P67910 (HLDD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
ADP-L-glycero-D-manno-heptose-6-epimerase
EC=5.1.3.20

Alternative name(s):
ADP-L-glycero-beta-D-manno-heptose-6-epimerase
Short name=ADP-glyceromanno-heptose 6-epimerase
Short name=ADP-hep 6-epimerase
Short name=AGME

Gene names

Name:	hldD
Synonyms:	htrM, rfaD, waaD
Ordered Locus Names:	b3619, JW3594

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	310 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the interconversion between ADP-D-glycero-beta-D-manno-heptose and ADP-L-glycero-beta-D-manno-heptose via an epimerization at carbon 6 of the heptose. Ref.9
Catalytic activity	ADP-D-glycero-D-manno-heptose = ADP-L-glycero-D-manno-heptose. HAMAP-Rule MF_01601
Cofactor	Binds 1 NADP+ per subunit. NAD+ can substitute for NADP+, but enzymatic activity is reduced. Ref.8 Ref.11
Enzyme regulation	Completely inhibited by ADP and ADP-glucose, and partially inhibited by ATP and NADH. HAMAP-Rule MF_01601
Pathway	Nucleotide-sugar biosynthesis; ADP-L-glycero-beta-D-manno-heptose biosynthesis; ADP-L-glycero-beta-D-manno-heptose from D-glycero-beta-D-manno-heptose 7-phosphate: step 4/4. Ref.12 Bacterial outer membrane biogenesis; LPS core biosynthesis. Ref.12
Subunit structure	Homopentamer. Ref.8 Ref.15
Induction	By heat shock. HAMAP-Rule MF_01601
Domain	Contains a large N-terminal NADP-binding domain associated with a modified Rossman fold, and a smaller C-terminal substrate-binding domain. HAMAP-Rule MF_01601
Miscellaneous	Essential for E.coli viability at elevated temperatures. Insertional inactivation of the gene by the Tn5 transposon results in E.coli being unable to form colonies at temperatures above 43 degrees Celsius. HAMAP-Rule MF_01601
Sequence similarities	Belongs to the sugar epimerase family. HldD subfamily.
Caution	Was originally (Ref.8) thought to be a homohexamer.
Biophysicochemical properties	Kinetic parameters: KM=0.1 mM for ADP-heptose Ref.8 Vmax=1.53 µmol/min/mg enzyme pH dependence: Optimum pH is 5.5-9.5. Temperature dependence: Optimum temperature is 42 degrees Celsius.

Ontologies

Keywords
Biological process	Carbohydrate metabolism Lipopolysaccharide biosynthesis Stress response
Ligand	NAD NADP
Molecular function	Isomerase
PTM	Acetylation
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	ADP-L-glycero-beta-D-manno-heptose biosynthetic process Inferred from electronic annotation. Source: UniProtKB-UniPathway lipopolysaccharide core region biosynthetic process Inferred from mutant phenotype PubMed 383699. Source: EcoCyc response to stress Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	cytosol Inferred from direct assay PubMed 16858726. Source: UniProtKB membrane Inferred from direct assay PubMed 16858726. Source: UniProtKB
Molecular_function	ADP-glyceromanno-heptose 6-epimerase activity Inferred from direct assay Ref.8. Source: EcoCyc NADP+ binding Inferred from direct assay Ref.11. Source: EcoCyc
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
menB	P0ABU0	2	EBI-543760,EBI-554195

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 310

310

ADP-L-glycero-D-manno-heptose-6-epimerase HAMAP-Rule MF_01601

PRO_0000205793

Regions

Nucleotide binding

10 – 11

2

NADP HAMAP-Rule MF_01601

Nucleotide binding

31 – 32

2

NADP HAMAP-Rule MF_01601

Nucleotide binding

75 – 79

5

NADP HAMAP-Rule MF_01601

Region

201 – 204

4

Substrate binding HAMAP-Rule MF_01601

Sites

Active site

140

1

Proton acceptor Ref.13

Active site

178

1

Proton acceptor Ref.13

Binding site

38

1

NADP

Binding site

53

1

NADP

Binding site

92

1

NADP

Binding site

144

1

NADP

Binding site

169

1

Substrate

Binding site

170

1

NADP; via amide nitrogen

Binding site

178

1

NADP

Binding site

180

1

Substrate; via carbonyl oxygen

Binding site

187

1

Substrate

Binding site

209

1

Substrate

Binding site

272

1

Substrate

Amino acid modifications

Modified residue

267

1

N6-acetyllysine Ref.14

Experimental info

Mutagenesis

140

1

Y → F: Severely compromises epimerase activitie. Ref.13

Mutagenesis

178

1

K → M: Severely compromises epimerase activitie. Ref.13

Mutagenesis

208

1

K → M: Activity similar to that of the wild-type. Ref.13

Mutagenesis

210

1

D → N: Activity similar to that of the wild-type. Ref.13

Secondary structure

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310

Helix Strand Turn

Details...

Beta strand

2 – 5

4

Turn

6 – 8

3

Helix

10 – 20

11

Turn

21 – 23

3

Beta strand

27 – 31

5

Helix

36 – 39

4

Helix

40 – 43

4

Beta strand

48 – 52

5

Helix

53 – 61

9

Beta strand

71 – 74

4

Helix

86 – 92

7

Helix

94 – 107

14

Beta strand

111 – 116

6

Helix

117 – 120

4

Helix

131 – 133

3

Helix

139 – 154

16

Helix

155 – 157

3

Beta strand

162 – 167

6

Beta strand

169 – 174

6

Helix

176 – 181

6

Helix

184 – 193

10

Beta strand

199 – 201

3

Helix

204 – 206

3

Beta strand

211 – 213

3

Helix

214 – 227

14

Beta strand

231 – 236

6

Helix

243 – 249

7

Beta strand

260 – 262

3

Helix

266 – 268

3

Helix

281 – 285

5

Helix

295 – 305

11

Sequences

	Sequence		Length	Mass (Da)
	P67910 [UniParc]. Last modified October 11, 2004. Version 1. Checksum: 4B9388A879CB7522	FASTA	310	34,893
	10 20 30 40 50 60 MIIVTGGAGF IGSNIVKALN DKGITDILVV DNLKDGTKFV NLVDLNIADY MDKEDFLIQI 70 80 90 100 110 120 MAGEEFGDVE AIFHEGACSS TTEWDGKYMM DNNYQYSKEL LHYCLEREIP FLYASSAATY 130 140 150 160 170 180 GGRTSDFIES REYEKPLNVY GYSKFLFDEY VRQILPEANS QIVGFRYFNV YGPREGHKGS 190 200 210 220 230 240 MASVAFHLNT QLNNGESPKL FEGSENFKRD FVYVGDVADV NLWFLENGVS GIFNLGTGRA 250 260 270 280 290 300 ESFQAVADAT LAYHKKGQIE YIPFPDKLKG RYQAFTQADL TNLRAAGYDK PFKTVAEGVT 310 EYMAWLNRDA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning, expression, and characterization of the Escherichia coli K-12 rfaD gene." Pegues J.C., Chen L., Gordon A.W., Ding L., Coleman W.G. Jr. J. Bacteriol. 172:4652-4660(1990) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-34. Strain: K12.
[2]	"The htrM gene, whose product is essential for Escherichia coli viability only at elevated temperatures, is identical to the rfaD gene." Raina S., Georgopoulos C. Nucleic Acids Res. 19:3811-3819(1991) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[3]	"Analysis of the Escherichia coli genome. V. DNA sequence of the region from 76.0 to 81.5 minutes." Sofia H.J., Burland V., Daniels D.L., Plunkett G. III, Blattner F.R. Nucleic Acids Res. 22:2576-2586(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"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.
[5]	"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.
[6]	"Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Link A.J., Robison K., Church G.M. Electrophoresis 18:1259-1313(1997) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-12. Strain: K12 / EMG2.
[7]	Frutiger S., Hughes G.J., Pasquali C., Hochstrasser D.F. Submitted (FEB-1996) to UniProtKB Cited for: PROTEIN SEQUENCE OF 1-11. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[8]	"Purification and properties of the Escherichia coli K-12 NAD-dependent nucleotide diphosphosugar epimerase, ADP-L-glycero-D-mannoheptose 6-epimerase." Ding L., Seto B.L., Ahmed S.A., Coleman W.G. Jr. J. Biol. Chem. 269:24384-24390(1994) [PubMed] [Europe PMC] [Abstract] Cited for: BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, COFACTOR. Strain: K12.
[9]	"The rfaD gene codes for ADP-L-glycero-D-mannoheptose-6-epimerase. An enzyme required for lipopolysaccharide core biosynthesis." Coleman W.G. Jr. J. Biol. Chem. 258:1985-1990(1983) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION. Strain: K12.
[10]	"Crystallization and preliminary X-ray diffraction studies of the lipopolysaccharide core biosynthetic enzyme ADP-L-glycero-D-mannoheptose 6-epimerase from Escherichia coli K-12." Ding L., Zhang Y., Deacon A.M., Ealick S.E., Ni Y.S., Sun P., Coleman W.G. Jr. Acta Crystallogr. D 55:685-688(1999) [PubMed] [Europe PMC] [Abstract] Cited for: CRYSTALLIZATION.
[11]	"Evidence that NADP+ is the physiological cofactor of ADP-L-glycero-D-mannoheptose 6-epimerase." Ni Y.S., McPhie P., Deacon A.M., Ealick S.E., Coleman W.G. Jr. J. Biol. Chem. 276:27329-27334(2001) [PubMed] [Europe PMC] [Abstract] Cited for: COFACTOR.
[12]	"Biosynthesis pathway of ADP-L-glycero-beta-D-manno-heptose in Escherichia coli." Kneidinger B., Marolda C., Graninger M., Zamyatina A., McArthur F., Kosma P., Valvano M.A., Messner P. J. Bacteriol. 184:363-369(2002) [PubMed] [Europe PMC] [Abstract] Cited for: ADP-L-GLYCERO-BETA-D-MANNO-HEPTOSE BIOSYNTHESIS PATHWAY. Strain: K12 / MG1655 / ATCC 47076.
[13]	"A two-base mechanism for Escherichia coli ADP-L-glycero-D-manno-heptose 6-epimerase." Morrison J.P., Tanner M.E. Biochemistry 46:3916-3924(2007) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF TYR-140; LYS-178; LYS-208 AND ASP-210, REACTION MECHANISM, ACTIVE SITE.
[14]	"Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli." Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F., Grishin N.V., Zhao Y. Mol. Cell. Proteomics 8:215-225(2009) [PubMed] [Europe PMC] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-267, MASS SPECTROMETRY. Strain: K12 / JW1106 and K12 / MG1655 / ATCC 47076.
[15]	"The crystal structure of ADP-L-glycero-D-mannoheptose 6-epimerase: catalysis with a twist." Deacon A.M., Ni Y.S., Coleman W.G. Jr., Ealick S.E. Structure 8:453-462(2000) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF COMPLEX WITH NADP AND ADP-GLUCOSE, SUBUNIT.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M33577 Genomic DNA. Translation: AAA24525.1.
X54492 Genomic DNA. Translation: CAA38364.1.
U00039 Genomic DNA. Translation: AAB18596.1.
U00096 Genomic DNA. Translation: AAC76643.1.
AP009048 Genomic DNA. Translation: BAE77673.1.

PIR

JU0299.

RefSeq

NP_418076.1. NC_000913.2.
YP_491814.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1EQ2	X-ray	2.00	A/B/C/D/E/F/G/H/I/J	1-310	[»]
2X6T	X-ray	2.36	A/B/C/D/E/F/G/H/I/J	1-310	[»]

ProteinModelPortal

P67910.

SMR

P67910. Positions 1-308.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-35958N.

IntAct

P67910. 38 interactions.

STRING

511145.b3619.

2D gel databases

SWISS-2DPAGE

P67910.

Proteomic databases

PaxDb

P67910.

PRIDE

P67910.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC76643; AAC76643; b3619.
BAE77673; BAE77673; BAE77673.

GeneID

12934299.
948134.

KEGG

ecj:Y75_p3555.
eco:b3619.

PATRIC

32122725. VBIEscCol129921_3739.

Organism-specific databases

EchoBASE

EB0831.

EcoGene

EG10838. hldD.

Phylogenomic databases

eggNOG

COG0451.

HOGENOM

HOG000167987.

KO

K03274.

OMA

AVNLWFW.

ProtClustDB

PRK11150.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10838-MONOMER.
ECOL316407:JW3594-MONOMER.
MetaCyc:EG10838-MONOMER.

SABIO-RK

P67910.

UniPathway

UPA00356; UER00440.
UPA00958.

Gene expression databases

Genevestigator

P67910.

Family and domain databases

Gene3D

3.40.50.720. 1 hit.

HAMAP

MF_01601. Heptose_epimerase.

InterPro

IPR001509. Epimerase_deHydtase.
IPR011912. Heptose_epim.
IPR016040. NAD(P)-bd_dom.
[Graphical view]

PANTHER

PTHR10366:SF29. PTHR10366:SF29. 1 hit.

Pfam

PF01370. Epimerase. 1 hit.
[Graphical view]

TIGRFAMs

TIGR02197. heptose_epim. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P67910.

Entry information

Entry name

HLDD_ECOLI

Accession

Primary (citable) accession number: P67910
Secondary accession number(s): P17963, Q2M7T3

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 11, 2004
Last sequence update:	October 11, 2004
Last modified:	May 1, 2013
This is version 90 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program