MENB_MYCTU
ID MENB_MYCTU Reviewed; 314 AA.
AC P9WNP5; L0T442; O06414; Q7D9N7;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 03-AUG-2022, entry version 47.
DE RecName: Full=1,4-dihydroxy-2-naphthoyl-CoA synthase {ECO:0000255|HAMAP-Rule:MF_01934};
DE Short=DHNA-CoA synthase {ECO:0000255|HAMAP-Rule:MF_01934};
DE EC=4.1.3.36 {ECO:0000255|HAMAP-Rule:MF_01934, ECO:0000269|PubMed:12909628, ECO:0000269|PubMed:20643650, ECO:0000269|PubMed:21830810};
GN Name=menB {ECO:0000255|HAMAP-Rule:MF_01934}; OrderedLocusNames=Rv0548c;
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83332;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=9634230; DOI=10.1038/31159;
RA Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E.,
RA Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K.,
RA Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K.,
RA Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
RA Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J.,
RA Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S.,
RA Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S.,
RA Barrell B.G.;
RT "Deciphering the biology of Mycobacterium tuberculosis from the complete
RT genome sequence.";
RL Nature 393:537-544(1998).
RN [2]
RP SITE, CATALYTIC ACTIVITY, AND MUTAGENESIS OF ASP-185.
RX PubMed=20643650; DOI=10.1074/jbc.m110.147702;
RA Jiang M., Chen M., Guo Z.F., Guo Z.;
RT "A bicarbonate cofactor modulates 1,4-dihydroxy-2-naphthoyl-coenzyme a
RT synthase in menaquinone biosynthesis of Escherichia coli.";
RL J. Biol. Chem. 285:30159-30169(2010).
RN [3]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21969609; DOI=10.1074/mcp.m111.011627;
RA Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B., Yadav A.K.,
RA Shrivastava P., Marimuthu A., Anand S., Sundaram H., Kingsbury R.,
RA Harsha H.C., Nair B., Prasad T.S., Chauhan D.S., Katoch K., Katoch V.M.,
RA Kumar P., Chaerkady R., Ramachandran S., Dash D., Pandey A.;
RT "Proteogenomic analysis of Mycobacterium tuberculosis by high resolution
RT mass spectrometry.";
RL Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS,
RP FUNCTION AS A DHNA-COA SYNTHASE, CATALYTIC ACTIVITY, MUTAGENESIS OF
RP ARG-133; ASP-185; ASP-192 AND TYR-287, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP SUBUNIT.
RX PubMed=12909628; DOI=10.1074/jbc.m307399200;
RA Truglio J.J., Theis K., Feng Y., Gajda R., Machutta C., Tonge P.J.,
RA Kisker C.;
RT "Crystal structure of Mycobacterium tuberculosis MenB, a key enzyme in
RT vitamin K2 biosynthesis.";
RL J. Biol. Chem. 278:42352-42360(2003).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS,
RP AND SUBUNIT.
RX PubMed=16131752; DOI=10.1107/s0907444905017531;
RA Johnston J.M., Arcus V.L., Baker E.N.;
RT "Structure of naphthoate synthase (MenB) from Mycobacterium tuberculosis in
RT both native and product-bound forms.";
RL Acta Crystallogr. D 61:1199-1206(2005).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) IN COMPLEX WITH THE SUBSTRATE ANALOG
RP O-SUCCINYLBENZOYL-N-COENZYME A, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, SITE, AND MUTAGENESIS OF ASP-185 AND SER-190.
RX PubMed=21830810; DOI=10.1021/bi200877x;
RA Li H.J., Li X., Liu N., Zhang H., Truglio J.J., Mishra S., Kisker C.,
RA Garcia-Diaz M., Tonge P.J.;
RT "Mechanism of the intramolecular Claisen condensation reaction catalyzed by
RT MenB, a crotonase superfamily member.";
RL Biochemistry 50:9532-9544(2011).
CC -!- FUNCTION: Converts o-succinylbenzoyl-CoA (OSB-CoA) to 1,4-dihydroxy-2-
CC naphthoyl-CoA (DHNA-CoA). {ECO:0000255|HAMAP-Rule:MF_01934,
CC ECO:0000269|PubMed:12909628}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-succinylbenzoyl-CoA + H(+) = 1,4-dihydroxy-2-naphthoyl-CoA +
CC H2O; Xref=Rhea:RHEA:26562, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:57364, ChEBI:CHEBI:58897; EC=4.1.3.36;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01934,
CC ECO:0000269|PubMed:12909628, ECO:0000269|PubMed:20643650,
CC ECO:0000269|PubMed:21830810};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=7.3 uM for O-succinylbenzoyl-CoA (at 25 degrees Celsius and pH
CC 7.0) {ECO:0000269|PubMed:12909628};
CC KM=22.4 uM for O-succinylbenzoyl-CoA (at 25 degrees Celsius and pH
CC 7.0) {ECO:0000269|PubMed:21830810};
CC Note=kcat is 14.9 min(-1) with O-succinylbenzoyl-CoA at 25 degrees
CC Celsius and pH 7.0 (PubMed:12909628). kcat is 4620 sec(-1) with O-
CC succinylbenzoyl-CoA at 25 degrees Celsius and pH 7.0
CC (PubMed:21830810). {ECO:0000269|PubMed:12909628,
CC ECO:0000269|PubMed:21830810};
CC -!- PATHWAY: Quinol/quinone metabolism; 1,4-dihydroxy-2-naphthoate
CC biosynthesis; 1,4-dihydroxy-2-naphthoate from chorismate: step 6/7.
CC {ECO:0000255|HAMAP-Rule:MF_01934}.
CC -!- PATHWAY: Quinol/quinone metabolism; menaquinone biosynthesis.
CC {ECO:0000255|HAMAP-Rule:MF_01934}.
CC -!- SUBUNIT: Homohexamer. Dimer of a homotrimer.
CC {ECO:0000269|PubMed:12909628, ECO:0000269|PubMed:16131752,
CC ECO:0000269|PubMed:21830810}.
CC -!- SIMILARITY: Belongs to the enoyl-CoA hydratase/isomerase family. MenB
CC subfamily. {ECO:0000255|HAMAP-Rule:MF_01934}.
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DR EMBL; AL123456; CCP43286.1; -; Genomic_DNA.
DR PIR; G70547; G70547.
DR RefSeq; NP_215062.1; NC_000962.3.
DR RefSeq; WP_003402911.1; NC_000962.3.
DR PDB; 1Q51; X-ray; 2.30 A; A/B/C/D/E/F/G/H/I/J/K/L=1-314.
DR PDB; 1Q52; X-ray; 1.80 A; A/B/C/D/E/F/G/H/I/J/K/L=1-314.
DR PDB; 1RJM; X-ray; 2.15 A; A/B/C=1-314.
DR PDB; 1RJN; X-ray; 2.30 A; A/B/C=1-314.
DR PDB; 3T8A; X-ray; 2.24 A; A/B/C=1-314.
DR PDB; 3T8B; X-ray; 1.65 A; A/B=1-314.
DR PDB; 4QII; X-ray; 1.64 A; A/B/C/D/E/F/G/H/I/J/K/L=1-314.
DR PDB; 4QIJ; X-ray; 2.20 A; A/B/C/D/E/F/G/H/I/J/K/L=1-314.
DR PDBsum; 1Q51; -.
DR PDBsum; 1Q52; -.
DR PDBsum; 1RJM; -.
DR PDBsum; 1RJN; -.
DR PDBsum; 3T8A; -.
DR PDBsum; 3T8B; -.
DR PDBsum; 4QII; -.
DR PDBsum; 4QIJ; -.
DR AlphaFoldDB; P9WNP5; -.
DR SMR; P9WNP5; -.
DR STRING; 83332.Rv0548c; -.
DR BindingDB; P9WNP5; -.
DR ChEMBL; CHEMBL1275214; -.
DR DrugBank; DB03059; Acetoacetyl-CoA.
DR DrugBank; DB01992; Coenzyme A.
DR PaxDb; P9WNP5; -.
DR DNASU; 887529; -.
DR GeneID; 887529; -.
DR KEGG; mtu:Rv0548c; -.
DR PATRIC; fig|83332.111.peg.604; -.
DR TubercuList; Rv0548c; -.
DR eggNOG; COG0447; Bacteria.
DR OMA; HAKRQTD; -.
DR PhylomeDB; P9WNP5; -.
DR BioCyc; MetaCyc:G185E-4681-MON; -.
DR BRENDA; 4.1.3.36; 3445.
DR UniPathway; UPA00079; -.
DR UniPathway; UPA01057; UER00167.
DR PRO; PR:P9WNP5; -.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0005886; C:plasma membrane; HDA:MTBBASE.
DR GO; GO:0008935; F:1,4-dihydroxy-2-naphthoyl-CoA synthase activity; IDA:UniProtKB.
DR GO; GO:0009234; P:menaquinone biosynthetic process; IDA:UniProtKB.
DR GO; GO:0034214; P:protein hexamerization; IDA:MTBBASE.
DR Gene3D; 1.10.12.10; -; 1.
DR HAMAP; MF_01934; MenB; 1.
DR InterPro; IPR029045; ClpP/crotonase-like_dom_sf.
DR InterPro; IPR010198; DHNA-CoA_synthase_MenB.
DR InterPro; IPR001753; Enoyl-CoA_hydra/iso.
DR InterPro; IPR014748; Enoyl-CoA_hydra_C.
DR PANTHER; PTHR43113; PTHR43113; 1.
DR Pfam; PF00378; ECH_1; 1.
DR SUPFAM; SSF52096; SSF52096; 1.
DR TIGRFAMs; TIGR01929; menB; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Lyase; Menaquinone biosynthesis; Reference proteome.
FT CHAIN 1..314
FT /note="1,4-dihydroxy-2-naphthoyl-CoA synthase"
FT /id="PRO_0000399471"
FT BINDING 58
FT /ligand="substrate"
FT /ligand_note="ligand shared between two neighboring
FT subunits"
FT /note="in other chain"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01934,
FT ECO:0000269|PubMed:12909628, ECO:0000269|PubMed:21830810"
FT BINDING 95
FT /ligand="substrate"
FT /ligand_note="ligand shared between two neighboring
FT subunits"
FT /note="in other chain"
FT /evidence="ECO:0000269|PubMed:12909628,
FT ECO:0000269|PubMed:21830810"
FT BINDING 103..107
FT /ligand="substrate"
FT /ligand_note="ligand shared between two neighboring
FT subunits"
FT /note="in other chain"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01934,
FT ECO:0000269|PubMed:12909628, ECO:0000269|PubMed:16131752,
FT ECO:0000269|PubMed:21830810"
FT BINDING 115
FT /ligand="substrate"
FT /ligand_note="ligand shared between two neighboring
FT subunits"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:P0ABU0, ECO:0000255|HAMAP-
FT Rule:MF_01934"
FT BINDING 157..161
FT /ligand="substrate"
FT /ligand_note="ligand shared between two neighboring
FT subunits"
FT /note="in other chain"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01934,
FT ECO:0000269|PubMed:12909628"
FT BINDING 184
FT /ligand="substrate"
FT /ligand_note="ligand shared between two neighboring
FT subunits"
FT /note="in other chain"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01934,
FT ECO:0000269|PubMed:12909628"
FT BINDING 190
FT /ligand="substrate"
FT /ligand_note="ligand shared between two neighboring
FT subunits"
FT /note="in other chain"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01934,
FT ECO:0000305|PubMed:21830810"
FT BINDING 287
FT /ligand="substrate"
FT /ligand_note="ligand shared between two neighboring
FT subunits"
FT /evidence="ECO:0000250|UniProtKB:P0ABU0, ECO:0000255|HAMAP-
FT Rule:MF_01934"
FT BINDING 302
FT /ligand="substrate"
FT /ligand_note="ligand shared between two neighboring
FT subunits"
FT /evidence="ECO:0000250|UniProtKB:P0ABU0, ECO:0000255|HAMAP-
FT Rule:MF_01934"
FT SITE 115
FT /note="Important for catalysis"
FT /evidence="ECO:0000250|UniProtKB:P0ABU0, ECO:0000255|HAMAP-
FT Rule:MF_01934"
FT SITE 185
FT /note="Important for catalysis"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01934,
FT ECO:0000305|PubMed:20643650, ECO:0000305|PubMed:21830810"
FT SITE 287
FT /note="Important for catalysis"
FT /evidence="ECO:0000250|UniProtKB:P0ABU0, ECO:0000255|HAMAP-
FT Rule:MF_01934, ECO:0000305|PubMed:12909628"
FT MUTAGEN 133
FT /note="R->A: Loss of DHNA-CoA synthase activity."
FT /evidence="ECO:0000269|PubMed:12909628"
FT MUTAGEN 185
FT /note="D->E: Nearly abolishes DHNA-CoA synthase activity."
FT /evidence="ECO:0000269|PubMed:21830810"
FT MUTAGEN 185
FT /note="D->G,N: Loss of DHNA-CoA synthase activity."
FT /evidence="ECO:0000269|PubMed:12909628,
FT ECO:0000269|PubMed:20643650"
FT MUTAGEN 190
FT /note="S->A: Reduces affinity for substrate. Nearly
FT abolishes DHNA-CoA synthase activity."
FT /evidence="ECO:0000269|PubMed:21830810"
FT MUTAGEN 192
FT /note="D->N: Loss of DHNA-CoA synthase activity."
FT /evidence="ECO:0000269|PubMed:12909628"
FT MUTAGEN 287
FT /note="Y->F: Loss of DHNA-CoA synthase activity."
FT /evidence="ECO:0000269|PubMed:12909628"
FT HELIX 22..24
FT /evidence="ECO:0007829|PDB:4QII"
FT STRAND 25..27
FT /evidence="ECO:0007829|PDB:4QII"
FT STRAND 35..52
FT /evidence="ECO:0007829|PDB:4QII"
FT HELIX 55..57
FT /evidence="ECO:0007829|PDB:4QII"
FT HELIX 63..77
FT /evidence="ECO:0007829|PDB:4QII"
FT STRAND 84..89
FT /evidence="ECO:0007829|PDB:4QII"
FT TURN 94..96
FT /evidence="ECO:0007829|PDB:4QII"
FT STRAND 100..102
FT /evidence="ECO:0007829|PDB:4QII"
FT HELIX 107..109
FT /evidence="ECO:0007829|PDB:4QII"
FT STRAND 118..122
FT /evidence="ECO:0007829|PDB:4QII"
FT HELIX 123..125
FT /evidence="ECO:0007829|PDB:4QII"
FT HELIX 126..131
FT /evidence="ECO:0007829|PDB:1Q52"
FT HELIX 136..145
FT /evidence="ECO:0007829|PDB:4QII"
FT STRAND 146..154
FT /evidence="ECO:0007829|PDB:4QII"
FT STRAND 156..159
FT /evidence="ECO:0007829|PDB:4QII"
FT HELIX 161..168
FT /evidence="ECO:0007829|PDB:4QII"
FT STRAND 169..175
FT /evidence="ECO:0007829|PDB:4QII"
FT TURN 176..178
FT /evidence="ECO:0007829|PDB:4QII"
FT STRAND 180..182
FT /evidence="ECO:0007829|PDB:4QII"
FT HELIX 185..188
FT /evidence="ECO:0007829|PDB:4QII"
FT STRAND 189..192
FT /evidence="ECO:0007829|PDB:3T8B"
FT TURN 195..197
FT /evidence="ECO:0007829|PDB:4QII"
FT HELIX 198..204
FT /evidence="ECO:0007829|PDB:4QII"
FT HELIX 206..215
FT /evidence="ECO:0007829|PDB:4QII"
FT STRAND 218..220
FT /evidence="ECO:0007829|PDB:3T8B"
FT HELIX 221..227
FT /evidence="ECO:0007829|PDB:4QII"
FT STRAND 231..234
FT /evidence="ECO:0007829|PDB:4QII"
FT HELIX 236..238
FT /evidence="ECO:0007829|PDB:4QII"
FT HELIX 239..251
FT /evidence="ECO:0007829|PDB:4QII"
FT HELIX 255..266
FT /evidence="ECO:0007829|PDB:4QII"
FT TURN 267..270
FT /evidence="ECO:0007829|PDB:4QII"
FT HELIX 271..287
FT /evidence="ECO:0007829|PDB:4QII"
FT HELIX 290..300
FT /evidence="ECO:0007829|PDB:4QII"
SQ SEQUENCE 314 AA; 34689 MW; AF2D192A9F607DC7 CRC64;
MVAPAGEQGR SSTALSDNPF DAKAWRLVDG FDDLTDITYH RHVDDATVRV AFNRPEVRNA
FRPHTVDELY RVLDHARMSP DVGVVLLTGN GPSPKDGGWA FCSGGDQRIR GRSGYQYASG
DTADTVDVAR AGRLHILEVQ RLIRFMPKVV ICLVNGWAAG GGHSLHVVCD LTLASREYAR
FKQTDADVGS FDGGYGSAYL ARQVGQKFAR EIFFLGRTYT AEQMHQMGAV NAVAEHAELE
TVGLQWAAEI NAKSPQAQRM LKFAFNLLDD GLVGQQLFAG EATRLAYMTD EAVEGRDAFL
QKRPPDWSPF PRYF
