MENI_ECOLI
ID MENI_ECOLI Reviewed; 136 AA.
AC P77781;
DT 27-APR-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1997, sequence version 1.
DT 03-AUG-2022, entry version 159.
DE RecName: Full=1,4-dihydroxy-2-naphthoyl-CoA hydrolase {ECO:0000255|HAMAP-Rule:MF_01936, ECO:0000305};
DE Short=DHNA-CoA hydrolase {ECO:0000255|HAMAP-Rule:MF_01936, ECO:0000305};
DE EC=3.1.2.28 {ECO:0000255|HAMAP-Rule:MF_01936, ECO:0000269|PubMed:23564174, ECO:0000269|PubMed:24992697};
DE AltName: Full=DHNA-CoA thioesterase {ECO:0000255|HAMAP-Rule:MF_01936, ECO:0000303|PubMed:23564174};
GN Name=menI {ECO:0000255|HAMAP-Rule:MF_01936, ECO:0000303|PubMed:23564174};
GN Synonyms=ydiI; OrderedLocusNames=b1686, JW1676;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
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 [2]
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 [3]
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 [4]
RP FUNCTION AS AN ESTERASE.
RX PubMed=15808744; DOI=10.1016/j.fmrre.2004.12.006;
RA Kuznetsova E., Proudfoot M., Sanders S.A., Reinking J., Savchenko A.,
RA Arrowsmith C.H., Edwards A.M., Yakunin A.F.;
RT "Enzyme genomics: application of general enzymatic screens to discover new
RT enzymes.";
RL FEMS Microbiol. Rev. 29:263-279(2005).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, PATHWAY, AND
RP DISRUPTION PHENOTYPE.
RC STRAIN=K12 / BW25113;
RX PubMed=23564174; DOI=10.1128/jb.00141-13;
RA Chen M., Ma X., Chen X., Jiang M., Song H., Guo Z.;
RT "Identification of a hotdog fold thioesterase involved in the biosynthesis
RT of menaquinone in Escherichia coli.";
RL J. Bacteriol. 195:2768-2775(2013).
RN [6]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, PATHWAY, AND
RP MUTAGENESIS OF VAL-68 AND TYR-71.
RX PubMed=24992697; DOI=10.1021/bi500333m;
RA Latham J.A., Chen D., Allen K.N., Dunaway-Mariano D.;
RT "Divergence of substrate specificity and function in the Escherichia coli
RT hotdog-fold thioesterase paralogs YdiI and YbdB.";
RL Biochemistry 53:4775-4787(2014).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
RA Kuzin A.P., Edstrom W., Vorobiev S.M., Lee I., Forouhar F., Ma L.,
RA Chiang Y., Rong X., Acton T.B., Montelione G.T., Hunt J.F., Tong L.;
RT "X-ray structure of YDII_ECOLI.";
RL Submitted (FEB-2004) to the PDB data bank.
RN [8]
RP X-RAY CRYSTALLOGRAPHY (1.34 ANGSTROMS) OF 2-136.
RX PubMed=16021622; DOI=10.1002/prot.20541;
RA Badger J., Sauder J.M., Adams J.M., Antonysamy S., Bain K., Bergseid M.G.,
RA Buchanan S.G., Buchanan M.D., Batiyenko Y., Christopher J.A., Emtage S.,
RA Eroshkina A., Feil I., Furlong E.B., Gajiwala K.S., Gao X., He D.,
RA Hendle J., Huber A., Hoda K., Kearins P., Kissinger C., Laubert B.,
RA Lewis H.A., Lin J., Loomis K., Lorimer D., Louie G., Maletic M.,
RA Marsh C.D., Miller I., Molinari J., Muller-Dieckmann H.J., Newman J.M.,
RA Noland B.W., Pagarigan B., Park F., Peat T.S., Post K.W., Radojicic S.,
RA Ramos A., Romero R., Rutter M.E., Sanderson W.E., Schwinn K.D., Tresser J.,
RA Winhoven J., Wright T.A., Wu L., Xu J., Harris T.J.R.;
RT "Structural analysis of a set of proteins resulting from a bacterial
RT genomics project.";
RL Proteins 60:787-796(2005).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.89 ANGSTROMS) IN COMPLEXES WITH SUBSTRATE ANALOGS,
RP SUBUNIT, MUTAGENESIS OF GLN-48; HIS-54; GLU-63; SER-64; SER-67; HIS-89;
RP ARG-91; HIS-106 AND SER-109, AND ACTIVE SITE.
RX PubMed=25010423; DOI=10.1021/bi500334v;
RA Wu R., Latham J.A., Chen D., Farelli J., Zhao H., Matthews K., Allen K.N.,
RA Dunaway-Mariano D.;
RT "Structure and catalysis in the Escherichia coli hotdog-fold thioesterase
RT paralogs YdiI and YbdB.";
RL Biochemistry 53:4788-4805(2014).
CC -!- FUNCTION: Catalyzes the hydrolysis of 1,4-dihydroxy-2-naphthoyl-CoA
CC (DHNA-CoA) to 1,4-dihydroxy-2-naphthoate (DHNA). Also shows significant
CC activity toward a wide range of acyl-CoA thioesters, and minimal
CC activity toward benzoyl-holoEntB. {ECO:0000269|PubMed:15808744,
CC ECO:0000269|PubMed:23564174, ECO:0000269|PubMed:24992697}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=1,4-dihydroxy-2-naphthoyl-CoA + H2O = 1,4-dihydroxy-2-
CC naphthoate + CoA + H(+); Xref=Rhea:RHEA:26309, ChEBI:CHEBI:11173,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:57287,
CC ChEBI:CHEBI:58897; EC=3.1.2.28; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01936, ECO:0000269|PubMed:23564174,
CC ECO:0000269|PubMed:24992697};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=2.5 uM for 1,4-dihydroxy-2-naphthoyl-CoA
CC {ECO:0000269|PubMed:23564174};
CC KM=8 uM for 1,4-dihydroxy-2-naphthoyl-CoA
CC {ECO:0000269|PubMed:24992697};
CC KM=1.3 uM for oleoyl-CoA {ECO:0000269|PubMed:24992697};
CC KM=1.5 uM for myristoyl-CoA {ECO:0000269|PubMed:24992697};
CC KM=1.559 uM for acetyl-CoA {ECO:0000269|PubMed:23564174};
CC KM=1.9 uM for palmitoyl-CoA {ECO:0000269|PubMed:24992697};
CC KM=2.2 uM for lauroyl-CoA {ECO:0000269|PubMed:24992697};
CC KM=8.0 uM for 1-hydroxy-2-naphthoyl-CoA
CC {ECO:0000269|PubMed:23564174};
CC KM=9 uM for 4-hydroxybenzoyl-CoA {ECO:0000269|PubMed:24992697};
CC KM=21 uM for hexanoyl-CoA {ECO:0000269|PubMed:24992697};
CC KM=25 uM for benzoyl-CoA {ECO:0000269|PubMed:24992697};
CC KM=26.5 uM for 3,5-dihydroxybenzoyl-CoA
CC {ECO:0000269|PubMed:23564174};
CC KM=26.9 uM for 3,4-dihydroxybenzoyl-CoA
CC {ECO:0000269|PubMed:23564174};
CC KM=30 uM for coumaroyl-CoA {ECO:0000269|PubMed:24992697};
CC KM=54 uM for benzoyl-ACP {ECO:0000269|PubMed:24992697};
CC KM=69.4 uM for beta-methylcrotonyl-CoA {ECO:0000269|PubMed:24992697};
CC KM=73 uM for salicylyl-CoA {ECO:0000269|PubMed:23564174};
CC KM=115 uM for beta-methylmalonyl-CoA {ECO:0000269|PubMed:24992697};
CC KM=120 uM for propionyl-CoA {ECO:0000269|PubMed:24992697};
CC KM=200 uM for 2,4-dihydroxybenzoyl-EntB
CC {ECO:0000269|PubMed:24992697};
CC Note=kcat is 6.2 sec(-1) with 1,4-dihydroxy-2-naphthoyl-CoA
CC (PubMed:23564174). kcat is 1.6 sec(-1) with 1,4-dihydroxy-2-
CC naphthoyl-CoA (PubMed:24992697). kcat is 0.12 sec(-1) with oleoyl-
CC CoA. kcat is 0.62 sec(-1) with myristoyl-CoA. kcat is 0.0044 sec(-1)
CC with acetyl-CoA. kcat is 0.58 sec(-1) with palmitoyl-CoA. kcat is
CC 0.74 sec(-1) with lauroyl-CoA. kcat is 14.8 sec(-1) with 1-hydroxy-2-
CC naphthoyl-CoA. kcat is 5.2 sec(-1) with 4-hydroxybenzoyl-CoA. kcat is
CC 0.3 sec(-1) with hexanoyl-CoA. kcat is 17.7 sec(-1) with benzoyl-CoA.
CC kcat is 12.6 sec(-1) with 3,5-dihydroxybenzoyl-CoA. kcat is 23.2
CC sec(-1) with 3,4-dihydroxybenzoyl-CoA. kcat is 8.4 sec(-1) with
CC coumaroyl-CoA. kcat is 0.083 sec(-1) with benzoyl-ACP. kcat is 0.5
CC sec(-1) with beta-methylcrotonyl-CoA. kcat is 93.0 sec(-1) with
CC salicylyl-CoA. kcat is 0.67 sec(-1) with beta-methylmalonyl-CoA. kcat
CC is 0.21 sec(-1) with propionyl-CoA. kcat is 0.0036 sec(-1) with 2,4-
CC dihydroxybenzoyl-EntB. {ECO:0000269|PubMed:23564174,
CC ECO:0000269|PubMed:24992697};
CC -!- PATHWAY: Quinol/quinone metabolism; 1,4-dihydroxy-2-naphthoate
CC biosynthesis; 1,4-dihydroxy-2-naphthoate from chorismate: step 7/7.
CC {ECO:0000255|HAMAP-Rule:MF_01936, ECO:0000269|PubMed:23564174,
CC ECO:0000269|PubMed:24992697}.
CC -!- PATHWAY: Quinol/quinone metabolism; menaquinone biosynthesis.
CC {ECO:0000255|HAMAP-Rule:MF_01936, ECO:0000269|PubMed:23564174,
CC ECO:0000269|PubMed:24992697}.
CC -!- SUBUNIT: Homotetramer. Dimer of dimers. {ECO:0000255|HAMAP-
CC Rule:MF_01936, ECO:0000269|PubMed:25010423}.
CC -!- DISRUPTION PHENOTYPE: Deletion results in a significant decrease in
CC menaquinone production. {ECO:0000269|PubMed:23564174}.
CC -!- SIMILARITY: Belongs to the thioesterase PaaI family.
CC {ECO:0000255|HAMAP-Rule:MF_01936}.
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DR EMBL; U00096; AAC74756.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA15452.1; -; Genomic_DNA.
DR PIR; F64926; F64926.
DR RefSeq; NP_416201.1; NC_000913.3.
DR RefSeq; WP_000637982.1; NZ_STEB01000003.1.
DR PDB; 1SBK; X-ray; 2.00 A; A/B/C/D=1-136.
DR PDB; 1VH5; X-ray; 1.34 A; A/B=2-136.
DR PDB; 1VI8; X-ray; 2.20 A; A/B/C/D/E/F/G/H=2-136.
DR PDB; 4K49; X-ray; 1.89 A; A/B/C/D=1-136.
DR PDB; 4K4A; X-ray; 1.89 A; A/B/C/D=1-136.
DR PDB; 4K4B; X-ray; 1.90 A; A/B/C/D/E/F/G/H=1-136.
DR PDBsum; 1SBK; -.
DR PDBsum; 1VH5; -.
DR PDBsum; 1VI8; -.
DR PDBsum; 4K49; -.
DR PDBsum; 4K4A; -.
DR PDBsum; 4K4B; -.
DR AlphaFoldDB; P77781; -.
DR SMR; P77781; -.
DR BioGRID; 4259131; 25.
DR DIP; DIP-11750N; -.
DR IntAct; P77781; 3.
DR STRING; 511145.b1686; -.
DR jPOST; P77781; -.
DR PaxDb; P77781; -.
DR PRIDE; P77781; -.
DR EnsemblBacteria; AAC74756; AAC74756; b1686.
DR EnsemblBacteria; BAA15452; BAA15452; BAA15452.
DR GeneID; 946190; -.
DR KEGG; ecj:JW1676; -.
DR KEGG; eco:b1686; -.
DR PATRIC; fig|511145.12.peg.1757; -.
DR EchoBASE; EB3725; -.
DR eggNOG; COG2050; Bacteria.
DR HOGENOM; CLU_089876_13_1_6; -.
DR InParanoid; P77781; -.
DR OMA; TTQVWQI; -.
DR PhylomeDB; P77781; -.
DR BioCyc; EcoCyc:G6912-MON; -.
DR BioCyc; MetaCyc:G6912-MON; -.
DR BRENDA; 3.1.2.2; 2026.
DR BRENDA; 3.1.2.28; 2026.
DR UniPathway; UPA00079; -.
DR UniPathway; UPA01057; UER01033.
DR EvolutionaryTrace; P77781; -.
DR PRO; PR:P77781; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0061522; F:1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity; IDA:EcoCyc.
DR GO; GO:0016289; F:CoA hydrolase activity; IDA:EcoCyc.
DR GO; GO:0016787; F:hydrolase activity; IDA:EcoCyc.
DR GO; GO:0009234; P:menaquinone biosynthetic process; IMP:CACAO.
DR HAMAP; MF_01936; MenI; 1.
DR InterPro; IPR029069; HotDog_dom_sf.
DR InterPro; IPR030863; MenI.
DR InterPro; IPR003736; PAAI_dom.
DR InterPro; IPR006683; Thioestr_dom.
DR Pfam; PF03061; 4HBT; 1.
DR SUPFAM; SSF54637; SSF54637; 1.
DR TIGRFAMs; TIGR00369; unchar_dom_1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Menaquinone biosynthesis; Reference proteome.
FT CHAIN 1..136
FT /note="1,4-dihydroxy-2-naphthoyl-CoA hydrolase"
FT /id="PRO_0000156678"
FT ACT_SITE 63
FT /note="Nucleophile or proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01936,
FT ECO:0000303|PubMed:25010423"
FT BINDING 82
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01936,
FT ECO:0000269|PubMed:25010423"
FT BINDING 89..92
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01936,
FT ECO:0000269|PubMed:25010423"
FT BINDING 106..111
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01936,
FT ECO:0000269|PubMed:25010423"
FT MUTAGEN 48
FT /note="Q->A: Almost loss of activity with benzoyl-CoA as
FT substrate."
FT /evidence="ECO:0000269|PubMed:25010423"
FT MUTAGEN 48
FT /note="Q->N: 51-fold decrease in catalytic efficiency
FT toward benzoyl-CoA."
FT /evidence="ECO:0000269|PubMed:25010423"
FT MUTAGEN 54
FT /note="H->A: 514-fold decrease in catalytic efficiency
FT toward benzoyl-CoA."
FT /evidence="ECO:0000269|PubMed:25010423"
FT MUTAGEN 54
FT /note="H->F: Almost loss of activity with benzoyl-CoA as
FT substrate."
FT /evidence="ECO:0000269|PubMed:25010423"
FT MUTAGEN 63
FT /note="E->A,Q: Loss of activity with benzoyl-CoA as
FT substrate."
FT /evidence="ECO:0000269|PubMed:25010423"
FT MUTAGEN 63
FT /note="E->D: Almost loss of activity with benzoyl-CoA as
FT substrate."
FT /evidence="ECO:0000269|PubMed:25010423"
FT MUTAGEN 64
FT /note="S->A: Almost no change in catalytic efficiency
FT toward benzoyl-CoA."
FT /evidence="ECO:0000269|PubMed:25010423"
FT MUTAGEN 67
FT /note="S->A: Almost no change in catalytic efficiency
FT toward benzoyl-CoA."
FT /evidence="ECO:0000269|PubMed:25010423"
FT MUTAGEN 68
FT /note="V->M: 10-fold decrease in catalytic efficiency
FT toward lauroyl-CoA. Does not affect catalytic efficiency
FT toward 1,4-dihydroxy-2-naphthoyl-CoA and benzoyl-CoA."
FT /evidence="ECO:0000269|PubMed:24992697"
FT MUTAGEN 71
FT /note="Y->A: Does not affect activity."
FT /evidence="ECO:0000269|PubMed:24992697"
FT MUTAGEN 89
FT /note="H->A: 156-fold decrease in catalytic efficiency
FT toward benzoyl-CoA."
FT /evidence="ECO:0000269|PubMed:25010423"
FT MUTAGEN 91
FT /note="R->A: 9-fold decrease in catalytic efficiency toward
FT benzoyl-CoA."
FT /evidence="ECO:0000269|PubMed:25010423"
FT MUTAGEN 106
FT /note="H->A: Almost no change in catalytic efficiency
FT toward benzoyl-CoA."
FT /evidence="ECO:0000269|PubMed:25010423"
FT MUTAGEN 109
FT /note="S->A: Almost no change in catalytic efficiency
FT toward benzoyl-CoA."
FT /evidence="ECO:0000269|PubMed:25010423"
FT HELIX 9..14
FT /evidence="ECO:0007829|PDB:1VH5"
FT TURN 15..18
FT /evidence="ECO:0007829|PDB:1VH5"
FT HELIX 20..23
FT /evidence="ECO:0007829|PDB:1VH5"
FT STRAND 27..31
FT /evidence="ECO:0007829|PDB:1VH5"
FT STRAND 36..41
FT /evidence="ECO:0007829|PDB:1VH5"
FT TURN 44..46
FT /evidence="ECO:0007829|PDB:1VH5"
FT STRAND 51..53
FT /evidence="ECO:0007829|PDB:1VH5"
FT HELIX 55..72
FT /evidence="ECO:0007829|PDB:1VH5"
FT STRAND 79..89
FT /evidence="ECO:0007829|PDB:1VH5"
FT STRAND 95..107
FT /evidence="ECO:0007829|PDB:1VH5"
FT STRAND 109..119
FT /evidence="ECO:0007829|PDB:1VH5"
FT STRAND 125..136
FT /evidence="ECO:0007829|PDB:1VH5"
SQ SEQUENCE 136 AA; 14945 MW; E7B995390E7244C3 CRC64;
MIWKRKITLE ALNAMGEGNM VGFLDIRFEH IGDDTLEATM PVDSRTKQPF GLLHGGASVV
LAESIGSVAG YLCTEGEQKV VGLEINANHV RSAREGRVRG VCKPLHLGSR HQVWQIEIFD
EKGRLCCSSR LTTAIL
