Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase

Gene

menD

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the thiamine diphosphate-dependent decarboxylation of 2-oxoglutarate and the subsequent addition of the resulting succinic semialdehyde-thiamine pyrophosphate anion to isochorismate to yield 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC).UniRule annotation

Catalytic activityi

Isochorismate + 2-oxoglutarate = 5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO2.UniRule annotation

Cofactori

Protein has several cofactor binding sites:
  • Mg2+UniRule annotation, Mn2+UniRule annotation
  • thiamine diphosphateUniRule annotationNote: Binds 1 thiamine pyrophosphate per subunit.UniRule annotation

Pathwayi: 1,4-dihydroxy-2-naphthoate biosynthesis

This protein is involved in step 2 of the subpathway that synthesizes 1,4-dihydroxy-2-naphthoate from chorismate.UniRule annotation
Proteins known to be involved in the 7 steps of the subpathway in this organism are:
  1. Isochorismate synthase MenF (menF)
  2. 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase (menD)
  3. Putative 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (menH)
  4. o-succinylbenzoate synthase (menC)
  5. 2-succinylbenzoate--CoA ligase (menE)
  6. 1,4-dihydroxy-2-naphthoyl-CoA synthase (menB)
  7. no protein annotated in this organism
This subpathway is part of the pathway 1,4-dihydroxy-2-naphthoate biosynthesis, which is itself part of Quinol/quinone metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes 1,4-dihydroxy-2-naphthoate from chorismate, the pathway 1,4-dihydroxy-2-naphthoate biosynthesis and in Quinol/quinone metabolism.

Pathwayi: menaquinone biosynthesis

This protein is involved in the pathway menaquinone biosynthesis, which is part of Quinol/quinone metabolism.UniRule annotation
View all proteins of this organism that are known to be involved in the pathway menaquinone biosynthesis and in Quinol/quinone metabolism.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Menaquinone biosynthesis

Keywords - Ligandi

Magnesium, Manganese, Metal-binding, Thiamine pyrophosphate

Enzyme and pathway databases

BioCyciBSUB:BSU30820-MONOMER.
MetaCyc:MONOMER-13808.
BRENDAi2.2.1.9. 658.
SABIO-RKP23970.
UniPathwayiUPA00079.
UPA01057; UER00164.

Names & Taxonomyi

Protein namesi
Recommended name:
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthaseUniRule annotation (EC:2.2.1.9UniRule annotation)
Short name:
SEPHCHC synthaseUniRule annotation
Alternative name(s):
Menaquinone biosynthesis protein MenDUniRule annotation
Gene namesi
Name:menDUniRule annotation
Ordered Locus Names:BSU30820
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 5805802-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthasePRO_0000090828Add
BLAST

Proteomic databases

PaxDbiP23970.

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100016766.

Structurei

Secondary structure

1
580
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi6 – 2015Combined sources
Beta strandi24 – 274Combined sources
Helixi34 – 429Combined sources
Beta strandi47 – 504Combined sources
Helixi54 – 6815Combined sources
Beta strandi72 – 765Combined sources
Helixi80 – 834Combined sources
Helixi86 – 9510Combined sources
Beta strandi99 – 1057Combined sources
Helixi108 – 1103Combined sources
Beta strandi111 – 1133Combined sources
Turni122 – 1254Combined sources
Helixi126 – 1283Combined sources
Beta strandi132 – 1343Combined sources
Helixi142 – 16019Combined sources
Beta strandi161 – 1633Combined sources
Beta strandi166 – 1727Combined sources
Beta strandi189 – 1924Combined sources
Beta strandi194 – 1985Combined sources
Beta strandi201 – 2033Combined sources
Helixi207 – 2093Combined sources
Helixi210 – 2189Combined sources
Beta strandi220 – 2267Combined sources
Helixi232 – 24514Combined sources
Beta strandi249 – 2513Combined sources
Helixi253 – 2553Combined sources
Beta strandi259 – 2624Combined sources
Helixi271 – 2744Combined sources
Helixi278 – 2847Combined sources
Beta strandi287 – 2948Combined sources
Helixi299 – 3079Combined sources
Beta strandi311 – 3166Combined sources
Beta strandi330 – 3334Combined sources
Helixi337 – 34610Combined sources
Helixi356 – 37318Combined sources
Helixi383 – 39311Combined sources
Beta strandi399 – 4024Combined sources
Helixi406 – 4149Combined sources
Beta strandi423 – 4253Combined sources
Turni428 – 4303Combined sources
Beta strandi433 – 4353Combined sources
Helixi436 – 44712Combined sources
Beta strandi451 – 4566Combined sources
Helixi457 – 4626Combined sources
Helixi464 – 4674Combined sources
Helixi468 – 4736Combined sources
Beta strandi477 – 4837Combined sources
Helixi488 – 4925Combined sources
Helixi494 – 4963Combined sources
Helixi499 – 5057Combined sources
Helixi515 – 5206Combined sources
Beta strandi524 – 5263Combined sources
Helixi531 – 5377Combined sources
Beta strandi547 – 5537Combined sources
Helixi556 – 57924Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2X7JX-ray2.35A/B/C/D1-580[»]
ProteinModelPortaliP23970.
SMRiP23970. Positions 2-580.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP23970.

Family & Domainsi

Sequence similaritiesi

Belongs to the TPP enzyme family. MenD subfamily.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105C4A. Bacteria.
COG1165. LUCA.
HOGENOMiHOG000218359.
InParanoidiP23970.
KOiK02551.
OMAiIFRILPG.
OrthoDBiEOG6NWBQW.
PhylomeDBiP23970.

Family and domain databases

Gene3Di3.40.50.1220. 1 hit.
3.40.50.970. 2 hits.
HAMAPiMF_01659. MenD.
InterProiIPR029035. DHS-like_NAD/FAD-binding_dom.
IPR004433. MenaQ_synth_MenD.
IPR032264. MenD_middle.
IPR029061. THDP-binding.
IPR012001. Thiamin_PyroP_enz_TPP-bd_dom.
IPR011766. TPP_enzyme-bd_C.
[Graphical view]
PfamiPF02775. TPP_enzyme_C. 1 hit.
PF16582. TPP_enzyme_M_2. 1 hit.
PF02776. TPP_enzyme_N. 1 hit.
[Graphical view]
PIRSFiPIRSF004983. MenD. 1 hit.
SUPFAMiSSF52467. SSF52467. 1 hit.
SSF52518. SSF52518. 2 hits.
TIGRFAMsiTIGR00173. menD. 1 hit.

Sequencei

Sequence statusi: Complete.

P23970-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTVNPITHYI GSFIDEFALS GITDAVVCPG SRSTPLAVLC AAHPDISVHV
60 70 80 90 100
QIDERSAGFF ALGLAKAKQR PVLLICTSGT AAANFYPAVV EAHYSRVPII
110 120 130 140 150
VLTADRPHEL REVGAPQAIN QHFLFGNFVK FFTDSALPEE SPQMLRYIRT
160 170 180 190 200
LASRAAGEAQ KRPMGPVHVN VPLREPLMPD LSDEPFGRMR TGRHVSVKTG
210 220 230 240 250
TQSVDRESLS DVAEMLAEAE KGMIVCGELH SDADKENIIA LSKALQYPIL
260 270 280 290 300
ADPLSNLRNG VHDKSTVIDA YDSFLKDDEL KRKLRPDVVI RFGPMPVSKP
310 320 330 340 350
VFLWLKDDPT IQQIVIDEDG GWRDPTQASA HMIHCNASVF AEEIMAGLTA
360 370 380 390 400
ATRSSEWLEK WQFVNGRFRE HLQTISSEDV SFEGNLYRIL QHLVPENSSL
410 420 430 440 450
FVGNSMPIRD VDTFFEKQDR PFRIYSNRGA NGIDGVVSSA MGVCEGTKAP
460 470 480 490 500
VTLVIGDLSF YHDLNGLLAA KKLGIPLTVI LVNNDGGGIF SFLPQASEKT
510 520 530 540 550
HFEDLFGTPT GLDFKHAAAL YGGTYSCPAS WDEFKTAYAP QADKPGLHLI
560 570 580
EIKTDRQSRV QLHRDMLNEA VREVKKQWEL
Length:580
Mass (Da):64,092
Last modified:July 15, 1999 - v3
Checksum:i3B416F8DA18FFAF2
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti112 – 1121E → R in AAA50398 (PubMed:8566759).Curated
Sequence conflicti112 – 1121E → R in AAC37014 (PubMed:8566759).Curated
Sequence conflicti152 – 1521A → P in AAC37014 (PubMed:8566759).Curated
Sequence conflicti540 – 58041PQADK…KQWEL → RRQTSPDSI in AAA50399 (PubMed:8566759).CuratedAdd
BLAST
Sequence conflicti540 – 58041PQADK…KQWEL → RRQTSPDSI in AAC37014 (PubMed:8566759).CuratedAdd
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M74521 Genomic DNA. Translation: AAA50398.1. Sequence problems.
M74521 Genomic DNA. Translation: AAA50399.1. Sequence problems.
M74538 Genomic DNA. Translation: AAC37014.1.
AF008220 Genomic DNA. Translation: AAC00224.1.
AL009126 Genomic DNA. Translation: CAB15060.1.
PIRiG69656.
RefSeqiNP_390960.1. NC_000964.3.
WP_003229050.1. NZ_JNCM01000036.1.

Genome annotation databases

EnsemblBacteriaiCAB15060; CAB15060; BSU30820.
GeneIDi937198.
KEGGibsu:BSU30820.
PATRICi18978068. VBIBacSub10457_3222.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M74521 Genomic DNA. Translation: AAA50398.1. Sequence problems.
M74521 Genomic DNA. Translation: AAA50399.1. Sequence problems.
M74538 Genomic DNA. Translation: AAC37014.1.
AF008220 Genomic DNA. Translation: AAC00224.1.
AL009126 Genomic DNA. Translation: CAB15060.1.
PIRiG69656.
RefSeqiNP_390960.1. NC_000964.3.
WP_003229050.1. NZ_JNCM01000036.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2X7JX-ray2.35A/B/C/D1-580[»]
ProteinModelPortaliP23970.
SMRiP23970. Positions 2-580.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100016766.

Proteomic databases

PaxDbiP23970.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB15060; CAB15060; BSU30820.
GeneIDi937198.
KEGGibsu:BSU30820.
PATRICi18978068. VBIBacSub10457_3222.

Phylogenomic databases

eggNOGiENOG4105C4A. Bacteria.
COG1165. LUCA.
HOGENOMiHOG000218359.
InParanoidiP23970.
KOiK02551.
OMAiIFRILPG.
OrthoDBiEOG6NWBQW.
PhylomeDBiP23970.

Enzyme and pathway databases

UniPathwayiUPA00079.
UPA01057; UER00164.
BioCyciBSUB:BSU30820-MONOMER.
MetaCyc:MONOMER-13808.
BRENDAi2.2.1.9. 658.
SABIO-RKP23970.

Miscellaneous databases

EvolutionaryTraceiP23970.

Family and domain databases

Gene3Di3.40.50.1220. 1 hit.
3.40.50.970. 2 hits.
HAMAPiMF_01659. MenD.
InterProiIPR029035. DHS-like_NAD/FAD-binding_dom.
IPR004433. MenaQ_synth_MenD.
IPR032264. MenD_middle.
IPR029061. THDP-binding.
IPR012001. Thiamin_PyroP_enz_TPP-bd_dom.
IPR011766. TPP_enzyme-bd_C.
[Graphical view]
PfamiPF02775. TPP_enzyme_C. 1 hit.
PF16582. TPP_enzyme_M_2. 1 hit.
PF02776. TPP_enzyme_N. 1 hit.
[Graphical view]
PIRSFiPIRSF004983. MenD. 1 hit.
SUPFAMiSSF52467. SSF52467. 1 hit.
SSF52518. SSF52518. 2 hits.
TIGRFAMsiTIGR00173. menD. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Sequence organization and regulation of the Bacillus subtilis menBE operon."
    Driscoll J.R., Taber H.W.
    J. Bacteriol. 174:5063-5071(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: PRELIMINARY NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168 / RB1.
  2. "Structural organization of a Bacillus subtilis operon encoding menaquinone biosynthetic enzymes."
    Rowland B., Hill K., Miller P., Driscoll J.R., Taber H.W.
    Gene 167:105-109(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168 / RB1.
  3. "Sequencing and functional annotation of the Bacillus subtilis genes in the 200 kb rrnB-dnaB region."
    Lapidus A., Galleron N., Sorokin A., Ehrlich S.D.
    Microbiology 143:3431-3441(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168.
  4. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
    Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
    , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
    Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 168.

Entry informationi

Entry nameiMEND_BACSU
AccessioniPrimary (citable) accession number: P23970
Secondary accession number(s): O34492, P23969
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 1, 1992
Last sequence update: July 15, 1999
Last modified: February 17, 2016
This is version 125 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Caution

Used to include what was called 'MenCF'.Curated

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.