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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)DescriptionActionsGraphical viewLength
ChainiPRO_00000908281 – 5802-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthaseAdd BLAST580

Proteomic databases

PaxDbiP23970.
PRIDEiP23970.

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100016766.

Structurei

Secondary structure

1580
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi6 – 20Combined sources15
Beta strandi24 – 27Combined sources4
Helixi34 – 42Combined sources9
Beta strandi47 – 50Combined sources4
Helixi54 – 68Combined sources15
Beta strandi72 – 76Combined sources5
Helixi80 – 83Combined sources4
Helixi86 – 95Combined sources10
Beta strandi99 – 105Combined sources7
Helixi108 – 110Combined sources3
Beta strandi111 – 113Combined sources3
Turni122 – 125Combined sources4
Helixi126 – 128Combined sources3
Beta strandi132 – 134Combined sources3
Helixi142 – 160Combined sources19
Beta strandi161 – 163Combined sources3
Beta strandi166 – 172Combined sources7
Beta strandi189 – 192Combined sources4
Beta strandi194 – 198Combined sources5
Beta strandi201 – 203Combined sources3
Helixi207 – 209Combined sources3
Helixi210 – 218Combined sources9
Beta strandi220 – 226Combined sources7
Helixi232 – 245Combined sources14
Beta strandi249 – 251Combined sources3
Helixi253 – 255Combined sources3
Beta strandi259 – 262Combined sources4
Helixi271 – 274Combined sources4
Helixi278 – 284Combined sources7
Beta strandi287 – 294Combined sources8
Helixi299 – 307Combined sources9
Beta strandi311 – 316Combined sources6
Beta strandi330 – 333Combined sources4
Helixi337 – 346Combined sources10
Helixi356 – 373Combined sources18
Helixi383 – 393Combined sources11
Beta strandi399 – 402Combined sources4
Helixi406 – 414Combined sources9
Beta strandi423 – 425Combined sources3
Turni428 – 430Combined sources3
Beta strandi433 – 435Combined sources3
Helixi436 – 447Combined sources12
Beta strandi451 – 456Combined sources6
Helixi457 – 462Combined sources6
Helixi464 – 467Combined sources4
Helixi468 – 473Combined sources6
Beta strandi477 – 483Combined sources7
Helixi488 – 492Combined sources5
Helixi494 – 496Combined sources3
Helixi499 – 505Combined sources7
Helixi515 – 520Combined sources6
Beta strandi524 – 526Combined sources3
Helixi531 – 537Combined sources7
Beta strandi547 – 553Combined sources7
Helixi556 – 579Combined sources24

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2X7JX-ray2.35A/B/C/D1-580[»]
ProteinModelPortaliP23970.
SMRiP23970.
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.
PhylomeDBiP23970.

Family and domain databases

Gene3Di3.40.50.1220. 1 hit.
3.40.50.970. 2 hits.
HAMAPiMF_01659. MenD. 1 hit.
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)DescriptionActionsGraphical viewLength
Sequence conflicti112E → R in AAA50398 (PubMed:8566759).Curated1
Sequence conflicti112E → R in AAC37014 (PubMed:8566759).Curated1
Sequence conflicti152A → P in AAC37014 (PubMed:8566759).Curated1
Sequence conflicti540 – 580PQADK…KQWEL → RRQTSPDSI in AAA50399 (PubMed:8566759).CuratedAdd BLAST41
Sequence conflicti540 – 580PQADK…KQWEL → RRQTSPDSI in AAC37014 (PubMed:8566759).CuratedAdd BLAST41

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2X7JX-ray2.35A/B/C/D1-580[»]
ProteinModelPortaliP23970.
SMRiP23970.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100016766.

Proteomic databases

PaxDbiP23970.
PRIDEiP23970.

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.
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. 1 hit.
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...

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: November 2, 2016
This is version 128 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.