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Protein

ADP-L-glycero-D-manno-heptose-6-epimerase

Gene

hldD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.2 Publications

Catalytic activityi

ADP-D-glycero-D-manno-heptose = ADP-L-glycero-D-manno-heptose.1 Publication

Cofactori

NADP+2 Publications, NAD+2 PublicationsNote: Binds 1 NADP+ per subunit. NAD+ can substitute for NADP+, but enzymatic activity is reduced.2 Publications

Enzyme regulationi

Completely inhibited by ADP and ADP-glucose, and partially inhibited by ATP and NADH.

Kineticsi

  1. KM=0.1 mM for ADP-heptose1 Publication
  1. Vmax=1.53 µmol/min/mg enzyme1 Publication

pH dependencei

Optimum pH is 5.5-9.5.1 Publication

Temperature dependencei

Optimum temperature is 42 degrees Celsius.1 Publication

Pathwayi: ADP-L-glycero-beta-D-manno-heptose biosynthesis

This protein is involved in step 4 of the subpathway that synthesizes ADP-L-glycero-beta-D-manno-heptose from D-glycero-beta-D-manno-heptose 7-phosphate.
Proteins known to be involved in the 4 steps of the subpathway in this organism are:
  1. Bifunctional protein HldE (hldE)
  2. D-glycero-beta-D-manno-heptose-1,7-bisphosphate 7-phosphatase (gmhB)
  3. Bifunctional protein HldE (hldE)
  4. ADP-L-glycero-D-manno-heptose-6-epimerase (hldD)
This subpathway is part of the pathway ADP-L-glycero-beta-D-manno-heptose biosynthesis, which is itself part of Nucleotide-sugar biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes ADP-L-glycero-beta-D-manno-heptose from D-glycero-beta-D-manno-heptose 7-phosphate, the pathway ADP-L-glycero-beta-D-manno-heptose biosynthesis and in Nucleotide-sugar biosynthesis.

Pathwayi: LPS core biosynthesis

This protein is involved in the pathway LPS core biosynthesis, which is part of Bacterial outer membrane biogenesis.
View all proteins of this organism that are known to be involved in the pathway LPS core biosynthesis and in Bacterial outer membrane biogenesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei38NADP1 Publication1
Binding sitei53NADP1 Publication1
Binding sitei92NADP1 Publication1
Active sitei140Proton acceptor1 Publication1
Binding sitei144NADP1 Publication1
Binding sitei169Substrate1 Publication1
Binding sitei170NADP; via amide nitrogen1 Publication1
Active sitei178Proton acceptor1 Publication1
Binding sitei178NADP1 Publication1
Binding sitei180Substrate; via carbonyl oxygen1 Publication1
Binding sitei187Substrate1 Publication1
Binding sitei209Substrate1 Publication1
Binding sitei272Substrate1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi10 – 11NADP1 Publication2
Nucleotide bindingi31 – 32NADP1 Publication2
Nucleotide bindingi75 – 79NADP1 Publication5

GO - Molecular functioni

  • ADP-glyceromanno-heptose 6-epimerase activity Source: EcoCyc
  • NADP+ binding Source: EcoCyc

GO - Biological processi

  • ADP-L-glycero-beta-D-manno-heptose biosynthetic process Source: UniProtKB-UniPathway
  • lipopolysaccharide core region biosynthetic process Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Carbohydrate metabolism, Lipopolysaccharide biosynthesis, Stress response

Keywords - Ligandi

NAD, NADP

Enzyme and pathway databases

BioCyciEcoCyc:EG10838-MONOMER.
ECOL316407:JW3594-MONOMER.
MetaCyc:EG10838-MONOMER.
BRENDAi5.1.3.20. 2026.
SABIO-RKP67910.
UniPathwayiUPA00356; UER00440.
UPA00958.

Names & Taxonomyi

Protein namesi
Recommended name:
ADP-L-glycero-D-manno-heptose-6-epimerase (EC:5.1.3.201 Publication)
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 namesi
Name:hldD
Synonyms:htrM, rfaD, waaD
Ordered Locus Names:b3619, JW3594
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10838. hldD.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: UniProtKB
  • membrane Source: UniProtKB
Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi140Y → F: Severely compromises epimerase activitie. 1 Publication1
Mutagenesisi178K → M: Severely compromises epimerase activitie. 1 Publication1
Mutagenesisi208K → M: Activity similar to that of the wild-type. 1 Publication1
Mutagenesisi210D → N: Activity similar to that of the wild-type. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002057931 – 310ADP-L-glycero-D-manno-heptose-6-epimeraseAdd BLAST310

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei267N6-acetyllysine1 Publication1

Keywords - PTMi

Acetylation

Proteomic databases

EPDiP67910.
PaxDbiP67910.
PRIDEiP67910.

2D gel databases

SWISS-2DPAGEP67910.

Expressioni

Inductioni

By heat shock.

Interactioni

Subunit structurei

Homopentamer.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
menBP0ABU02EBI-543760,EBI-554195

Protein-protein interaction databases

BioGridi4263293. 559 interactors.
DIPiDIP-35958N.
IntActiP67910. 39 interactors.
STRINGi511145.b3619.

Structurei

Secondary structure

1310
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 5Combined sources4
Turni6 – 8Combined sources3
Helixi10 – 20Combined sources11
Turni21 – 23Combined sources3
Beta strandi27 – 31Combined sources5
Helixi36 – 39Combined sources4
Helixi40 – 43Combined sources4
Beta strandi48 – 52Combined sources5
Helixi53 – 61Combined sources9
Beta strandi71 – 74Combined sources4
Helixi86 – 92Combined sources7
Helixi94 – 107Combined sources14
Beta strandi111 – 116Combined sources6
Helixi117 – 120Combined sources4
Helixi131 – 133Combined sources3
Helixi139 – 154Combined sources16
Helixi155 – 157Combined sources3
Beta strandi162 – 167Combined sources6
Beta strandi169 – 174Combined sources6
Helixi176 – 181Combined sources6
Helixi184 – 193Combined sources10
Beta strandi199 – 203Combined sources5
Helixi204 – 206Combined sources3
Beta strandi211 – 213Combined sources3
Helixi214 – 227Combined sources14
Beta strandi231 – 236Combined sources6
Helixi243 – 249Combined sources7
Helixi251 – 254Combined sources4
Beta strandi260 – 262Combined sources3
Helixi266 – 268Combined sources3
Turni269 – 271Combined sources3
Helixi281 – 285Combined sources5
Helixi295 – 305Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1EQ2X-ray2.00A/B/C/D/E/F/G/H/I/J1-310[»]
2X6TX-ray2.36A/B/C/D/E/F/G/H/I/J1-310[»]
ProteinModelPortaliP67910.
SMRiP67910.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP67910.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni201 – 204Substrate binding1 Publication4

Domaini

Contains a large N-terminal NADP-binding domain associated with a modified Rossman fold, and a smaller C-terminal substrate-binding domain.

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105CUI. Bacteria.
COG0451. LUCA.
HOGENOMiHOG000167987.
InParanoidiP67910.
KOiK03274.
OMAiMENNYRY.
PhylomeDBiP67910.

Family and domain databases

CDDicd05248. ADP_GME_SDR_e. 1 hit.
Gene3Di3.40.50.720. 1 hit.
HAMAPiMF_01601. Heptose_epimerase. 1 hit.
InterProiIPR001509. Epimerase_deHydtase.
IPR011912. Heptose_epim.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF01370. Epimerase. 1 hit.
[Graphical view]
SUPFAMiSSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR02197. heptose_epim. 1 hit.

Sequencei

Sequence statusi: Complete.

P67910-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIIVTGGAGF IGSNIVKALN DKGITDILVV DNLKDGTKFV NLVDLNIADY
60 70 80 90 100
MDKEDFLIQI MAGEEFGDVE AIFHEGACSS TTEWDGKYMM DNNYQYSKEL
110 120 130 140 150
LHYCLEREIP FLYASSAATY GGRTSDFIES REYEKPLNVY GYSKFLFDEY
160 170 180 190 200
VRQILPEANS QIVGFRYFNV YGPREGHKGS MASVAFHLNT QLNNGESPKL
210 220 230 240 250
FEGSENFKRD FVYVGDVADV NLWFLENGVS GIFNLGTGRA ESFQAVADAT
260 270 280 290 300
LAYHKKGQIE YIPFPDKLKG RYQAFTQADL TNLRAAGYDK PFKTVAEGVT
310
EYMAWLNRDA
Length:310
Mass (Da):34,893
Last modified:October 11, 2004 - v1
Checksum:i4B9388A879CB7522
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiJU0299.
RefSeqiNP_418076.1. NC_000913.3.
WP_000587764.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76643; AAC76643; b3619.
BAE77673; BAE77673; BAE77673.
GeneIDi948134.
KEGGiecj:JW3594.
eco:b3619.
PATRICi32122725. VBIEscCol129921_3739.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiJU0299.
RefSeqiNP_418076.1. NC_000913.3.
WP_000587764.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1EQ2X-ray2.00A/B/C/D/E/F/G/H/I/J1-310[»]
2X6TX-ray2.36A/B/C/D/E/F/G/H/I/J1-310[»]
ProteinModelPortaliP67910.
SMRiP67910.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263293. 559 interactors.
DIPiDIP-35958N.
IntActiP67910. 39 interactors.
STRINGi511145.b3619.

2D gel databases

SWISS-2DPAGEP67910.

Proteomic databases

EPDiP67910.
PaxDbiP67910.
PRIDEiP67910.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76643; AAC76643; b3619.
BAE77673; BAE77673; BAE77673.
GeneIDi948134.
KEGGiecj:JW3594.
eco:b3619.
PATRICi32122725. VBIEscCol129921_3739.

Organism-specific databases

EchoBASEiEB0831.
EcoGeneiEG10838. hldD.

Phylogenomic databases

eggNOGiENOG4105CUI. Bacteria.
COG0451. LUCA.
HOGENOMiHOG000167987.
InParanoidiP67910.
KOiK03274.
OMAiMENNYRY.
PhylomeDBiP67910.

Enzyme and pathway databases

UniPathwayiUPA00356; UER00440.
UPA00958.
BioCyciEcoCyc:EG10838-MONOMER.
ECOL316407:JW3594-MONOMER.
MetaCyc:EG10838-MONOMER.
BRENDAi5.1.3.20. 2026.
SABIO-RKP67910.

Miscellaneous databases

EvolutionaryTraceiP67910.
PROiP67910.

Family and domain databases

CDDicd05248. ADP_GME_SDR_e. 1 hit.
Gene3Di3.40.50.720. 1 hit.
HAMAPiMF_01601. Heptose_epimerase. 1 hit.
InterProiIPR001509. Epimerase_deHydtase.
IPR011912. Heptose_epim.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF01370. Epimerase. 1 hit.
[Graphical view]
SUPFAMiSSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR02197. heptose_epim. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiHLDD_ECOLI
AccessioniPrimary (citable) accession number: P67910
Secondary accession number(s): P17963, Q2M7T3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 11, 2004
Last sequence update: October 11, 2004
Last modified: November 30, 2016
This is version 117 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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.

Caution

Was originally thought to be a homohexamer.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.