P27830 (RMLB2_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
dTDP-glucose 4,6-dehydratase 2
EC=4.2.1.46

Gene names

Name:	rffG
Ordered Locus Names:	b3788, JW5598

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	355 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the dehydration of dTDP-D-glucose to form dTDP-6-deoxy-D-xylo-4-hexulose via a three-step process involving oxidation, dehydration and reduction. Ref.5
Catalytic activity	dTDP-alpha-D-glucose = dTDP-4-dehydro-6-deoxy-alpha-D-glucose + H2O.
Cofactor	Binds 1 NAD ion per monomer.
Pathway	Carbohydrate biosynthesis; dTDP-L-rhamnose biosynthesis. Bacterial outer membrane biogenesis; LPS O-antigen biosynthesis.
Subunit structure	Homodimer. Ref.8
Sequence similarities	Belongs to the sugar epimerase family. dTDP-glucose dehydratase subfamily.
Caution	Was originally (Ref.1) thought to be rffE, the UDP-N-acetylglucosamine epimerase.

Ontologies

Keywords
Biological process	Lipopolysaccharide biosynthesis
Ligand	NAD
Molecular function	Lyase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	O antigen biosynthetic process Inferred from electronic annotation. Source: UniProtKB-UniPathway dTDP-rhamnose biosynthetic process Inferred from electronic annotation. Source: UniProtKB-UniPathway extracellular polysaccharide biosynthetic process Inferred from direct assay Ref.5. Source: UniProtKB lipopolysaccharide biosynthetic process Inferred from direct assay Ref.5. Source: UniProtKB
Molecular_function	coenzyme binding Inferred from electronic annotation. Source: InterPro dTDP-glucose 4,6-dehydratase activity Inferred from direct assay Ref.5. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 355

355

dTDP-glucose 4,6-dehydratase 2

PRO_0000183236

Regions

Nucleotide binding

8 – 14

7

NAD

Nucleotide binding

33 – 36

4

NAD

Nucleotide binding

59 – 60

2

NAD

Nucleotide binding

160 – 164

5

NAD

Region

134 – 136

3

Substrate binding By similarity

Region

199 – 200

2

Substrate binding By similarity

Region

215 – 217

3

Substrate binding By similarity

Region

294 – 297

4

Substrate binding By similarity

Sites

Active site

135

1

Proton donor Ref.6 Ref.7

Active site

136

1

Proton acceptor Ref.6 Ref.7

Active site

160

1

Proton acceptor Ref.6 Ref.7

Binding site

81

1

NAD; via carbonyl oxygen

Binding site

85

1

Substrate; via carbonyl oxygen By similarity

Binding site

100

1

NAD

Binding site

189

1

Substrate By similarity

Binding site

190

1

NAD; via amide nitrogen

Binding site

224

1

Substrate By similarity

Binding site

259

1

Substrate By similarity

Experimental info

Sequence conflict

314 – 315

2

WL → CV in AAA67588. Ref.1

Secondary structure

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355

Helix Strand Turn

Details...

Beta strand

3 – 7

5

Turn

8 – 10

3

Helix

12 – 24

13

Beta strand

28 – 32

5

Helix

41 – 43

3

Turn

44 – 49

6

Beta strand

53 – 56

4

Helix

63 – 73

11

Beta strand

76 – 80

5

Beta strand

91 – 93

3

Helix

96 – 101

6

Helix

103 – 117

15

Helix

121 – 126

6

Beta strand

128 – 134

7

Helix

135 – 138

4

Beta strand

143 – 145

3

Helix

159 – 178

20

Beta strand

182 – 187

6

Beta strand

189 – 192

4

Helix

200 – 209

10

Beta strand

226 – 228

3

Helix

229 – 242

14

Beta strand

248 – 251

4

Helix

259 – 273

15

Helix

284 – 287

4

Helix

306 – 311

6

Helix

320 – 333

14

Helix

335 – 343

9

Helix

345 – 348

4

Sequences

	Sequence		Length	Mass (Da)
	P27830 [UniParc]. Last modified November 23, 2004. Version 3. Checksum: 34DBD1EFB42DB9B3	FASTA	355	39,754
	10 20 30 40 50 60 MRKILITGGA GFIGSALVRY IINETSDAVV VVDKLTYAGN LMSLAPVAQS ERFAFEKVDI 70 80 90 100 110 120 CDRAELARVF TEHQPDCVMH LAAESHVDRS IDGPAAFIET NIVGTYTLLE AARAYWNALT 130 140 150 160 170 180 EDKKSAFRFH HISTDEVYGD LHSTDDFFTE TTPYAPSSPY SASKASSDHL VRAWLRTYGL 190 200 210 220 230 240 PTLITNCSNN YGPYHFPEKL IPLMILNALA GKSLPVYGNG QQIRDWLYVE DHARALYCVA 250 260 270 280 290 300 TTGKVGETYN IGGHNERKNL DVVETICELL EELAPNKPHG VAHYRDLITF VADRPGHDLR 310 320 330 340 350 YAIDASKIAR ELGWLPQETF ESGMRKTVQW YLANESWWKQ VQDGSYQGER LGLKG

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes." Daniels D.L., Plunkett G. III, Burland V.D., Blattner F.R. Science 257:771-778(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[2]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"Escherichia coli K-12: a cooperatively developed annotation snapshot -- 2005." Riley M., Abe T., Arnaud M.B., Berlyn M.K.B., Blattner F.R., Chaudhuri R.R., Glasner J.D., Horiuchi T., Keseler I.M., Kosuge T., Mori H., Perna N.T., Plunkett G. III, Rudd K.E., Serres M.H., Thomas G.H., Thomson N.R., Wishart D., Wanner B.L. Nucleic Acids Res. 34:1-9(2006) [PubMed] [Europe PMC] [Abstract] Cited for: SEQUENCE REVISION TO 314-315.
[4]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"Genetic analysis of the dTDP-rhamnose biosynthesis region of the Escherichia coli VW187 (O7:K1) rfb gene cluster: identification of functional homologs of rfbB and rfbA in the rff cluster and correct location of the rffE gene." Marolda C.L., Valvano M.A. J. Bacteriol. 177:5539-5546(1995) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN DTDP-RHAMNOSE BIOSYNTHESIS.
[6]	"Probing catalysis by Escherichia coli dTDP-glucose-4,6-dehydratase: identification and preliminary characterization of functional amino acid residues at the active site." Hegeman A.D., Gross J.W., Frey P.A. Biochemistry 40:6598-6610(2001) [PubMed] [Europe PMC] [Abstract] Cited for: ACTIVE SITES.
[7]	"Dehydration is catalyzed by glutamate-136 and aspartic acid-135 active site residues in Escherichia coli dTDP-glucose 4,6-dehydratase." Gross J.W., Hegeman A.D., Gerratana B., Frey P.A. Biochemistry 40:12497-12504(2001) [PubMed] [Europe PMC] [Abstract] Cited for: ACTIVE SITES.
[8]	"Molecular structure of dTDP-glucose 4,6-dehydratase from E. coli." Thoden J.B., Hegeman A.D., Frey P.A., Holden H.M. Submitted (OCT-1998) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH NAD, SUBUNIT.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M87049 Genomic DNA. Translation: AAA67588.1.
U00096 Genomic DNA. Translation: AAT48213.1.
AP009048 Genomic DNA. Translation: BAE77510.1.

PIR

G65182.

RefSeq

YP_026255.1. NC_000913.2.
YP_491651.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1BXK	X-ray	1.90	A/B	1-350	[»]

ProteinModelPortal

P27830.

SMR

P27830. Positions 1-350.

ModBase

Search...

Protein-protein interaction databases

STRING

511145.b3788.

Proteomic databases

PaxDb

P27830.

PRIDE

P27830.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAT48213; AAT48213; b3788.
BAE77510; BAE77510; BAE77510.

GeneID

12933083.
948300.

KEGG

ecj:Y75_p3387.
eco:b3788.

PATRIC

32123069. VBIEscCol129921_3904.

Organism-specific databases

EchoBASE

EB1422.

EcoGene

EG11453. rffG.

Phylogenomic databases

eggNOG

COG1088.

HOGENOM

HOG000168006.

KO

K01710.

OMA

RAYRQQM.

ProtClustDB

PRK10217.

Enzyme and pathway databases

BioCyc

EcoCyc:DTDPGLUCDEHYDRAT2-MONOMER.
ECOL316407:JW5598-MONOMER.
MetaCyc:DTDPGLUCDEHYDRAT2-MONOMER.

SABIO-RK

P27830.

UniPathway

UPA00124.
UPA00281.

Gene expression databases

Genevestigator

P27830.

Family and domain databases

Gene3D

3.40.50.720. 1 hit.

InterPro

IPR005888. dTDP_Gluc_deHydtase.
IPR001509. Epimerase_deHydtase.
IPR016040. NAD(P)-bd_dom.
[Graphical view]

PANTHER

PTHR10366:SF41. PTHR10366:SF41. 1 hit.

Pfam

PF01370. Epimerase. 1 hit.
[Graphical view]

TIGRFAMs

TIGR01181. dTDP_gluc_dehyt. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P27830.

Entry information

Entry name

RMLB2_ECOLI

Accession

Primary (citable) accession number: P27830
Secondary accession number(s): P76754, Q2M896, Q6BF01

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1992
Last sequence update:	November 23, 2004
Last modified:	May 29, 2013
This is version 116 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program