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Information on EC 2.7.1.181 - polymannosyl GlcNAc-diphospho-ditrans,octacis-undecaprenol kinase and Organism(s) Escherichia coli and UniProt Accession J7I4B7

for references in articles please use BRENDA:EC2.7.1.181
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IUBMB Comments
The enzyme is involved in the biosynthesis of the polymannose O-polysaccharide in the outer leaflet of the membrane of Escherichia coli serotype O9a. O-Polysaccharide structures vary extensively because of differences in the number and type of sugars in the repeat unit. The dual kinase/methylase WbdD also catalyses the methylation of 3-phospho-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-[alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)]n-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol (cf. EC 2.1.1.294, 3-O-phospho-polymannosyl GlcNAc-diphospho-ditrans,octacis-undecaprenol 3-phospho-methyltransferase).
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Escherichia coli
UNIPROT: J7I4B7
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The taxonomic range for the selected organisms is: Escherichia coli
The expected taxonomic range for this enzyme is: Bacteria, Archaea
Synonyms
wbdd kinase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
WbdDO9a
-
-
PATHWAY SOURCE
PATHWAYS
-
-, -
SYSTEMATIC NAME
IUBMB Comments
ATP:alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-[alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)]n-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol 3-phosphotransferase
The enzyme is involved in the biosynthesis of the polymannose O-polysaccharide in the outer leaflet of the membrane of Escherichia coli serotype O9a. O-Polysaccharide structures vary extensively because of differences in the number and type of sugars in the repeat unit. The dual kinase/methylase WbdD also catalyses the methylation of 3-phospho-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-[alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)]n-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol (cf. EC 2.1.1.294, 3-O-phospho-polymannosyl GlcNAc-diphospho-ditrans,octacis-undecaprenol 3-phospho-methyltransferase).
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ATP + 2-alpha-D-mannosyl-D-mannose
ADP + 3-O-phospho-2-alpha-D-mannosyl-D-mannose
show the reaction diagram
-
-
-
?
ATP + alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-[alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)]n-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol
ADP + 3-O-phospho-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-[alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)]n-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol
show the reaction diagram
-
-
-
?
ATP + D-mannose
ADP + 3-O-phospho-D-mannose
show the reaction diagram
-
-
-
?
ATP + 8-azidooctyl alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man
ADP + 8-azidooctyl 3-O-phospho-alpha-D-mannopyranosyl-(1->2)-alpha-D-mannopyranosyl-(1->3)-alpha-D-mannopyranosyl-(1->3)-alpha-D-mannopyranoside
show the reaction diagram
-
the substrate is an an 8-azidooctyl glycoside derivatives of the Escherichia coli serotype O9a O-chain repeating unit. WbdD shows dual kinase and methyltransferase activity
-
-
?
ATP + alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)]n-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol
ADP + 3-O-phospho-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)]n-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol
show the reaction diagram
additional information
?
-
enzyme WbdD is bifunctional and shows both kinase and methyltransferase activities
-
-
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
ATP + alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-[alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)]n-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol
ADP + 3-O-phospho-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-[alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)]n-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol
show the reaction diagram
-
-
-
?
ATP + alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)]n-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol
ADP + 3-O-phospho-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)]n-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30
-
assay at
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
-
the WbdD protein is tethered to the membrane via a C-terminal region containing amphipathic helices located between residues 601 and 669
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
chain-terminator enzyme WbdD caps the nonreducing end of the glycan with a methylphosphate moiety and thereby establishes chain-length distribution. A carbohydrate-binding module (CBM) in the ABC transporter recognizes terminated glycans, ensuring that only mature O-antigen polysaccharide (O-PS) is exported and incorporated into LPS. Enzyme WbdD is bifunctional and shows both kinase and methyltransferase activities. WbdD mutants reveal that although the kinase activity is solely responsible for chain-length regulation, both activities are essential for CBM recognition and export. Direct interaction between the CBM and the terminal methyl group. CBM can bind the O-PS only with the native repeat unit, revealing that methylphosphate is essential but not sufficient for substrate recognition and export. Essential to this chain-length regulation strategy is a quality control mechanism on the ABC transporter protein complex, which ensures that only terminated (and chain-regulated) O-PS is exported for assembly on the cell surface. O-PS ABC transporters are composed of homodimers of the transmembrane domain protein (Wzm) and the nucleotide-binding domain protein (Wzt). Wzt possesses a C-terminal CBM, which is specific for its cognate O-PS. Binding of O-PS by the CBM is a prerequisite for transport, and removal or mutation of the CBM abrogates export. WbdD kinase activity is solely responsible for arresting O9a O-PS polymerization. Catalytic mechanism, overview
malfunction
physiological function
additional information
structural requirements for glycan recognition by the CBM, overview
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
WBDD_ECOLX
708
0
81732
Swiss-Prot
-
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
65500
-
x * 65500, soluble His6-tagged truncated derivative comprising amino acids 1 to 600 of WbdD
81731
-
x * 81731, calculated from sequence
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
2.2 A resolution structure reveals a bacterial methyltransferase domain joined to a eukaryotic kinase domain. The kinase domain is again fused to an extended C-terminal coiled-coil domain reminiscent of eukaryotic Myotonic Dystrophy Protein Kinase family kinases. Structures of co-complexes with two known eukaryotic protein kinase inhibitors which are potent inhibitors in vitro, but do not show any in vivo activity
crystallization and modeling by molecular-replacement to obtain high-resolution diffraction, and development of methods to control the hydration status
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D350A
88.8% of wild-type activity with substrate 2-alpha-D-mannosyl-D-mannose, 95.2% with substrate D-mannose
D351A
0.9% of wild-type activity with substrate 2-alpha-D-mannosyl-D-mannose, 1.1% with substrate D-mannose
D351E
4.5% of wild-type activity with substrate 2-alpha-D-mannosyl-D-mannose, 1.5% with substrate D-mannose
DELTA398-418
6.7% of wild-type activity with substrate 2-alpha-D-mannosyl-D-mannose, 4.7% with substrate D-mannose
E274A
45.4% of wild-type activity with substrate 2-alpha-D-mannosyl-D-mannose, 66.6% with substrate D-mannose
H132A
complete loss of activity
H133A
complete loss of activity
N34D/Q35E/H197E
complete loss of activity
R203A
complete loss of activity
R270A
72.8% of wild-type activity with substrate 2-alpha-D-mannosyl-D-mannose, 85.7% with substrate D-mannose
W355F
72.4% of wild-type activity with substrate 2-alpha-D-mannosyl-D-mannose, 1.9% with substrate D-mannose
W355H
48.7% of wild-type activity with substrate 2-alpha-D-mannosyl-D-mannose, 50.7% with substrate D-mannose
Y16F
complete loss of activity
Y230F
0.1% of wild-type activity with substrate 2-alpha-D-mannosyl-D-mannose, 2.5% with substrate D-mannose
additional information
uncoupling of WbdD kinase and methyltransferase activities, revealing that although the kinase activity is solely responsible for chain-length regulation, both activities are essential for CBM recognition and export
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
soluble His6-tagged truncated derivative comprising amino acids 1 to 600 of WbdD
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene wbdD, genetic organization
overexpression of WbdD decreases O-polysaccharide chain length. O-polysaccharide chain length is not reduced by overexpressing the heterologous plasmid encoded WbdD proteins. The WbdD proteins are therefore specific for a given serotype
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
analysis
strategy for improving poor 3.5 A resolution initial phases by density modification and cross-crystal averaging with an additional data set to build a crude model
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Clarke, B.R.; Cuthbertson, L.; Whitfield, C.
Nonreducing terminal modifications determine the chain length of polymannose O antigens of Escherichia coli and couple chain termination to polymer export via an ATP-binding cassette transporter
J. Biol. Chem.
279
35709-35718
2004
Escherichia coli, Escherichia coli O9a
Manually annotated by BRENDA team
Clarke, B.R.; Greenfield, L.K.; Bouwman, C.; Whitfield, C.
Coordination of polymerization, chain termination, and export in assembly of the Escherichia coli lipopolysaccharide O9a antigen in an ATP-binding cassette transporter-dependent pathway
J. Biol. Chem.
284
30662-30672
2009
Escherichia coli, Escherichia coli O9a
Manually annotated by BRENDA team
Clarke, B.R.; Richards, M.R.; Greenfield, L.K.; Hou, D.; Lowary, T.L.; Whitfield, C.
In vitro reconstruction of the chain termination reaction in biosynthesis of the Escherichia coli O9a O-polysaccharide; the chain-length regulator, WbdD, catalyzes the addition of methyl phosphate to the non-reducing terminus of the growing glycan
J. Biol. Chem.
286
41391-41401
2011
Escherichia coli, Escherichia coli O9a
Manually annotated by BRENDA team
Hagelueken, G.; Huang, H.; Harlos, K.; Clarke, B.R.; Whitfield, C.; Naismith, J.H.
Crystallization, dehydration and experimental phasing of WbdD, a bifunctional kinase and methyltransferase from Escherichia coli O9a
Acta Crystallogr. Sect. D
68
1371-1379
2012
Escherichia coli (J7I4B7), Escherichia coli O9a (J7I4B7)
Manually annotated by BRENDA team
Hagelueken, G.; Huang, H.; Clarke, B.R.; Lebl, T.; Whitfield, C.; Naismith, J.H.
Structure of WbdD: a bifunctional kinase and methyltransferase that regulates the chain length of the O antigen in Escherichia coli O9a
Mol. Microbiol.
86
730-742
2012
Escherichia coli (J7I4B7), Escherichia coli O9a (J7I4B7)
Manually annotated by BRENDA team
Mann, E.; Kelly, S.; Al-Abdul-Wahid, M.; Clarke, B.; Ovchinnikova, O.; Liu, B.; Whitfield, C.
Substrate recognition by a carbohydrate-binding module in the prototypical ABC transporter for lipopolysaccharide O-antigen from Escherichia coli O9a
J. Biol. Chem.
294
14978-14990
2019
Escherichia coli (J7I4B7)
-
Manually annotated by BRENDA team