ID MENB_ECOLI Reviewed; 285 AA.
AC P0ABU0; P27290;
DT 25-OCT-2005, integrated into UniProtKB/Swiss-Prot.
DT 25-OCT-2005, sequence version 1.
DT 27-MAR-2024, entry version 138.
DE RecName: Full=1,4-dihydroxy-2-naphthoyl-CoA synthase {ECO:0000255|HAMAP-Rule:MF_01934, ECO:0000303|PubMed:21830810};
DE Short=DHNA-CoA synthase {ECO:0000255|HAMAP-Rule:MF_01934, ECO:0000303|PubMed:23658663};
DE EC=4.1.3.36 {ECO:0000255|HAMAP-Rule:MF_01934, ECO:0000269|PubMed:20643650, ECO:0000269|PubMed:21830810, ECO:0000269|PubMed:22606952, ECO:0000269|PubMed:23658663};
GN Name=menB {ECO:0000255|HAMAP-Rule:MF_01934};
GN OrderedLocusNames=b2262, JW2257;
OS Escherichia coli (strain K12).
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=1629162; DOI=10.1128/jb.174.15.5057-5062.1992;
RA Sharma V., Suvarna K., Meganathan R., Hudspeth M.E.;
RT "Menaquinone (vitamin K2) biosynthesis: nucleotide sequence and expression
RT of the menB gene from Escherichia coli.";
RL J. Bacteriol. 174:5057-5062(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9205837; DOI=10.1093/dnares/4.2.91;
RA Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K.,
RA Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T., Oyama S.,
RA Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H.,
RA Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.;
RT "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12
RT genome corresponding to 50.0-68.8 min on the linkage map and analysis of
RT its sequence features.";
RL DNA Res. 4:91-113(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-6.
RC STRAIN=K12;
RA Sharma V., Hudspeth M.E., Meganathan R.;
RL Submitted (JUL-1994) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP FUNCTION IN MENAQUINONE BIOSYNTHESIS.
RX PubMed=1091286; DOI=10.1021/bi00673a029;
RA Young I.G.;
RT "Biosynthesis of bacterial menaquinones. Menaquinone mutants of Escherichia
RT coli.";
RL Biochemistry 14:399-406(1975).
RN [7]
RP FUNCTION AS A DHNA-COA SYNTHASE, CATALYTIC ACTIVITY, MUTAGENESIS OF
RP GLN-154; GLY-156 AND TRP-184, COFACTOR, ACTIVITY REGULATION, AND SUBUNIT.
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 [8]
RP X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) IN COMPLEX WITH THE SUBSTRATE ANALOG
RP O-SUCCINYLBENZOYL-N-COENZYME A, CATALYTIC ACTIVITY, FUNCTION, SUBUNIT,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND MUTAGENESIS OF TYR-97 AND GLY-156.
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).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.19 ANGSTROMS) IN COMPLEX WITH HYDROGENCARBONATE,
RP CATALYTIC ACTIVITY, COFACTOR, AND SUBUNIT.
RX PubMed=22606952; DOI=10.1021/bi300486j;
RA Sun Y., Song H., Li J., Jiang M., Li Y., Zhou J., Guo Z.;
RT "Active site binding and catalytic role of bicarbonate in 1,4-dihydroxy-2-
RT naphthoyl coenzyme A synthases from vitamin K biosynthetic pathways.";
RL Biochemistry 51:4580-4589(2012).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) IN COMPLEX WITH THE SUBSTRATE ANALOG
RP 1-HYDROXY-2-NAPHTHOYL-COA, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, SUBUNIT,
RP MUTAGENESIS OF LYS-89; ARG-91; ARG-267; PHE-270 AND LYS-273, AND
RP BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=23658663; DOI=10.1371/journal.pone.0063095;
RA Sun Y., Song H., Li J., Li Y., Jiang M., Zhou J., Guo Z.;
RT "Structural basis of the induced-fit mechanism of 1,4-dihydroxy-2-naphthoyl
RT coenzyme A synthase from the crotonase fold superfamily.";
RL PLoS ONE 8:E63095-E63095(2013).
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:1091286, ECO:0000269|PubMed:20643650,
CC ECO:0000269|PubMed:21830810, ECO:0000269|PubMed:23658663}.
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:20643650, ECO:0000269|PubMed:21830810,
CC ECO:0000269|PubMed:22606952, ECO:0000269|PubMed:23658663};
CC -!- COFACTOR:
CC Name=hydrogencarbonate; Xref=ChEBI:CHEBI:17544;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01934,
CC ECO:0000269|PubMed:20643650, ECO:0000305|PubMed:22606952};
CC Note=The hydrogencarbonate anion plays the same catalytic role (proton
CC acceptor) as the side-chain carboxylate group of the essential 'Asp-
CC 185' found in actinobacteria, archaea, bacteroidetes, and
CC deltaproteobacteria. {ECO:0000269|PubMed:20643650,
CC ECO:0000305|PubMed:22606952};
CC -!- ACTIVITY REGULATION: Inhibited by sulfite and nitrate.
CC {ECO:0000269|PubMed:20643650}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=26 uM for o-succinylbenzoyl-CoA {ECO:0000269|PubMed:21830810};
CC KM=2.8 uM for o-succinylbenzoyl-CoA {ECO:0000269|PubMed:23658663};
CC Note=kcat is 620 sec(-1) with o-succinylbenzoyl-CoA as
CC substrate(PubMed:21830810). kcat is 1.24 min(-1) with o-
CC succinylbenzoyl-CoA as substrate (PubMed:23658663). All assays are
CC performed at pH 7.0 at 25 degrees Celsius and in the presence of 20
CC mM NaHCO(3). {ECO:0000269|PubMed:21830810,
CC ECO:0000269|PubMed:23658663};
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:20643650, ECO:0000269|PubMed:21830810,
CC ECO:0000269|PubMed:22606952, ECO:0000269|PubMed:23658663}.
CC -!- INTERACTION:
CC P0ABU0; P67910: hldD; NbExp=3; IntAct=EBI-554195, EBI-543760;
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; M93421; AAA23682.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75322.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA16086.1; -; Genomic_DNA.
DR EMBL; L35030; AAA24152.1; -; Genomic_DNA.
DR PIR; A42714; D64997.
DR RefSeq; NP_416765.1; NC_000913.3.
DR RefSeq; WP_000639996.1; NZ_STEB01000008.1.
DR PDB; 3T88; X-ray; 2.00 A; A/B/C/D/E/F=1-285.
DR PDB; 3T89; X-ray; 1.95 A; A/B/C/D/E/F=1-285.
DR PDB; 4ELS; X-ray; 2.30 A; A/B/C/D/E/F=1-285.
DR PDB; 4ELW; X-ray; 2.55 A; A/B/C/D/E/F=1-285.
DR PDB; 4ELX; X-ray; 2.19 A; A/B/C/D/E/F=1-285.
DR PDB; 4I42; X-ray; 1.85 A; A/B/C/D/E/F/G/H/I/J/K/L=1-285.
DR PDBsum; 3T88; -.
DR PDBsum; 3T89; -.
DR PDBsum; 4ELS; -.
DR PDBsum; 4ELW; -.
DR PDBsum; 4ELX; -.
DR PDBsum; 4I42; -.
DR AlphaFoldDB; P0ABU0; -.
DR SMR; P0ABU0; -.
DR BioGRID; 4260504; 18.
DR BioGRID; 851088; 1.
DR DIP; DIP-47854N; -.
DR IntAct; P0ABU0; 6.
DR STRING; 511145.b2262; -.
DR jPOST; P0ABU0; -.
DR PaxDb; 511145-b2262; -.
DR EnsemblBacteria; AAC75322; AAC75322; b2262.
DR GeneID; 75205687; -.
DR GeneID; 946747; -.
DR KEGG; ecj:JW2257; -.
DR KEGG; eco:b2262; -.
DR PATRIC; fig|511145.12.peg.2355; -.
DR EchoBASE; EB1342; -.
DR eggNOG; COG0447; Bacteria.
DR HOGENOM; CLU_009834_7_7_6; -.
DR InParanoid; P0ABU0; -.
DR OMA; FCDARED; -.
DR OrthoDB; 9807606at2; -.
DR PhylomeDB; P0ABU0; -.
DR BioCyc; EcoCyc:NAPHTHOATE-SYN-MONOMER; -.
DR BioCyc; MetaCyc:NAPHTHOATE-SYN-MONOMER; -.
DR UniPathway; UPA00079; -.
DR UniPathway; UPA01057; UER00167.
DR PRO; PR:P0ABU0; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0008935; F:1,4-dihydroxy-2-naphthoyl-CoA synthase activity; IDA:EcoliWiki.
DR GO; GO:0071890; F:bicarbonate binding; IDA:UniProtKB.
DR GO; GO:0009234; P:menaquinone biosynthetic process; IMP:EcoCyc.
DR CDD; cd06558; crotonase-like; 1.
DR Gene3D; 1.10.12.10; Lyase 2-enoyl-coa Hydratase, Chain A, domain 2; 1.
DR HAMAP; MF_01934; MenB; 1.
DR InterPro; IPR029045; ClpP/crotonase-like_dom_sf.
DR InterPro; IPR010198; DHNA-CoA_synthase_MenB.
DR InterPro; IPR018376; Enoyl-CoA_hyd/isom_CS.
DR InterPro; IPR001753; Enoyl-CoA_hydra/iso.
DR InterPro; IPR014748; Enoyl-CoA_hydra_C.
DR NCBIfam; TIGR01929; menB; 1.
DR PANTHER; PTHR43113:SF1; 1,4-DIHYDROXY-2-NAPHTHOYL-COA SYNTHASE, PEROXISOMAL; 1.
DR PANTHER; PTHR43113; NUCLEOSIDE-DIPHOSPHATE-SUGAR EPIMERASE; 1.
DR Pfam; PF00378; ECH_1; 1.
DR SUPFAM; SSF52096; ClpP/crotonase; 1.
DR PROSITE; PS00166; ENOYL_COA_HYDRATASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Lyase; Menaquinone biosynthesis; Reference proteome.
FT CHAIN 1..285
FT /note="1,4-dihydroxy-2-naphthoyl-CoA synthase"
FT /id="PRO_0000109325"
FT BINDING 45
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:21830810, ECO:0000269|PubMed:23658663"
FT BINDING 84..89
FT /ligand="substrate"
FT /ligand_note="ligand shared between two neighboring
FT subunits"
FT /note="in other chain"
FT /evidence="ECO:0000269|PubMed:21830810,
FT ECO:0000269|PubMed:23658663"
FT BINDING 97
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:21830810"
FT BINDING 129..133
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:21830810, ECO:0000269|PubMed:23658663"
FT BINDING 154..156
FT /ligand="hydrogencarbonate"
FT /ligand_id="ChEBI:CHEBI:17544"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01934,
FT ECO:0000269|PubMed:22606952"
FT BINDING 155
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:21830810, ECO:0000269|PubMed:23658663"
FT BINDING 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:23658663"
FT BINDING 258
FT /ligand="substrate"
FT /ligand_note="ligand shared between two neighboring
FT subunits"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01934,
FT ECO:0000269|PubMed:21830810"
FT BINDING 273
FT /ligand="substrate"
FT /ligand_note="ligand shared between two neighboring
FT subunits"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01934,
FT ECO:0000269|PubMed:21830810, ECO:0000269|PubMed:23658663"
FT SITE 97
FT /note="Important for catalysis"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01934,
FT ECO:0000305|PubMed:21830810"
FT SITE 258
FT /note="Important for catalysis"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01934,
FT ECO:0000305|PubMed:21830810"
FT MUTAGEN 89
FT /note="K->A: Strongly decreases affinity for substrate and
FT DHNA-CoA synthase activity."
FT /evidence="ECO:0000269|PubMed:23658663"
FT MUTAGEN 91
FT /note="R->A: Loss of DHNA-CoA synthase activity."
FT /evidence="ECO:0000269|PubMed:23658663"
FT MUTAGEN 97
FT /note="Y->F: Loss of DHNA-CoA synthase activity."
FT /evidence="ECO:0000269|PubMed:21830810"
FT MUTAGEN 154
FT /note="Q->A: Reduces the specific DHNA-CoA synthase
FT activity by 15-fold, whereas its affinity for
FT hydrogencarbonate is reduced by 36-fold."
FT /evidence="ECO:0000269|PubMed:20643650"
FT MUTAGEN 156
FT /note="G->D: Loss of DHNA-CoA synthase activity."
FT /evidence="ECO:0000269|PubMed:20643650,
FT ECO:0000269|PubMed:21830810"
FT MUTAGEN 184
FT /note="W->F: Reduces the specific DHNA-CoA synthase
FT activity by 530-fold, whereas its affinity for
FT hydrogencarbonate is reduced by 20-fold."
FT /evidence="ECO:0000269|PubMed:20643650"
FT MUTAGEN 267
FT /note="R->A: Strongly decreases affinity for substrate and
FT DHNA-CoA synthase activity."
FT /evidence="ECO:0000269|PubMed:23658663"
FT MUTAGEN 270
FT /note="F->A: Strongly decreases affinity for substrate and
FT DHNA-CoA synthase activity."
FT /evidence="ECO:0000269|PubMed:23658663"
FT MUTAGEN 273
FT /note="K->A: Impairs protein folding."
FT /evidence="ECO:0000269|PubMed:23658663"
FT HELIX 6..9
FT /evidence="ECO:0007829|PDB:4I42"
FT STRAND 15..17
FT /evidence="ECO:0007829|PDB:4I42"
FT STRAND 23..30
FT /evidence="ECO:0007829|PDB:4I42"
FT STRAND 33..39
FT /evidence="ECO:0007829|PDB:4I42"
FT HELIX 42..44
FT /evidence="ECO:0007829|PDB:4I42"
FT HELIX 50..65
FT /evidence="ECO:0007829|PDB:4I42"
FT STRAND 71..83
FT /evidence="ECO:0007829|PDB:4I42"
FT HELIX 88..90
FT /evidence="ECO:0007829|PDB:4I42"
FT STRAND 93..98
FT /evidence="ECO:0007829|PDB:4I42"
FT TURN 105..107
FT /evidence="ECO:0007829|PDB:4ELX"
FT HELIX 108..117
FT /evidence="ECO:0007829|PDB:4I42"
FT STRAND 122..126
FT /evidence="ECO:0007829|PDB:4I42"
FT STRAND 128..131
FT /evidence="ECO:0007829|PDB:4I42"
FT HELIX 133..140
FT /evidence="ECO:0007829|PDB:4I42"
FT STRAND 141..147
FT /evidence="ECO:0007829|PDB:4I42"
FT STRAND 151..153
FT /evidence="ECO:0007829|PDB:4I42"
FT HELIX 156..159
FT /evidence="ECO:0007829|PDB:4I42"
FT TURN 166..168
FT /evidence="ECO:0007829|PDB:4I42"
FT HELIX 169..175
FT /evidence="ECO:0007829|PDB:4I42"
FT HELIX 177..186
FT /evidence="ECO:0007829|PDB:4I42"
FT HELIX 192..197
FT /evidence="ECO:0007829|PDB:4I42"
FT STRAND 200..205
FT /evidence="ECO:0007829|PDB:4I42"
FT HELIX 207..209
FT /evidence="ECO:0007829|PDB:4I42"
FT HELIX 210..222
FT /evidence="ECO:0007829|PDB:4I42"
FT HELIX 226..238
FT /evidence="ECO:0007829|PDB:4I42"
FT HELIX 242..258
FT /evidence="ECO:0007829|PDB:4I42"
FT HELIX 261..271
FT /evidence="ECO:0007829|PDB:4I42"
FT HELIX 278..280
FT /evidence="ECO:0007829|PDB:3T88"
SQ SEQUENCE 285 AA; 31633 MW; C38E7206924408E6 CRC64;
MIYPDEAMLY APVEWHDCSE GFEDIRYEKS TDGIAKITIN RPQVRNAFRP LTVKEMIQAL
ADARYDDNIG VIILTGAGDK AFCSGGDQKV RGDYGGYKDD SGVHHLNVLD FQRQIRTCPK
PVVAMVAGYS IGGGHVLHMM CDLTIAADNA IFGQTGPKVG SFDGGWGASY MARIVGQKKA
REIWFLCRQY DAKQALDMGL VNTVVPLADL EKETVRWCRE MLQNSPMALR CLKAALNADC
DGQAGLQELA GNATMLFYMT EEGQEGRNAF NQKRQPDFSK FKRNP
//
