITE FOR RESIDUE TRS A1322

(no "SS Bond" information available for 1E7R)

Asymmetric Unit

No.	Residues
1	Gln A:117	-	Pro A:118

(no "SAP(SNP)/Variant" information available for 1E7R)

(no "PROSITE Motif" information available for 1E7R)

(no "Exon" information available for 1E7R)

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
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Chain A from PDB  Type:PROTEIN  Length:314
 aligned with FCL_ECOLI | P32055 from UniProtKB/Swiss-Prot  Length:321

    Alignment length:314
                                    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    
            FCL_ECOLI     3 KQRVFIAGHRGMVGSAIRRQLEQRGDVELVLRTRDELNLLDSRAVHDFFASERIDQVYLAAAKVGGIVANNTYPADFIYQNMMIESNIIHAAHQNDVNKLLFLGSSCIYPKLAKQPMAESELLQGTLEPTNEPYAIAKIAGIKLCESYNRQYGRDYRSVMPTNLYGPHDNFHPSNSHVIPALLRRFHEATAQNAPDVVVWGSGTPMREFLHVDDMAAASIHVMELAHEVWLENTQPMLSHINVGTGVDCTIRELAQTIAKVVGYKGRVVFDASKPDGTPRKLLDVTRLHQLGWYHEISLEAGLASTYQWFLENQ 316
               SCOP domains d1e7ra_ A: GDP-4-keto-6-deoxy-d-mannose epimerase/reductase (GDP-fucose synthetase)                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1e7rA01 A:3-167,A:210-248,A:284-299 NAD(P)-binding Rossmann-like Domain                                                                                              1e7rA02 A:168-209,A:249-283,A:300-316     1e7rA01 A:3-167,A:210-248,A:284-299    1e7rA02                            1e7rA01         1e7rA02           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhh....eeee..........hhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh........hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.eee...........hhhhhhhhhhhhhhhhh..eeeee.....ee.eeehhhhhhhhhhhhhhhhhhhhhh.......eee.....eehhhhhhhhhhhhh...eeeee.............hhhhhhh......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e7r A   3 KQRVFIAGHRGMVGSAIRRQLEQRGDVELVLRTRDELNLLDSRAVHDFFASERIDQVYLAAAKVGGIVANNTYPADFIYQNMMIESNIIHAAHQNDVNKLLFLGSSCIYPKLAKQPMAESELLQGTLEPTNEPEAIAKIAGIKLCESYNRQYGRDYRSVMPTNLYGPHDNFHPSNSHVIPALLRRFHEATAQSAPDVVVWGSGTPMREFLHVDDMAAASIHVMELAHEVWLENTQPMLSHINVGTGVDCTIRELAQTIAKVVGYKGRVVFDASKPDGTPRKLLDVTRLHQLGWYHEISLEAGLASTYQWFLENQ 316
                                    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

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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: NAD(P)-binding Rossmann-like Domain (1244)

Escherichia coli. Organism_taxid: 562. (49)

1e7rA01

A:3-167,A:210-248,A:284-299

Architecture: Alpha-Beta Complex (3881)

Topology: UDP-galactose 4-epimerase; domain 1 (99)

Homologous Superfamily: UDP-galactose 4-epimerase, domain 1 (99)

Escherichia coli. Organism_taxid: 562. (15)

1e7rA02

A:168-209,A:249-283,A:300-316

(no "Pfam Domain" information available for 1E7R)

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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		TRS	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		UVW	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
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	Cis Peptide Bonds
		Gln A:117 - Pro A:118	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	1e7r
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	5.1.3.-
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UniProtKB/Swiss-Prot
	FCL_ECOLI \| P32055	:	1bsv 1bws 1e6u 1e7q 1e7s 1fxs 1gfs

1bsv	GDP-FUCOSE SYNTHETASE FROM ESCHERICHIA COLI COMPLEX WITH NADPH
1bws	CRYSTAL STRUCTURE OF GDP-4-KETO-6-DEOXY-D-MANNOSE EPIMERASE/REDUCTASE FROM ESCHERICHIA COLI A KEY ENZYME IN THE BIOSYNTHESIS OF GDP-L-FUCOSE
1e6u	GDP 4-KETO-6-DEOXY-D-MANNOSE EPIMERASE REDUCTASE
1e7q	GDP 4-KETO-6-DEOXY-D-MANNOSE EPIMERASE REDUCTASE S107A
1e7s	GDP 4-KETO-6-DEOXY-D-MANNOSE EPIMERASE REDUCTASE K140R
1fxs	GDP-FUCOSE SYNTHETASE FROM ESCHERICHIA COLI COMPLEX WITH NADP
1gfs	GDP-FUCOSE SYNTHETASE FROM E. COLI

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 6)

Sites (6, 6)

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

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (2, 2)

Pfam Domains (0, 0)

Gene Ontology (12, 12)

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