MEND_ECOLI
ID MEND_ECOLI Reviewed; 556 AA.
AC P17109; P76478; P78180; P78181;
DT 01-AUG-1990, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 4.
DT 03-AUG-2022, entry version 176.
DE RecName: Full=2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase {ECO:0000255|HAMAP-Rule:MF_01659};
DE Short=SEPHCHC synthase {ECO:0000255|HAMAP-Rule:MF_01659};
DE EC=2.2.1.9 {ECO:0000255|HAMAP-Rule:MF_01659};
DE AltName: Full=Menaquinone biosynthesis protein MenD {ECO:0000255|HAMAP-Rule:MF_01659};
GN Name=menD {ECO:0000255|HAMAP-Rule:MF_01659};
GN OrderedLocusNames=b2264, JW5374;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=8764478; DOI=10.1016/0378-1097(96)00173-5;
RA Daruwala R., Kwon O., Meganathan R., Hudspeth M.E.S.;
RT "A new isochorismate synthase specifically involved in menaquinone (vitamin
RT K2) biosynthesis encoded by the menF gene.";
RL FEMS Microbiol. Lett. 140:159-163(1996).
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 1-507.
RX PubMed=2666397; DOI=10.1128/jb.171.8.4349-4354.1989;
RA Popp J.L.;
RT "Sequence and overexpression of the menD gene from Escherichia coli.";
RL J. Bacteriol. 171:4349-4354(1989).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 536-556.
RC STRAIN=K12;
RA Sharma V., Hudspeth M.E., Meganathan R.;
RL Submitted (JUL-1994) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP INDUCTION, AND PRELIMINARY FUNCTION.
RC STRAIN=K12;
RX PubMed=1459959; DOI=10.1128/jb.174.24.8111-8118.1992;
RA Palaniappan C., Sharma V., Hudspeth M.E., Meganathan R.;
RT "Menaquinone (vitamin K2) biosynthesis: evidence that the Escherichia coli
RT menD gene encodes both 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic
RT acid synthase and alpha-ketoglutarate decarboxylase activities.";
RL J. Bacteriol. 174:8111-8118(1992).
RN [8]
RP SUBUNIT, COFACTOR, MUTAGENESIS OF GLU-55, AND BIOPHYSICOCHEMICAL
RP PROPERTIES.
RX PubMed=14621995; DOI=10.1021/bi035224j;
RA Bhasin M., Billinsky J.L., Palmer D.R.J.;
RT "Steady-state kinetics and molecular evolution of Escherichia coli MenD
RT [(1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase],
RT an anomalous thiamin diphosphate-dependent decarboxylase-carboligase.";
RL Biochemistry 42:13496-13504(2003).
RN [9]
RP CRYSTALLIZATION, COFACTOR, AND SUBUNIT.
RX PubMed=16511076; DOI=10.1107/s1744309105010997;
RA Sieminska E.A.L., Macova A., Palmer D.R.J., Sanders D.A.R.;
RT "Crystallization and preliminary X-ray analysis of (1R,6R)-2-succinyl-6-
RT hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) synthase (MenD) from
RT Escherichia coli.";
RL Acta Crystallogr. F 61:489-492(2005).
RN [10]
RP FUNCTION AS A SEPHCHC SYNTHASE, CATALYTIC ACTIVITY, COFACTOR, AND
RP BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=17760421; DOI=10.1021/bi700810x;
RA Jiang M., Cao Y., Guo Z.-F., Chen M., Chen X., Guo Z.;
RT "Menaquinone biosynthesis in Escherichia coli: identification of 2-
RT succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate as a novel
RT intermediate and re-evaluation of MenD activity.";
RL Biochemistry 46:10979-10989(2007).
CC -!- FUNCTION: Catalyzes the thiamine diphosphate-dependent decarboxylation
CC of 2-oxoglutarate and the subsequent addition of the resulting succinic
CC semialdehyde-thiamine pyrophosphate anion to isochorismate to yield 2-
CC succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC).
CC {ECO:0000255|HAMAP-Rule:MF_01659, ECO:0000269|PubMed:17760421}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-oxoglutarate + H(+) + isochorismate = 5-enolpyruvoyl-6-
CC hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO2;
CC Xref=Rhea:RHEA:25593, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:16810, ChEBI:CHEBI:29780, ChEBI:CHEBI:58818; EC=2.2.1.9;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01659,
CC ECO:0000269|PubMed:17760421};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01659};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01659};
CC -!- COFACTOR:
CC Name=thiamine diphosphate; Xref=ChEBI:CHEBI:58937;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01659};
CC Note=Binds 1 thiamine pyrophosphate per subunit. {ECO:0000255|HAMAP-
CC Rule:MF_01659};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=53 nM for isochorismate (at 22.5 degrees Celsius and pH 7.8)
CC {ECO:0000269|PubMed:14621995, ECO:0000269|PubMed:17760421};
CC KM=1.5 uM for 2-oxoglutarate (at 22.5 degrees Celsius and pH 7.8)
CC {ECO:0000269|PubMed:14621995, ECO:0000269|PubMed:17760421};
CC KM=2.4 uM for thiamine diphosphate (at 22.5 degrees Celsius and pH
CC 7.8) {ECO:0000269|PubMed:14621995, ECO:0000269|PubMed:17760421};
CC KM=80 uM for magnesium ions (at 22.5 degrees Celsius and pH 7.8)
CC {ECO:0000269|PubMed:14621995, ECO:0000269|PubMed:17760421};
CC pH dependence:
CC Optimum pH is 7-8. {ECO:0000269|PubMed:14621995,
CC ECO:0000269|PubMed:17760421};
CC -!- PATHWAY: Quinol/quinone metabolism; 1,4-dihydroxy-2-naphthoate
CC biosynthesis; 1,4-dihydroxy-2-naphthoate from chorismate: step 2/7.
CC {ECO:0000255|HAMAP-Rule:MF_01659}.
CC -!- PATHWAY: Quinol/quinone metabolism; menaquinone biosynthesis.
CC {ECO:0000255|HAMAP-Rule:MF_01659}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_01659,
CC ECO:0000269|PubMed:14621995, ECO:0000269|PubMed:16511076}.
CC -!- INDUCTION: By isopropyl-beta-D-thiogalactoside (IPTG).
CC {ECO:0000269|PubMed:1459959}.
CC -!- SIMILARITY: Belongs to the TPP enzyme family. MenD subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_01659, ECO:0000305}.
CC -!- CAUTION: Was originally thought (PubMed:1459959, PubMed:14621995 and
CC PubMed:16511076) to be a 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-
CC carboxylate (SHCHC) synthase but further protein analysis clearly
CC suggests that it is a 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-
CC 1-carboxylate (SEPHCHC) synthase. {ECO:0000305|PubMed:17760421}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA24153.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; U54790; AAC44304.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75324.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA16089.2; -; Genomic_DNA.
DR EMBL; M21787; AAA24153.1; ALT_FRAME; Genomic_DNA.
DR EMBL; L04464; AAB59060.1; -; Genomic_DNA.
DR EMBL; L35030; AAA24150.1; -; Genomic_DNA.
DR PIR; F64997; F64997.
DR RefSeq; NP_416767.1; NC_000913.3.
DR RefSeq; WP_001295284.1; NZ_STEB01000008.1.
DR PDB; 2JLA; X-ray; 2.81 A; A/B/C/D=1-556.
DR PDB; 2JLC; X-ray; 2.50 A; A/B=1-556.
DR PDB; 3FLM; X-ray; 2.70 A; A/B=1-556.
DR PDB; 3HWW; X-ray; 1.95 A; A/D=1-556.
DR PDB; 3HWX; X-ray; 2.60 A; 1/A/B/I/J/R/S/Z=1-556.
DR PDB; 5EJ4; X-ray; 1.77 A; A/B/C/D/E/F/G/H=1-556.
DR PDB; 5EJ5; X-ray; 2.30 A; A/B/C/D/E/F/G/H=1-556.
DR PDB; 5EJ6; X-ray; 2.24 A; A/B/C/D/E/F/G/H=1-556.
DR PDB; 5EJ7; X-ray; 1.56 A; A/B/C/D/E/F/G/H=1-556.
DR PDB; 5EJ8; X-ray; 1.34 A; A/B/C/D/E/F/G/H=1-556.
DR PDB; 5EJ9; X-ray; 1.72 A; A/B/C/D/E/F/G/H=1-556.
DR PDB; 5EJA; X-ray; 1.60 A; A/B/C/D/E/F/G/H=1-556.
DR PDB; 5EJM; X-ray; 1.72 A; A/B/C/D/E/F/G/H=1-556.
DR PDB; 5Z2P; X-ray; 2.30 A; A/B/C/D/E/F/G/H=1-556.
DR PDB; 5Z2R; X-ray; 2.30 A; A/B/C/D/E/F/G/H=1-556.
DR PDB; 5Z2U; X-ray; 2.35 A; A/B/C/D/E/F/G/H=1-556.
DR PDBsum; 2JLA; -.
DR PDBsum; 2JLC; -.
DR PDBsum; 3FLM; -.
DR PDBsum; 3HWW; -.
DR PDBsum; 3HWX; -.
DR PDBsum; 5EJ4; -.
DR PDBsum; 5EJ5; -.
DR PDBsum; 5EJ6; -.
DR PDBsum; 5EJ7; -.
DR PDBsum; 5EJ8; -.
DR PDBsum; 5EJ9; -.
DR PDBsum; 5EJA; -.
DR PDBsum; 5EJM; -.
DR PDBsum; 5Z2P; -.
DR PDBsum; 5Z2R; -.
DR PDBsum; 5Z2U; -.
DR AlphaFoldDB; P17109; -.
DR SMR; P17109; -.
DR BioGRID; 4260506; 9.
DR BioGRID; 851061; 2.
DR DIP; DIP-10185N; -.
DR IntAct; P17109; 1.
DR STRING; 511145.b2264; -.
DR jPOST; P17109; -.
DR PaxDb; P17109; -.
DR PRIDE; P17109; -.
DR EnsemblBacteria; AAC75324; AAC75324; b2264.
DR EnsemblBacteria; BAA16089; BAA16089; BAA16089.
DR GeneID; 946720; -.
DR KEGG; ecj:JW5374; -.
DR KEGG; eco:b2264; -.
DR PATRIC; fig|511145.12.peg.2357; -.
DR EchoBASE; EB0574; -.
DR eggNOG; COG1165; Bacteria.
DR HOGENOM; CLU_006051_3_0_6; -.
DR InParanoid; P17109; -.
DR OMA; FCNRGTS; -.
DR PhylomeDB; P17109; -.
DR BioCyc; EcoCyc:MEND-MON; -.
DR BioCyc; MetaCyc:MEND-MON; -.
DR BRENDA; 2.2.1.9; 2026.
DR SABIO-RK; P17109; -.
DR UniPathway; UPA00079; -.
DR UniPathway; UPA01057; UER00164.
DR EvolutionaryTrace; P17109; -.
DR PRO; PR:P17109; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0070204; F:2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity; IDA:EcoCyc.
DR GO; GO:0000287; F:magnesium ion binding; IDA:EcoCyc.
DR GO; GO:0030145; F:manganese ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0030976; F:thiamine pyrophosphate binding; IDA:EcoCyc.
DR GO; GO:0009234; P:menaquinone biosynthetic process; IMP:EcoCyc.
DR DisProt; DP02750; -.
DR HAMAP; MF_01659; MenD; 1.
DR InterPro; IPR004433; MenaQ_synth_MenD.
DR InterPro; IPR032264; MenD_middle.
DR InterPro; IPR029061; THDP-binding.
DR InterPro; IPR012001; Thiamin_PyroP_enz_TPP-bd_dom.
DR InterPro; IPR011766; TPP_enzyme-bd_C.
DR PANTHER; PTHR42916; PTHR42916; 1.
DR Pfam; PF02775; TPP_enzyme_C; 1.
DR Pfam; PF16582; TPP_enzyme_M_2; 1.
DR Pfam; PF02776; TPP_enzyme_N; 1.
DR PIRSF; PIRSF004983; MenD; 1.
DR SUPFAM; SSF52518; SSF52518; 2.
DR TIGRFAMs; TIGR00173; menD; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Magnesium; Manganese; Menaquinone biosynthesis;
KW Metal-binding; Reference proteome; Thiamine pyrophosphate; Transferase.
FT CHAIN 1..556
FT /note="2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-
FT carboxylate synthase"
FT /id="PRO_0000090829"
FT MUTAGEN 55
FT /note="E->Q: Loss of activity."
FT /evidence="ECO:0000269|PubMed:14621995"
FT CONFLICT 42
FT /note="Missing (in Ref. 5; AAA24153)"
FT /evidence="ECO:0000305"
FT CONFLICT 163..183
FT /note="GVHINCPFAEPLYGEMDDTGL -> ESISTARLLNRCMAKWTIPGF (in
FT Ref. 5; AAA24153)"
FT /evidence="ECO:0000305"
FT CONFLICT 398
FT /note="Missing (in Ref. 5; AAA24153)"
FT /evidence="ECO:0000305"
FT CONFLICT 543..556
FT /note="AQTLQQLLAQVSHL -> RKRSSNFWRR (in Ref. 6; AAB59060)"
FT /evidence="ECO:0000305"
FT HELIX 3..19
FT /evidence="ECO:0007829|PDB:5EJ8"
FT TURN 20..22
FT /evidence="ECO:0007829|PDB:5EJ8"
FT STRAND 25..28
FT /evidence="ECO:0007829|PDB:5EJ8"
FT TURN 32..34
FT /evidence="ECO:0007829|PDB:3FLM"
FT HELIX 35..43
FT /evidence="ECO:0007829|PDB:5EJ8"
FT STRAND 48..51
FT /evidence="ECO:0007829|PDB:5EJ8"
FT HELIX 55..69
FT /evidence="ECO:0007829|PDB:5EJ8"
FT STRAND 73..77
FT /evidence="ECO:0007829|PDB:5EJ8"
FT HELIX 81..84
FT /evidence="ECO:0007829|PDB:5EJ8"
FT HELIX 87..96
FT /evidence="ECO:0007829|PDB:5EJ8"
FT STRAND 100..106
FT /evidence="ECO:0007829|PDB:5EJ8"
FT HELIX 109..111
FT /evidence="ECO:0007829|PDB:5EJ8"
FT STRAND 112..114
FT /evidence="ECO:0007829|PDB:5EJ8"
FT TURN 123..128
FT /evidence="ECO:0007829|PDB:5EJ8"
FT STRAND 130..135
FT /evidence="ECO:0007829|PDB:5EJ8"
FT HELIX 145..157
FT /evidence="ECO:0007829|PDB:5EJ8"
FT STRAND 164..169
FT /evidence="ECO:0007829|PDB:5EJ8"
FT HELIX 183..187
FT /evidence="ECO:0007829|PDB:5EJ8"
FT HELIX 188..194
FT /evidence="ECO:0007829|PDB:5EJ8"
FT STRAND 199..201
FT /evidence="ECO:0007829|PDB:5EJ8"
FT STRAND 205..207
FT /evidence="ECO:0007829|PDB:5EJ8"
FT HELIX 214..217
FT /evidence="ECO:0007829|PDB:5EJ8"
FT STRAND 222..226
FT /evidence="ECO:0007829|PDB:5EJ8"
FT HELIX 231..244
FT /evidence="ECO:0007829|PDB:5EJ8"
FT STRAND 248..250
FT /evidence="ECO:0007829|PDB:5EJ8"
FT TURN 252..254
FT /evidence="ECO:0007829|PDB:5EJ8"
FT HELIX 263..266
FT /evidence="ECO:0007829|PDB:5EJ8"
FT HELIX 270..276
FT /evidence="ECO:0007829|PDB:5EJ8"
FT STRAND 280..287
FT /evidence="ECO:0007829|PDB:5EJ8"
FT HELIX 292..300
FT /evidence="ECO:0007829|PDB:5EJ8"
FT STRAND 304..312
FT /evidence="ECO:0007829|PDB:5EJ8"
FT STRAND 322..328
FT /evidence="ECO:0007829|PDB:5EJ8"
FT HELIX 330..336
FT /evidence="ECO:0007829|PDB:5EJ8"
FT HELIX 349..361
FT /evidence="ECO:0007829|PDB:5EJ8"
FT TURN 362..365
FT /evidence="ECO:0007829|PDB:2JLC"
FT STRAND 366..368
FT /evidence="ECO:0007829|PDB:5EJ9"
FT HELIX 369..374
FT /evidence="ECO:0007829|PDB:5EJ8"
FT HELIX 376..379
FT /evidence="ECO:0007829|PDB:5EJ8"
FT STRAND 385..388
FT /evidence="ECO:0007829|PDB:5EJ8"
FT HELIX 392..400
FT /evidence="ECO:0007829|PDB:5EJ8"
FT STRAND 409..411
FT /evidence="ECO:0007829|PDB:2JLC"
FT STRAND 418..420
FT /evidence="ECO:0007829|PDB:5EJ8"
FT HELIX 421..432
FT /evidence="ECO:0007829|PDB:5EJ8"
FT STRAND 436..441
FT /evidence="ECO:0007829|PDB:5EJ8"
FT HELIX 442..447
FT /evidence="ECO:0007829|PDB:5EJ8"
FT HELIX 449..456
FT /evidence="ECO:0007829|PDB:5EJ8"
FT STRAND 462..468
FT /evidence="ECO:0007829|PDB:5EJ8"
FT HELIX 474..477
FT /evidence="ECO:0007829|PDB:5EJ8"
FT HELIX 482..488
FT /evidence="ECO:0007829|PDB:5EJ8"
FT HELIX 498..503
FT /evidence="ECO:0007829|PDB:5EJ8"
FT STRAND 507..509
FT /evidence="ECO:0007829|PDB:5EJ8"
FT HELIX 514..524
FT /evidence="ECO:0007829|PDB:5EJ8"
FT STRAND 527..536
FT /evidence="ECO:0007829|PDB:5EJ8"
FT HELIX 541..554
FT /evidence="ECO:0007829|PDB:5EJ8"
SQ SEQUENCE 556 AA; 61367 MW; 278201D02243E76D CRC64;
MSVSAFNRRW AAVILEALTR HGVRHICIAP GSRSTPLTLA AAENSAFIHH THFDERGLGH
LALGLAKVSK QPVAVIVTSG TAVANLYPAL IEAGLTGEKL ILLTADRPPE LIDCGANQAI
RQPGMFASHP THSISLPRPT QDIPARWLVS TIDHALGTLH AGGVHINCPF AEPLYGEMDD
TGLSWQQRLG DWWQDDKPWL REAPRLESEK QRDWFFWRQK RGVVVAGRMS AEEGKKVALW
AQTLGWPLIG DVLSQTGQPL PCADLWLGNA KATSELQQAQ IVVQLGSSLT GKRLLQWQAS
CEPEEYWIVD DIEGRLDPAH HRGRRLIANI ADWLELHPAE KRQPWCVEIP RLAEQAMQAV
IARRDAFGEA QLAHRICDYL PEQGQLFVGN SLVVRLIDAL SQLPAGYPVY SNRGASGIDG
LLSTAAGVQR ASGKPTLAIV GDLSALYDLN ALALLRQVSA PLVLIVVNNN GGQIFSLLPT
PQSERERFYL MPQNVHFEHA AAMFELKYHR PQNWQELETA FADAWRTPTT TVIEMVVNDT
DGAQTLQQLL AQVSHL
