WBDD_ECOLX
ID WBDD_ECOLX Reviewed; 708 AA.
AC J7I4B7;
DT 29-OCT-2014, integrated into UniProtKB/Swiss-Prot.
DT 31-OCT-2012, sequence version 1.
DT 03-AUG-2022, entry version 31.
DE RecName: Full=O-antigen chain terminator bifunctional methyltransferase/kinase WbdD {ECO:0000305};
DE Includes:
DE RecName: Full=3-O-phospho-polymannosyl GlcNAc-diphospho-ditrans,octacis-undecaprenol 3-phospho-methyltransferase {ECO:0000305};
DE EC=2.1.1.294 {ECO:0000269|PubMed:21990359};
DE Includes:
DE RecName: Full=Polymannosyl GlcNAc-diphospho-ditrans,octacis-undecaprenol kinase {ECO:0000305};
DE EC=2.7.1.181 {ECO:0000269|PubMed:21990359};
GN Name=wbdD {ECO:0000303|PubMed:15184370};
OS Escherichia coli.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=562 {ECO:0000312|EMBL:AFQ31610.1};
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, AND PATHWAY.
RC STRAIN=O9a:K30 / E69;
RX PubMed=15184370; DOI=10.1074/jbc.m404738200;
RA Clarke B.R., Cuthbertson L., Whitfield C.;
RT "Nonreducing terminal modifications determine the chain length of
RT polymannose O antigens of Escherichia coli and couple chain termination to
RT polymer export via an ATP-binding cassette transporter.";
RL J. Biol. Chem. 279:35709-35718(2004).
RN [2]
RP FUNCTION, INTERACTION WITH WBDA, SUBCELLULAR LOCATION, AND DOMAIN.
RC STRAIN=O9a:K30 / E69;
RX PubMed=19734145; DOI=10.1074/jbc.m109.052878;
RA Clarke B.R., Greenfield L.K., Bouwman C., Whitfield C.;
RT "Coordination of polymerization, chain termination, and export in assembly
RT of the Escherichia coli lipopolysaccharide O9a antigen in an ATP-binding
RT cassette transporter-dependent pathway.";
RL J. Biol. Chem. 284:30662-30672(2009).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, AND PATHWAY.
RC STRAIN=O9a;
RX PubMed=21990359; DOI=10.1074/jbc.m111.295857;
RA Clarke B.R., Richards M.R., Greenfield L.K., Hou D., Lowary T.L.,
RA Whitfield C.;
RT "In vitro reconstruction of the chain termination reaction in biosynthesis
RT of the Escherichia coli O9a O-polysaccharide: the chain-length regulator,
RT WbdD, catalyzes the addition of methyl phosphate to the non-reducing
RT terminus of the growing glycan.";
RL J. Biol. Chem. 286:41391-41401(2011).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (3.00 ANGSTROMS) OF 2-556 IN COMPLEX WITH ADP AND
RP S-ADENOSYL-L-METHIONINE.
RC STRAIN=O9a;
RX PubMed=22993091; DOI=10.1107/s0907444912029599;
RA Hagelueken G., Huang H., Harlos K., Clarke B.R., Whitfield C.,
RA Naismith J.H.;
RT "Crystallization, dehydration and experimental phasing of WbdD, a
RT bifunctional kinase and methyltransferase from Escherichia coli O9a.";
RL Acta Crystallogr. D 68:1371-1379(2012).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) OF 2-556 IN COMPLEX WITH AMP; ATP
RP AND S-ADENOSYL-L-METHIONINE, SUBUNIT, AND MUTAGENESIS OF TYR-16; ASN-34;
RP GLN-35; HIS-132; HIS-133; HIS-197; ARG-203; TYR-230; ARG-270; GLU-274;
RP ASP-350; ASP-351 AND TRP-355.
RC STRAIN=O9a;
RX PubMed=22970759; DOI=10.1111/mmi.12014;
RA Hagelueken G., Huang H., Clarke B.R., Lebl T., Whitfield C., Naismith J.H.;
RT "Structure of WbdD: a bifunctional kinase and methyltransferase that
RT regulates the chain length of the O antigen in Escherichia coli O9a.";
RL Mol. Microbiol. 86:730-742(2012).
CC -!- FUNCTION: Regulates the length of the LPS O-antigen polysaccharide
CC chain. Stops the polymerization of the chain by phosphorylating and
CC then methylating the phosphate on the terminal sugar. This terminal
CC modification is essential for export of the O-antigen across the inner
CC membrane. WbdD is also required for correct localization of the WbdA
CC mannosyltransferase. {ECO:0000269|PubMed:15184370,
CC ECO:0000269|PubMed:19734145, ECO:0000269|PubMed:21990359}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3-O-phospho-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-[alpha-D-
CC Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->2)-alpha-D-Man-
CC (1->2)](n)-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-
CC alpha-D-GlcNAc-di-trans,octa-cis-undecaprenyl diphosphate + S-
CC adenosyl-L-methionine = 3-O-methylphospho-alpha-D-Man-(1->2)-alpha-D-
CC Man-(1->2)-[alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->2)-
CC alpha-D-Man-(1->2)](n)-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-
CC Man-(1->3)-alpha-D-GlcNAc-di-trans,octa-cis-undecaprenyl diphosphate
CC + S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:36639, Rhea:RHEA-
CC COMP:9559, Rhea:RHEA-COMP:9560, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74008, ChEBI:CHEBI:74009; EC=2.1.1.294;
CC Evidence={ECO:0000269|PubMed:21990359};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-[alpha-D-Man-(1->3)-
CC alpha-D-Man-(1->3)-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)](n)-alpha-D-
CC Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-GlcNAc-di-
CC trans,octa-cis-undecaprenyl diphosphate + ATP = 3-O-phospho-alpha-D-
CC Man-(1->2)-alpha-D-Man-(1->2)-[alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-
CC alpha-D-Man-(1->2)-alpha-D-Man-(1->2)](n)-alpha-D-Man-(1->3)-alpha-D-
CC Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-GlcNAc-di-trans,octa-cis-
CC undecaprenyl diphosphate + ADP + H(+); Xref=Rhea:RHEA:40371,
CC Rhea:RHEA-COMP:9558, Rhea:RHEA-COMP:9559, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:74008, ChEBI:CHEBI:74010,
CC ChEBI:CHEBI:456216; EC=2.7.1.181;
CC Evidence={ECO:0000269|PubMed:21990359};
CC -!- PATHWAY: Bacterial outer membrane biogenesis; LPS O-antigen
CC biosynthesis. {ECO:0000269|PubMed:15184370,
CC ECO:0000269|PubMed:21990359}.
CC -!- SUBUNIT: Homotrimer in solution. Interacts with WbdA.
CC {ECO:0000269|PubMed:19734145, ECO:0000269|PubMed:22970759}.
CC -!- SUBCELLULAR LOCATION: Cell inner membrane
CC {ECO:0000269|PubMed:19734145}; Peripheral membrane protein
CC {ECO:0000269|PubMed:19734145}; Cytoplasmic side
CC {ECO:0000269|PubMed:19734145}.
CC -!- DOMAIN: The N-terminal part contains the methyltransferase and kinase
CC domains that are essential for chain termination and polymer export.
CC The C-terminal region is required for targeting both WbdD and WbdA to
CC the inner membrane. {ECO:0000269|PubMed:19734145}.
CC -!- SIMILARITY: Belongs to the WbdD family. {ECO:0000305}.
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DR EMBL; JX235676; AFQ31610.1; -; Genomic_DNA.
DR PDB; 4AX8; X-ray; 3.00 A; A=2-556.
DR PDB; 4AZS; X-ray; 2.15 A; A=2-556.
DR PDB; 4AZT; X-ray; 2.34 A; A=2-556.
DR PDB; 4AZV; X-ray; 3.29 A; A=2-556.
DR PDB; 4AZW; X-ray; 2.47 A; A=2-458.
DR PDBsum; 4AX8; -.
DR PDBsum; 4AZS; -.
DR PDBsum; 4AZT; -.
DR PDBsum; 4AZV; -.
DR PDBsum; 4AZW; -.
DR AlphaFoldDB; J7I4B7; -.
DR SMR; J7I4B7; -.
DR PRIDE; J7I4B7; -.
DR KEGG; ag:AFQ31610; -.
DR BioCyc; MetaCyc:MON-20266; -.
DR BRENDA; 2.1.1.294; 2026.
DR BRENDA; 2.7.1.181; 2026.
DR UniPathway; UPA00281; -.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0008168; F:methyltransferase activity; IEA:UniProtKB-KW.
DR GO; GO:0004672; F:protein kinase activity; IEA:InterPro.
DR GO; GO:0032259; P:methylation; IEA:UniProtKB-KW.
DR GO; GO:0009243; P:O antigen biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0006468; P:protein phosphorylation; IEA:InterPro.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR011009; Kinase-like_dom_sf.
DR InterPro; IPR025714; Methyltranfer_dom.
DR InterPro; IPR000719; Prot_kinase_dom.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR Pfam; PF13847; Methyltransf_31; 1.
DR Pfam; PF00069; Pkinase; 1.
DR SMART; SM00220; S_TKc; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR SUPFAM; SSF56112; SSF56112; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Cell inner membrane; Cell membrane; Coiled coil;
KW Kinase; Lipopolysaccharide biosynthesis; Membrane; Methyltransferase;
KW Nucleotide-binding; S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..708
FT /note="O-antigen chain terminator bifunctional
FT methyltransferase/kinase WbdD"
FT /id="PRO_0000430676"
FT REGION 1..210
FT /note="Methyltransferase"
FT /evidence="ECO:0000303|PubMed:22970759,
FT ECO:0000303|PubMed:22993091"
FT REGION 211..459
FT /note="Kinase"
FT /evidence="ECO:0000303|PubMed:22970759,
FT ECO:0000303|PubMed:22993091"
FT REGION 601..669
FT /note="Required for membrane-binding"
FT /evidence="ECO:0000269|PubMed:19734145"
FT REGION 687..708
FT /note="Required for localizing WbdA to the membrane"
FT /evidence="ECO:0000269|PubMed:19734145"
FT COILED 485..594
FT /evidence="ECO:0000255"
FT BINDING 16..17
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:22970759,
FT ECO:0000269|PubMed:22993091"
FT BINDING 36
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:22970759,
FT ECO:0000269|PubMed:22993091"
FT BINDING 61
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:22970759,
FT ECO:0000269|PubMed:22993091"
FT BINDING 82..87
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:22970759,
FT ECO:0000269|PubMed:22993091"
FT BINDING 108..111
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:22970759,
FT ECO:0000269|PubMed:22993091"
FT BINDING 128
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:22970759,
FT ECO:0000269|PubMed:22993091"
FT BINDING 229
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:22970759,
FT ECO:0000269|PubMed:22993091"
FT BINDING 237
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:22970759"
FT BINDING 241..243
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:22970759,
FT ECO:0000269|PubMed:22993091"
FT BINDING 252
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:22970759,
FT ECO:0000269|PubMed:22993091"
FT BINDING 274
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:22970759"
FT BINDING 309..311
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:22970759,
FT ECO:0000269|PubMed:22993091"
FT BINDING 358
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:22970759"
FT BINDING 369
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:22970759,
FT ECO:0000269|PubMed:22993091"
FT MUTAGEN 16
FT /note="Y->F: Loss of methyltransferase activity."
FT /evidence="ECO:0000269|PubMed:22970759"
FT MUTAGEN 34
FT /note="N->D: 90% decrease in methyltransferase activity;
FT when associated with E-35 and E-197."
FT /evidence="ECO:0000269|PubMed:22970759"
FT MUTAGEN 35
FT /note="Q->E: 90% decrease in methyltransferase activity;
FT when associated with D-34 and E-197."
FT /evidence="ECO:0000269|PubMed:22970759"
FT MUTAGEN 132
FT /note="H->A: Loss of methyltransferase activity."
FT /evidence="ECO:0000269|PubMed:22970759"
FT MUTAGEN 133
FT /note="H->A: Loss of methyltransferase activity."
FT /evidence="ECO:0000269|PubMed:22970759"
FT MUTAGEN 197
FT /note="H->E: 90% decrease in methyltransferase activity;
FT when associated with D-34 and E-35."
FT /evidence="ECO:0000269|PubMed:22970759"
FT MUTAGEN 203
FT /note="R->A: Loss of methyltransferase activity."
FT /evidence="ECO:0000269|PubMed:22970759"
FT MUTAGEN 230
FT /note="Y->F: Loss of kinase activity."
FT /evidence="ECO:0000269|PubMed:22970759"
FT MUTAGEN 270
FT /note="R->A: Decrease in kinase activity."
FT /evidence="ECO:0000269|PubMed:22970759"
FT MUTAGEN 274
FT /note="E->A: Decrease in kinase activity."
FT /evidence="ECO:0000269|PubMed:22970759"
FT MUTAGEN 350
FT /note="D->A: 10% decrease in kinase activity."
FT /evidence="ECO:0000269|PubMed:22970759"
FT MUTAGEN 351
FT /note="D->A,E: Loss of kinase activity."
FT /evidence="ECO:0000269|PubMed:22970759"
FT MUTAGEN 355
FT /note="W->F: Decrease in kinase activity."
FT /evidence="ECO:0000269|PubMed:22970759"
FT MUTAGEN 355
FT /note="W->H: 50% decrease in kinase activity."
FT /evidence="ECO:0000269|PubMed:22970759"
FT HELIX 5..10
FT /evidence="ECO:0007829|PDB:4AX8"
FT HELIX 23..28
FT /evidence="ECO:0007829|PDB:4AX8"
FT HELIX 34..51
FT /evidence="ECO:0007829|PDB:4AX8"
FT STRAND 56..61
FT /evidence="ECO:0007829|PDB:4AX8"
FT HELIX 66..72
FT /evidence="ECO:0007829|PDB:4AX8"
FT TURN 73..75
FT /evidence="ECO:0007829|PDB:4AX8"
FT STRAND 77..83
FT /evidence="ECO:0007829|PDB:4AX8"
FT HELIX 85..96
FT /evidence="ECO:0007829|PDB:4AX8"
FT STRAND 103..107
FT /evidence="ECO:0007829|PDB:4AX8"
FT HELIX 110..116
FT /evidence="ECO:0007829|PDB:4AX8"
FT STRAND 123..129
FT /evidence="ECO:0007829|PDB:4AX8"
FT HELIX 131..138
FT /evidence="ECO:0007829|PDB:4AX8"
FT HELIX 140..153
FT /evidence="ECO:0007829|PDB:4AX8"
FT STRAND 154..160
FT /evidence="ECO:0007829|PDB:4AX8"
FT STRAND 166..168
FT /evidence="ECO:0007829|PDB:4AX8"
FT HELIX 169..173
FT /evidence="ECO:0007829|PDB:4AX8"
FT HELIX 178..181
FT /evidence="ECO:0007829|PDB:4AX8"
FT TURN 182..184
FT /evidence="ECO:0007829|PDB:4AX8"
FT STRAND 185..194
FT /evidence="ECO:0007829|PDB:4AX8"
FT STRAND 197..200
FT /evidence="ECO:0007829|PDB:4AX8"
FT STRAND 203..215
FT /evidence="ECO:0007829|PDB:4AX8"
FT STRAND 218..221
FT /evidence="ECO:0007829|PDB:4AX8"
FT STRAND 223..230
FT /evidence="ECO:0007829|PDB:4AX8"
FT TURN 234..239
FT /evidence="ECO:0007829|PDB:4AX8"
FT STRAND 241..245
FT /evidence="ECO:0007829|PDB:4AX8"
FT STRAND 247..257
FT /evidence="ECO:0007829|PDB:4AX8"
FT HELIX 259..261
FT /evidence="ECO:0007829|PDB:4AX8"
FT HELIX 265..283
FT /evidence="ECO:0007829|PDB:4AX8"
FT STRAND 294..299
FT /evidence="ECO:0007829|PDB:4AX8"
FT STRAND 301..309
FT /evidence="ECO:0007829|PDB:4AX8"
FT STRAND 313..315
FT /evidence="ECO:0007829|PDB:4AX8"
FT HELIX 316..321
FT /evidence="ECO:0007829|PDB:4AX8"
FT HELIX 328..344
FT /evidence="ECO:0007829|PDB:4AX8"
FT STRAND 348..350
FT /evidence="ECO:0007829|PDB:4AX8"
FT HELIX 354..356
FT /evidence="ECO:0007829|PDB:4AX8"
FT STRAND 357..359
FT /evidence="ECO:0007829|PDB:4AX8"
FT STRAND 365..367
FT /evidence="ECO:0007829|PDB:4AX8"
FT STRAND 373..375
FT /evidence="ECO:0007829|PDB:4AX8"
FT HELIX 384..397
FT /evidence="ECO:0007829|PDB:4AX8"
FT HELIX 422..430
FT /evidence="ECO:0007829|PDB:4AX8"
FT HELIX 434..436
FT /evidence="ECO:0007829|PDB:4AX8"
FT HELIX 439..447
FT /evidence="ECO:0007829|PDB:4AX8"
FT HELIX 448..451
FT /evidence="ECO:0007829|PDB:4AX8"
FT HELIX 455..457
FT /evidence="ECO:0007829|PDB:4AX8"
FT HELIX 462..472
FT /evidence="ECO:0007829|PDB:4AX8"
SQ SEQUENCE 708 AA; 81732 MW; 436C35C76096E3F7 CRC64;
MTKDLNTLVS ELPEIYQTIF GHPEWDGDAA RDCNQRLDLI TEQYDNLSRA LGRPLNVLDL
GCAQGFFSLS LASKGATIVG IDFQQENINV CRALAEENPD FAAEFRVGRI EEVIAALEEG
EFDLAIGLSV FHHIVHLHGI DEVKRLLSRL ADVTQAVILE LAVKEEPFYW GVSQPDDPRE
LIEQCAFYRL IGEFDTHLSP VPRPMYLVSN HRVLINDFNQ PFQHWQNQPY AGAGLAHKRS
RRYFFGEDYV CKFFYYDMPH GILTAEESQR NKYELHNEIK FLTQPPAGFD APAVLAHGEN
AQSGWLVMEK LPGRLLSDML AAGEEIDREK ILGSLLRSLA ALEKQGFWHD DVRPWNVMVD
ARQHARLIDF GSIVTTPQDC SWPTNLVQSF FVFVNELFAE NKSWNGFWRS APVHPFNLPQ
PWSNWLYAVW QEPVERWNFV LLLALFEKKA KLPSAEQQRG ATEQWIIAQE TVLLELQSRV
RNESAGSEAL RGQIHTLEQQ MAQLQSAQDA FVEKAQQQVE VSHELTWLGE NMEQLAALLQ
TAQAHAQADV QPELPPETAE LLQRLEAANR EIHHLSNENQ QLRQEIEKIH RSRSWRMTKG
YRYLGLQIHL LRQYGFVQRC KHFIKRVLRF VFSFMRKHPQ VKHTAVNGLH KLGLYQPAYR
LYRRMNPLPH SQYQADAQIL SQTELQVMHP ELLPPEVYEI YLKLTKNK
