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1,4-dihydroxy-2-naphthoyl-CoA hydrolase (DHNA-CoA hydrolase) (EC 3.1.2.28) (DHNA-CoA thioesterase)

 MENI_ECOLI              Reviewed;         136 AA.
P77781;
27-APR-2001, integrated into UniProtKB/Swiss-Prot.
01-FEB-1997, sequence version 1.
28-MAR-2018, entry version 137.
RecName: Full=1,4-dihydroxy-2-naphthoyl-CoA hydrolase {ECO:0000255|HAMAP-Rule:MF_01936, ECO:0000305};
Short=DHNA-CoA hydrolase {ECO:0000255|HAMAP-Rule:MF_01936, ECO:0000305};
EC=3.1.2.28 {ECO:0000255|HAMAP-Rule:MF_01936, ECO:0000269|PubMed:23564174, ECO:0000269|PubMed:24992697};
AltName: Full=DHNA-CoA thioesterase {ECO:0000255|HAMAP-Rule:MF_01936, ECO:0000303|PubMed:23564174};
Name=menI {ECO:0000255|HAMAP-Rule:MF_01936,
ECO:0000303|PubMed:23564174}; Synonyms=ydiI;
OrderedLocusNames=b1686, JW1676;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=9205837; DOI=10.1093/dnares/4.2.91;
Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K.,
Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N.,
Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H.,
Oshima T., Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S.,
Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C.,
Yamagata S., Horiuchi T.;
"Construction of a contiguous 874-kb sequence of the Escherichia coli-
K12 genome corresponding to 50.0-68.8 min on the linkage map and
analysis of its sequence features.";
DNA Res. 4:91-113(1997).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
Mau B., Shao Y.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[4]
FUNCTION AS AN ESTERASE.
PubMed=15808744; DOI=10.1016/j.fmrre.2004.12.006;
Kuznetsova E., Proudfoot M., Sanders S.A., Reinking J., Savchenko A.,
Arrowsmith C.H., Edwards A.M., Yakunin A.F.;
"Enzyme genomics: application of general enzymatic screens to discover
new enzymes.";
FEMS Microbiol. Rev. 29:263-279(2005).
[5]
FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, PATHWAY,
AND DISRUPTION PHENOTYPE.
STRAIN=K12 / BW25113;
PubMed=23564174; DOI=10.1128/JB.00141-13;
Chen M., Ma X., Chen X., Jiang M., Song H., Guo Z.;
"Identification of a hotdog fold thioesterase involved in the
biosynthesis of menaquinone in Escherichia coli.";
J. Bacteriol. 195:2768-2775(2013).
[6]
FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, PATHWAY,
AND MUTAGENESIS OF VAL-68 AND TYR-71.
PubMed=24992697; DOI=10.1021/bi500333m;
Latham J.A., Chen D., Allen K.N., Dunaway-Mariano D.;
"Divergence of substrate specificity and function in the Escherichia
coli hotdog-fold thioesterase paralogs YdiI and YbdB.";
Biochemistry 53:4775-4787(2014).
[7]
X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Kuzin A.P., Edstrom W., Vorobiev S.M., Lee I., Forouhar F., Ma L.,
Chiang Y., Rong X., Acton T.B., Montelione G.T., Hunt J.F., Tong L.;
"X-ray structure of YDII_ECOLI.";
Submitted (FEB-2004) to the PDB data bank.
[8]
X-RAY CRYSTALLOGRAPHY (1.34 ANGSTROMS) OF 2-136.
PubMed=16021622; DOI=10.1002/prot.20541;
Badger J., Sauder J.M., Adams J.M., Antonysamy S., Bain K.,
Bergseid M.G., Buchanan S.G., Buchanan M.D., Batiyenko Y.,
Christopher J.A., Emtage S., Eroshkina A., Feil I., Furlong E.B.,
Gajiwala K.S., Gao X., He D., Hendle J., Huber A., Hoda K.,
Kearins P., Kissinger C., Laubert B., Lewis H.A., Lin J., Loomis K.,
Lorimer D., Louie G., Maletic M., Marsh C.D., Miller I., Molinari J.,
Muller-Dieckmann H.J., Newman J.M., Noland B.W., Pagarigan B.,
Park F., Peat T.S., Post K.W., Radojicic S., Ramos A., Romero R.,
Rutter M.E., Sanderson W.E., Schwinn K.D., Tresser J., Winhoven J.,
Wright T.A., Wu L., Xu J., Harris T.J.R.;
"Structural analysis of a set of proteins resulting from a bacterial
genomics project.";
Proteins 60:787-796(2005).
[9]
X-RAY CRYSTALLOGRAPHY (1.89 ANGSTROMS) IN COMPLEXES WITH SUBSTRATE
ANALOGS, SUBUNIT, MUTAGENESIS OF GLN-48; HIS-54; GLU-63; SER-64;
SER-67; HIS-89; ARG-91; HIS-106 AND SER-109, AND ACTIVE SITE.
PubMed=25010423; DOI=10.1021/bi500334v;
Wu R., Latham J.A., Chen D., Farelli J., Zhao H., Matthews K.,
Allen K.N., Dunaway-Mariano D.;
"Structure and catalysis in the Escherichia coli hotdog-fold
thioesterase paralogs YdiI and YbdB.";
Biochemistry 53:4788-4805(2014).
-!- FUNCTION: Catalyzes the hydrolysis of 1,4-dihydroxy-2-naphthoyl-
CoA (DHNA-CoA) to 1,4-dihydroxy-2-naphthoate (DHNA). Also shows
significant activity toward a wide range of acyl-CoA thioesters,
and minimal activity toward benzoyl-holoEntB.
{ECO:0000269|PubMed:15808744, ECO:0000269|PubMed:23564174,
ECO:0000269|PubMed:24992697}.
-!- CATALYTIC ACTIVITY: 1,4-dihydroxy-2-naphthoyl-CoA + H(2)O = 1,4-
dihydroxy-2-naphthoate + CoA. {ECO:0000255|HAMAP-Rule:MF_01936,
ECO:0000269|PubMed:23564174, ECO:0000269|PubMed:24992697}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=2.5 uM for 1,4-dihydroxy-2-naphthoyl-CoA
{ECO:0000269|PubMed:23564174};
KM=8 uM for 1,4-dihydroxy-2-naphthoyl-CoA
{ECO:0000269|PubMed:24992697};
KM=1.3 uM for oleoyl-CoA {ECO:0000269|PubMed:24992697};
KM=1.5 uM for myristoyl-CoA {ECO:0000269|PubMed:24992697};
KM=1.559 uM for acetyl-CoA {ECO:0000269|PubMed:23564174};
KM=1.9 uM for palmitoyl-CoA {ECO:0000269|PubMed:24992697};
KM=2.2 uM for lauroyl-CoA {ECO:0000269|PubMed:24992697};
KM=8.0 uM for 1-hydroxy-2-naphthoyl-CoA
{ECO:0000269|PubMed:23564174};
KM=9 uM for 4-hydroxybenzoyl-CoA {ECO:0000269|PubMed:24992697};
KM=21 uM for hexanoyl-CoA {ECO:0000269|PubMed:24992697};
KM=25 uM for benzoyl-CoA {ECO:0000269|PubMed:24992697};
KM=26.5 uM for 3,5-dihydroxybenzoyl-CoA
{ECO:0000269|PubMed:23564174};
KM=26.9 uM for 3,4-dihydroxybenzoyl-CoA
{ECO:0000269|PubMed:23564174};
KM=30 uM for coumaroyl-CoA {ECO:0000269|PubMed:24992697};
KM=54 uM for benzoyl-ACP {ECO:0000269|PubMed:24992697};
KM=69.4 uM for beta-methylcrotonyl-CoA
{ECO:0000269|PubMed:24992697};
KM=73 uM for salicylyl-CoA {ECO:0000269|PubMed:23564174};
KM=115 uM for beta-methylmalonyl-CoA
{ECO:0000269|PubMed:24992697};
KM=120 uM for propionyl-CoA {ECO:0000269|PubMed:24992697};
KM=200 uM for 2,4-dihydroxybenzoyl-EntB
{ECO:0000269|PubMed:24992697};
Note=kcat is 6.2 sec(-1) with 1,4-dihydroxy-2-naphthoyl-CoA
(PubMed:23564174). kcat is 1.6 sec(-1) with 1,4-dihydroxy-2-
naphthoyl-CoA (PubMed:24992697). kcat is 0.12 sec(-1) with
oleoyl-CoA. kcat is 0.62 sec(-1) with myristoyl-CoA. kcat is
0.0044 sec(-1) with acetyl-CoA. kcat is 0.58 sec(-1) with
palmitoyl-CoA. kcat is 0.74 sec(-1) with lauroyl-CoA. kcat is
14.8 sec(-1) with 1-hydroxy-2-naphthoyl-CoA. kcat is 5.2 sec(-1)
with 4-hydroxybenzoyl-CoA. kcat is 0.3 sec(-1) with hexanoyl-
CoA. kcat is 17.7 sec(-1) with benzoyl-CoA. kcat is 12.6 sec(-1)
with 3,5-dihydroxybenzoyl-CoA. kcat is 23.2 sec(-1) with 3,4-
dihydroxybenzoyl-CoA. kcat is 8.4 sec(-1) with coumaroyl-CoA.
kcat is 0.083 sec(-1) with benzoyl-ACP. kcat is 0.5 sec(-1) with
beta-methylcrotonyl-CoA. kcat is 93.0 sec(-1) with salicylyl-
CoA. kcat is 0.67 sec(-1) with beta-methylmalonyl-CoA. kcat is
0.21 sec(-1) with propionyl-CoA. kcat is 0.0036 sec(-1) with
2,4-dihydroxybenzoyl-EntB. {ECO:0000269|PubMed:23564174,
ECO:0000269|PubMed:24992697};
-!- PATHWAY: Quinol/quinone metabolism; 1,4-dihydroxy-2-naphthoate
biosynthesis; 1,4-dihydroxy-2-naphthoate from chorismate: step
7/7. {ECO:0000255|HAMAP-Rule:MF_01936,
ECO:0000269|PubMed:23564174, ECO:0000269|PubMed:24992697}.
-!- PATHWAY: Quinol/quinone metabolism; menaquinone biosynthesis.
{ECO:0000255|HAMAP-Rule:MF_01936, ECO:0000269|PubMed:23564174,
ECO:0000269|PubMed:24992697}.
-!- SUBUNIT: Homotetramer. Dimer of dimers. {ECO:0000255|HAMAP-
Rule:MF_01936, ECO:0000269|PubMed:25010423}.
-!- DISRUPTION PHENOTYPE: Deletion results in a significant decrease
in menaquinone production. {ECO:0000269|PubMed:23564174}.
-!- SIMILARITY: Belongs to the thioesterase PaaI family.
{ECO:0000255|HAMAP-Rule:MF_01936}.
-----------------------------------------------------------------------
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EMBL; U00096; AAC74756.1; -; Genomic_DNA.
EMBL; AP009048; BAA15452.1; -; Genomic_DNA.
PIR; F64926; F64926.
RefSeq; NP_416201.1; NC_000913.3.
RefSeq; WP_000637982.1; NZ_LN832404.1.
PDB; 1SBK; X-ray; 2.00 A; A/B/C/D=1-136.
PDB; 1VH5; X-ray; 1.34 A; A/B=2-136.
PDB; 1VI8; X-ray; 2.20 A; A/B/C/D/E/F/G/H=2-136.
PDB; 4K49; X-ray; 1.89 A; A/B/C/D=1-136.
PDB; 4K4A; X-ray; 1.89 A; A/B/C/D=1-136.
PDB; 4K4B; X-ray; 1.90 A; A/B/C/D/E/F/G/H=1-136.
PDBsum; 1SBK; -.
PDBsum; 1VH5; -.
PDBsum; 1VI8; -.
PDBsum; 4K49; -.
PDBsum; 4K4A; -.
PDBsum; 4K4B; -.
ProteinModelPortal; P77781; -.
SMR; P77781; -.
BioGrid; 4259131; 25.
DIP; DIP-11750N; -.
IntAct; P77781; 3.
STRING; 316385.ECDH10B_1821; -.
PaxDb; P77781; -.
PRIDE; P77781; -.
EnsemblBacteria; AAC74756; AAC74756; b1686.
EnsemblBacteria; BAA15452; BAA15452; BAA15452.
GeneID; 946190; -.
KEGG; ecj:JW1676; -.
KEGG; eco:b1686; -.
PATRIC; fig|511145.12.peg.1757; -.
EchoBASE; EB3725; -.
EcoGene; EG13968; menI.
eggNOG; ENOG4105KA0; Bacteria.
eggNOG; COG2050; LUCA.
HOGENOM; HOG000066991; -.
InParanoid; P77781; -.
KO; K19222; -.
OMA; KNTLMET; -.
PhylomeDB; P77781; -.
BioCyc; EcoCyc:G6912-MONOMER; -.
BioCyc; MetaCyc:G6912-MONOMER; -.
BRENDA; 3.1.2.2; 2026.
UniPathway; UPA00079; -.
UniPathway; UPA01057; UER01033.
EvolutionaryTrace; P77781; -.
PRO; PR:P77781; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0061522; F:1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity; IDA:EcoCyc.
GO; GO:0016289; F:CoA hydrolase activity; IDA:EcoCyc.
GO; GO:0016787; F:hydrolase activity; IDA:EcoCyc.
GO; GO:0009234; P:menaquinone biosynthetic process; IMP:CACAO.
HAMAP; MF_01936; MenI; 1.
InterPro; IPR029069; HotDog_dom_sf.
InterPro; IPR030863; MenI.
InterPro; IPR003736; PAAI_dom.
InterPro; IPR006683; Thioestr_dom.
Pfam; PF03061; 4HBT; 1.
SUPFAM; SSF54637; SSF54637; 1.
TIGRFAMs; TIGR00369; unchar_dom_1; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Hydrolase; Menaquinone biosynthesis;
Reference proteome.
CHAIN 1 136 1,4-dihydroxy-2-naphthoyl-CoA hydrolase.
/FTId=PRO_0000156678.
REGION 89 92 Substrate binding. {ECO:0000255|HAMAP-
Rule:MF_01936,
ECO:0000269|PubMed:25010423}.
REGION 106 111 Substrate binding. {ECO:0000255|HAMAP-
Rule:MF_01936,
ECO:0000269|PubMed:25010423}.
ACT_SITE 63 63 Nucleophile or proton acceptor.
{ECO:0000255|HAMAP-Rule:MF_01936,
ECO:0000303|PubMed:25010423}.
BINDING 82 82 Substrate; via carbonyl oxygen.
{ECO:0000255|HAMAP-Rule:MF_01936,
ECO:0000269|PubMed:25010423}.
MUTAGEN 48 48 Q->A: Almost loss of activity with
benzoyl-CoA as substrate.
{ECO:0000269|PubMed:25010423}.
MUTAGEN 48 48 Q->N: 51-fold decrease in catalytic
efficiency toward benzoyl-CoA.
{ECO:0000269|PubMed:25010423}.
MUTAGEN 54 54 H->A: 514-fold decrease in catalytic
efficiency toward benzoyl-CoA.
{ECO:0000269|PubMed:25010423}.
MUTAGEN 54 54 H->F: Almost loss of activity with
benzoyl-CoA as substrate.
{ECO:0000269|PubMed:25010423}.
MUTAGEN 63 63 E->A,Q: Loss of activity with benzoyl-CoA
as substrate.
{ECO:0000269|PubMed:25010423}.
MUTAGEN 63 63 E->D: Almost loss of activity with
benzoyl-CoA as substrate.
{ECO:0000269|PubMed:25010423}.
MUTAGEN 64 64 S->A: Almost no change in catalytic
efficiency toward benzoyl-CoA.
{ECO:0000269|PubMed:25010423}.
MUTAGEN 67 67 S->A: Almost no change in catalytic
efficiency toward benzoyl-CoA.
{ECO:0000269|PubMed:25010423}.
MUTAGEN 68 68 V->M: 10-fold decrease in catalytic
efficiency toward lauroyl-CoA. Does not
affect catalytic efficiency toward 1,4-
dihydroxy-2-naphthoyl-CoA and benzoyl-
CoA. {ECO:0000269|PubMed:24992697}.
MUTAGEN 71 71 Y->A: Does not affect activity.
{ECO:0000269|PubMed:24992697}.
MUTAGEN 89 89 H->A: 156-fold decrease in catalytic
efficiency toward benzoyl-CoA.
{ECO:0000269|PubMed:25010423}.
MUTAGEN 91 91 R->A: 9-fold decrease in catalytic
efficiency toward benzoyl-CoA.
{ECO:0000269|PubMed:25010423}.
MUTAGEN 106 106 H->A: Almost no change in catalytic
efficiency toward benzoyl-CoA.
{ECO:0000269|PubMed:25010423}.
MUTAGEN 109 109 S->A: Almost no change in catalytic
efficiency toward benzoyl-CoA.
{ECO:0000269|PubMed:25010423}.
HELIX 9 14 {ECO:0000244|PDB:1VH5}.
TURN 15 18 {ECO:0000244|PDB:1VH5}.
HELIX 20 23 {ECO:0000244|PDB:1VH5}.
STRAND 27 31 {ECO:0000244|PDB:1VH5}.
STRAND 36 41 {ECO:0000244|PDB:1VH5}.
TURN 44 46 {ECO:0000244|PDB:1VH5}.
STRAND 51 53 {ECO:0000244|PDB:1VH5}.
HELIX 55 72 {ECO:0000244|PDB:1VH5}.
STRAND 79 89 {ECO:0000244|PDB:1VH5}.
STRAND 95 107 {ECO:0000244|PDB:1VH5}.
STRAND 109 119 {ECO:0000244|PDB:1VH5}.
STRAND 125 136 {ECO:0000244|PDB:1VH5}.
SEQUENCE 136 AA; 14945 MW; E7B995390E7244C3 CRC64;
MIWKRKITLE ALNAMGEGNM VGFLDIRFEH IGDDTLEATM PVDSRTKQPF GLLHGGASVV
LAESIGSVAG YLCTEGEQKV VGLEINANHV RSAREGRVRG VCKPLHLGSR HQVWQIEIFD
EKGRLCCSSR LTTAIL


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