MEND_BACSU
ID MEND_BACSU Reviewed; 580 AA.
AC P23970; O34492; P23969;
DT 01-MAR-1992, integrated into UniProtKB/Swiss-Prot.
DT 15-JUL-1999, sequence version 3.
DT 03-AUG-2022, entry version 149.
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}; OrderedLocusNames=BSU30820;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP PRELIMINARY NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168 / RB1;
RX PubMed=1629163; DOI=10.1128/jb.174.15.5063-5071.1992;
RA Driscoll J.R., Taber H.W.;
RT "Sequence organization and regulation of the Bacillus subtilis menBE
RT operon.";
RL J. Bacteriol. 174:5063-5071(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168 / RB1;
RX PubMed=8566759; DOI=10.1016/0378-1119(95)00662-1;
RA Rowland B., Hill K., Miller P., Driscoll J.R., Taber H.W.;
RT "Structural organization of a Bacillus subtilis operon encoding menaquinone
RT biosynthetic enzymes.";
RL Gene 167:105-109(1995).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9387221; DOI=10.1099/00221287-143-11-3431;
RA Lapidus A., Galleron N., Sorokin A., Ehrlich S.D.;
RT "Sequencing and functional annotation of the Bacillus subtilis genes in the
RT 200 kb rrnB-dnaB region.";
RL Microbiology 143:3431-3441(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
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}.
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 -!- 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 -!- 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 -!- SIMILARITY: Belongs to the TPP enzyme family. MenD subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_01659}.
CC -!- CAUTION: Used to include what was called 'MenCF'. {ECO:0000305}.
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DR EMBL; M74521; AAA50398.1; ALT_SEQ; Genomic_DNA.
DR EMBL; M74521; AAA50399.1; ALT_SEQ; Genomic_DNA.
DR EMBL; M74538; AAC37014.1; -; Genomic_DNA.
DR EMBL; AF008220; AAC00224.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB15060.1; -; Genomic_DNA.
DR PIR; G69656; G69656.
DR RefSeq; NP_390960.1; NC_000964.3.
DR RefSeq; WP_003229050.1; NZ_JNCM01000036.1.
DR PDB; 2X7J; X-ray; 2.35 A; A/B/C/D=1-580.
DR PDBsum; 2X7J; -.
DR AlphaFoldDB; P23970; -.
DR SMR; P23970; -.
DR STRING; 224308.BSU30820; -.
DR PaxDb; P23970; -.
DR PRIDE; P23970; -.
DR EnsemblBacteria; CAB15060; CAB15060; BSU_30820.
DR GeneID; 937198; -.
DR KEGG; bsu:BSU30820; -.
DR PATRIC; fig|224308.179.peg.3340; -.
DR eggNOG; COG1165; Bacteria.
DR InParanoid; P23970; -.
DR OMA; FCNRGTS; -.
DR PhylomeDB; P23970; -.
DR BioCyc; BSUB:BSU30820-MON; -.
DR BioCyc; MetaCyc:MON-13808; -.
DR BRENDA; 2.2.1.9; 658.
DR SABIO-RK; P23970; -.
DR UniPathway; UPA00079; -.
DR UniPathway; UPA01057; UER00164.
DR EvolutionaryTrace; P23970; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0070204; F:2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0030145; F:manganese ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0030976; F:thiamine pyrophosphate binding; IEA:UniProtKB-UniRule.
DR GO; GO:0009234; P:menaquinone biosynthetic process; IEA:UniProtKB-UniRule.
DR HAMAP; MF_01659; MenD; 1.
DR InterPro; IPR029035; DHS-like_NAD/FAD-binding_dom.
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; SSF52467; SSF52467; 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..580
FT /note="2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-
FT carboxylate synthase"
FT /id="PRO_0000090828"
FT CONFLICT 112
FT /note="E -> R (in Ref. 2; AAA50398/AAC37014)"
FT /evidence="ECO:0000305"
FT CONFLICT 152
FT /note="A -> P (in Ref. 2; AAC37014)"
FT /evidence="ECO:0000305"
FT CONFLICT 540..580
FT /note="PQADKPGLHLIEIKTDRQSRVQLHRDMLNEAVREVKKQWEL -> RRQTSPD
FT SI (in Ref. 2; AAA50399/AAC37014)"
FT /evidence="ECO:0000305"
FT HELIX 6..20
FT /evidence="ECO:0007829|PDB:2X7J"
FT STRAND 24..27
FT /evidence="ECO:0007829|PDB:2X7J"
FT HELIX 34..42
FT /evidence="ECO:0007829|PDB:2X7J"
FT STRAND 47..50
FT /evidence="ECO:0007829|PDB:2X7J"
FT HELIX 54..68
FT /evidence="ECO:0007829|PDB:2X7J"
FT STRAND 72..76
FT /evidence="ECO:0007829|PDB:2X7J"
FT HELIX 80..83
FT /evidence="ECO:0007829|PDB:2X7J"
FT HELIX 86..95
FT /evidence="ECO:0007829|PDB:2X7J"
FT STRAND 99..105
FT /evidence="ECO:0007829|PDB:2X7J"
FT HELIX 108..110
FT /evidence="ECO:0007829|PDB:2X7J"
FT STRAND 111..113
FT /evidence="ECO:0007829|PDB:2X7J"
FT TURN 122..125
FT /evidence="ECO:0007829|PDB:2X7J"
FT HELIX 126..128
FT /evidence="ECO:0007829|PDB:2X7J"
FT STRAND 132..134
FT /evidence="ECO:0007829|PDB:2X7J"
FT HELIX 142..160
FT /evidence="ECO:0007829|PDB:2X7J"
FT STRAND 161..163
FT /evidence="ECO:0007829|PDB:2X7J"
FT STRAND 166..172
FT /evidence="ECO:0007829|PDB:2X7J"
FT STRAND 189..192
FT /evidence="ECO:0007829|PDB:2X7J"
FT STRAND 194..198
FT /evidence="ECO:0007829|PDB:2X7J"
FT STRAND 201..203
FT /evidence="ECO:0007829|PDB:2X7J"
FT HELIX 207..209
FT /evidence="ECO:0007829|PDB:2X7J"
FT HELIX 210..218
FT /evidence="ECO:0007829|PDB:2X7J"
FT STRAND 220..226
FT /evidence="ECO:0007829|PDB:2X7J"
FT HELIX 232..245
FT /evidence="ECO:0007829|PDB:2X7J"
FT STRAND 249..251
FT /evidence="ECO:0007829|PDB:2X7J"
FT HELIX 253..255
FT /evidence="ECO:0007829|PDB:2X7J"
FT STRAND 259..262
FT /evidence="ECO:0007829|PDB:2X7J"
FT HELIX 271..274
FT /evidence="ECO:0007829|PDB:2X7J"
FT HELIX 278..284
FT /evidence="ECO:0007829|PDB:2X7J"
FT STRAND 287..294
FT /evidence="ECO:0007829|PDB:2X7J"
FT HELIX 299..307
FT /evidence="ECO:0007829|PDB:2X7J"
FT STRAND 311..316
FT /evidence="ECO:0007829|PDB:2X7J"
FT STRAND 330..333
FT /evidence="ECO:0007829|PDB:2X7J"
FT HELIX 337..346
FT /evidence="ECO:0007829|PDB:2X7J"
FT HELIX 356..373
FT /evidence="ECO:0007829|PDB:2X7J"
FT HELIX 383..393
FT /evidence="ECO:0007829|PDB:2X7J"
FT STRAND 399..402
FT /evidence="ECO:0007829|PDB:2X7J"
FT HELIX 406..414
FT /evidence="ECO:0007829|PDB:2X7J"
FT STRAND 423..425
FT /evidence="ECO:0007829|PDB:2X7J"
FT TURN 428..430
FT /evidence="ECO:0007829|PDB:2X7J"
FT STRAND 433..435
FT /evidence="ECO:0007829|PDB:2X7J"
FT HELIX 436..447
FT /evidence="ECO:0007829|PDB:2X7J"
FT STRAND 451..456
FT /evidence="ECO:0007829|PDB:2X7J"
FT HELIX 457..462
FT /evidence="ECO:0007829|PDB:2X7J"
FT HELIX 464..467
FT /evidence="ECO:0007829|PDB:2X7J"
FT HELIX 468..473
FT /evidence="ECO:0007829|PDB:2X7J"
FT STRAND 477..483
FT /evidence="ECO:0007829|PDB:2X7J"
FT HELIX 488..492
FT /evidence="ECO:0007829|PDB:2X7J"
FT HELIX 494..496
FT /evidence="ECO:0007829|PDB:2X7J"
FT HELIX 499..505
FT /evidence="ECO:0007829|PDB:2X7J"
FT HELIX 515..520
FT /evidence="ECO:0007829|PDB:2X7J"
FT STRAND 524..526
FT /evidence="ECO:0007829|PDB:2X7J"
FT HELIX 531..537
FT /evidence="ECO:0007829|PDB:2X7J"
FT STRAND 547..553
FT /evidence="ECO:0007829|PDB:2X7J"
FT HELIX 556..579
FT /evidence="ECO:0007829|PDB:2X7J"
SQ SEQUENCE 580 AA; 64092 MW; 3B416F8DA18FFAF2 CRC64;
MTVNPITHYI GSFIDEFALS GITDAVVCPG SRSTPLAVLC AAHPDISVHV QIDERSAGFF
ALGLAKAKQR PVLLICTSGT AAANFYPAVV EAHYSRVPII VLTADRPHEL REVGAPQAIN
QHFLFGNFVK FFTDSALPEE SPQMLRYIRT LASRAAGEAQ KRPMGPVHVN VPLREPLMPD
LSDEPFGRMR TGRHVSVKTG TQSVDRESLS DVAEMLAEAE KGMIVCGELH SDADKENIIA
LSKALQYPIL ADPLSNLRNG VHDKSTVIDA YDSFLKDDEL KRKLRPDVVI RFGPMPVSKP
VFLWLKDDPT IQQIVIDEDG GWRDPTQASA HMIHCNASVF AEEIMAGLTA ATRSSEWLEK
WQFVNGRFRE HLQTISSEDV SFEGNLYRIL QHLVPENSSL FVGNSMPIRD VDTFFEKQDR
PFRIYSNRGA NGIDGVVSSA MGVCEGTKAP VTLVIGDLSF YHDLNGLLAA KKLGIPLTVI
LVNNDGGGIF SFLPQASEKT HFEDLFGTPT GLDFKHAAAL YGGTYSCPAS WDEFKTAYAP
QADKPGLHLI EIKTDRQSRV QLHRDMLNEA VREVKKQWEL
