UniProtKB - P17109 (MEND_ECOLI)
Protein
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
Gene
menD
Organism
Escherichia coli (strain K12)
Status
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 annotation1 Publication
Caution
Was originally thought (PubMed:1459959, PubMed:14621995 and PubMed:16511076) to be a 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) synthase but further protein analysis clearly suggests that it is a 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC) synthase.1 Publication
Catalytic activityi
- 2-oxoglutarate + H+ + isochorismate = 5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO2UniRule annotation1 PublicationEC:2.2.1.9UniRule annotation1 Publication
Cofactori
Protein has several cofactor binding sites:- Mg2+UniRule annotation, Mn2+UniRule annotation
- thiamine diphosphateUniRule annotationNote: Binds 1 thiamine pyrophosphate per subunit.UniRule annotation
Kineticsi
- KM=53 nM for isochorismate (at 22.5 degrees Celsius and pH 7.8)2 Publications
- KM=1.5 µM for 2-oxoglutarate (at 22.5 degrees Celsius and pH 7.8)2 Publications
- KM=2.4 µM for thiamine diphosphate (at 22.5 degrees Celsius and pH 7.8)2 Publications
- KM=80 µM for magnesium ions (at 22.5 degrees Celsius and pH 7.8)2 Publications
pH dependencei
Optimum pH is 7-8.2 Publications
: 1,4-dihydroxy-2-naphthoate biosynthesis Pathwayi
This protein is involved in step 2 of the subpathway that synthesizes 1,4-dihydroxy-2-naphthoate from chorismate.UniRule annotationProteins known to be involved in the 7 steps of the subpathway in this organism are:
- Isochorismate synthase MenF (menF), Isochorismate synthase MenF (menF)
- 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase (menD), 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase (menD)
- 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (menH), 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (menH)
- o-succinylbenzoate synthase (menC), o-succinylbenzoate synthase (menC)
- 2-succinylbenzoate--CoA ligase (menE), 2-succinylbenzoate--CoA ligase (menE)
- 1,4-dihydroxy-2-naphthoyl-CoA synthase (menB), 1,4-dihydroxy-2-naphthoyl-CoA synthase (menB)
- 1,4-dihydroxy-2-naphthoyl-CoA hydrolase (menI), 1,4-dihydroxy-2-naphthoyl-CoA hydrolase (menI)
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 annotationView all proteins of this organism that are known to be involved in the pathway menaquinone biosynthesis and in Quinol/quinone metabolism.
GO - Molecular functioni
- 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity Source: EcoCyc
- magnesium ion binding Source: EcoCyc
- manganese ion binding Source: UniProtKB-UniRule
- thiamine pyrophosphate binding Source: EcoCyc
GO - Biological processi
- menaquinone biosynthetic process Source: EcoCyc
Keywordsi
Molecular function | Transferase |
Biological process | Menaquinone biosynthesis |
Ligand | Magnesium, Manganese, Metal-binding, Thiamine pyrophosphate |
Enzyme and pathway databases
BioCyci | EcoCyc:MEND-MONOMER MetaCyc:MEND-MONOMER |
BRENDAi | 2.2.1.9, 2165 |
SABIO-RKi | P17109 |
UniPathwayi | UPA00079 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:b2264, JW5374 |
Organismi | Escherichia coli (strain K12) |
Taxonomic identifieri | 83333 [NCBI] |
Taxonomic lineagei | Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia › |
Proteomesi |
|
Pathology & Biotechi
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 55 | E → Q: Loss of activity. 1 Publication | 1 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000090829 | 1 – 556 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthaseAdd BLAST | 556 |
Proteomic databases
jPOSTi | P17109 |
PaxDbi | P17109 |
PRIDEi | P17109 |
Expressioni
Inductioni
By isopropyl-beta-D-thiogalactoside (IPTG).1 Publication
Interactioni
Subunit structurei
Homodimer.
UniRule annotation2 PublicationsProtein-protein interaction databases
BioGRIDi | 4260506, 9 interactors 851061, 2 interactors |
DIPi | DIP-10185N |
IntActi | P17109, 1 interactor |
STRINGi | 511145.b2264 |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
SMRi | P17109 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | P17109 |
Family & Domainsi
Sequence similaritiesi
Phylogenomic databases
eggNOGi | COG1165, Bacteria |
HOGENOMi | CLU_006051_3_0_6 |
InParanoidi | P17109 |
PhylomeDBi | P17109 |
Family and domain databases
HAMAPi | MF_01659, MenD, 1 hit |
InterProi | View protein in InterPro IPR004433, MenaQ_synth_MenD IPR032264, MenD_middle IPR029061, THDP-binding IPR012001, Thiamin_PyroP_enz_TPP-bd_dom IPR011766, TPP_enzyme-bd_C |
PANTHERi | PTHR42916, PTHR42916, 1 hit |
Pfami | View protein in Pfam PF02775, TPP_enzyme_C, 1 hit PF16582, TPP_enzyme_M_2, 1 hit PF02776, TPP_enzyme_N, 1 hit |
PIRSFi | PIRSF004983, MenD, 1 hit |
SUPFAMi | SSF52518, SSF52518, 2 hits |
TIGRFAMsi | TIGR00173, menD, 1 hit |
i Sequence
Sequence statusi: Complete.
P17109-1 [UniParc]FASTAAdd to basket
10 20 30 40 50
MSVSAFNRRW AAVILEALTR HGVRHICIAP GSRSTPLTLA AAENSAFIHH
60 70 80 90 100
THFDERGLGH LALGLAKVSK QPVAVIVTSG TAVANLYPAL IEAGLTGEKL
110 120 130 140 150
ILLTADRPPE LIDCGANQAI RQPGMFASHP THSISLPRPT QDIPARWLVS
160 170 180 190 200
TIDHALGTLH AGGVHINCPF AEPLYGEMDD TGLSWQQRLG DWWQDDKPWL
210 220 230 240 250
REAPRLESEK QRDWFFWRQK RGVVVAGRMS AEEGKKVALW AQTLGWPLIG
260 270 280 290 300
DVLSQTGQPL PCADLWLGNA KATSELQQAQ IVVQLGSSLT GKRLLQWQAS
310 320 330 340 350
CEPEEYWIVD DIEGRLDPAH HRGRRLIANI ADWLELHPAE KRQPWCVEIP
360 370 380 390 400
RLAEQAMQAV IARRDAFGEA QLAHRICDYL PEQGQLFVGN SLVVRLIDAL
410 420 430 440 450
SQLPAGYPVY SNRGASGIDG LLSTAAGVQR ASGKPTLAIV GDLSALYDLN
460 470 480 490 500
ALALLRQVSA PLVLIVVNNN GGQIFSLLPT PQSERERFYL MPQNVHFEHA
510 520 530 540 550
AAMFELKYHR PQNWQELETA FADAWRTPTT TVIEMVVNDT DGAQTLQQLL
AQVSHL
Sequence cautioni
The sequence AAA24153 differs from that shown. Reason: Frameshift.Curated
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 42 | Missing in AAA24153 (PubMed:2666397).Curated | 1 | |
Sequence conflicti | 163 – 183 | GVHIN…DDTGL → ESISTARLLNRCMAKWTIPG F in AAA24153 (PubMed:2666397).CuratedAdd BLAST | 21 | |
Sequence conflicti | 398 | Missing in AAA24153 (PubMed:2666397).Curated | 1 | |
Sequence conflicti | 543 – 556 | AQTLQ…QVSHL → RKRSSNFWRR in AAB59060 (Ref. 6) CuratedAdd BLAST | 14 |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | U54790 Genomic DNA Translation: AAC44304.1 U00096 Genomic DNA Translation: AAC75324.1 AP009048 Genomic DNA Translation: BAA16089.2 M21787 Genomic DNA Translation: AAA24153.1 Frameshift. L04464 Genomic DNA Translation: AAB59060.1 L35030 Genomic DNA Translation: AAA24150.1 |
PIRi | F64997 |
RefSeqi | NP_416767.1, NC_000913.3 WP_001295284.1, NZ_STEB01000008.1 |
Genome annotation databases
EnsemblBacteriai | AAC75324; AAC75324; b2264 BAA16089; BAA16089; BAA16089 |
GeneIDi | 946720 |
KEGGi | ecj:JW5374 eco:b2264 |
PATRICi | fig|511145.12.peg.2357 |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | U54790 Genomic DNA Translation: AAC44304.1 U00096 Genomic DNA Translation: AAC75324.1 AP009048 Genomic DNA Translation: BAA16089.2 M21787 Genomic DNA Translation: AAA24153.1 Frameshift. L04464 Genomic DNA Translation: AAB59060.1 L35030 Genomic DNA Translation: AAA24150.1 |
PIRi | F64997 |
RefSeqi | NP_416767.1, NC_000913.3 WP_001295284.1, NZ_STEB01000008.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
2JLA | X-ray | 2.81 | A/B/C/D | 1-556 | [»] | |
2JLC | X-ray | 2.50 | A/B | 1-556 | [»] | |
3FLM | X-ray | 2.70 | A/B | 1-556 | [»] | |
3HWW | X-ray | 1.95 | A/D | 1-556 | [»] | |
3HWX | X-ray | 2.60 | 1/A/B/I/J/R/S/Z | 1-556 | [»] | |
5EJ4 | X-ray | 1.77 | A/B/C/D/E/F/G/H | 1-556 | [»] | |
5EJ5 | X-ray | 2.30 | A/B/C/D/E/F/G/H | 1-556 | [»] | |
5EJ6 | X-ray | 2.24 | A/B/C/D/E/F/G/H | 1-556 | [»] | |
5EJ7 | X-ray | 1.56 | A/B/C/D/E/F/G/H | 1-556 | [»] | |
5EJ8 | X-ray | 1.34 | A/B/C/D/E/F/G/H | 1-556 | [»] | |
5EJ9 | X-ray | 1.72 | A/B/C/D/E/F/G/H | 1-556 | [»] | |
5EJA | X-ray | 1.60 | A/B/C/D/E/F/G/H | 1-556 | [»] | |
5EJM | X-ray | 1.72 | A/B/C/D/E/F/G/H | 1-556 | [»] | |
5Z2P | X-ray | 2.30 | A/B/C/D/E/F/G/H | 1-556 | [»] | |
5Z2R | X-ray | 2.30 | A/B/C/D/E/F/G/H | 1-556 | [»] | |
5Z2U | X-ray | 2.35 | A/B/C/D/E/F/G/H | 1-556 | [»] | |
SMRi | P17109 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 4260506, 9 interactors 851061, 2 interactors |
DIPi | DIP-10185N |
IntActi | P17109, 1 interactor |
STRINGi | 511145.b2264 |
Proteomic databases
jPOSTi | P17109 |
PaxDbi | P17109 |
PRIDEi | P17109 |
Genome annotation databases
EnsemblBacteriai | AAC75324; AAC75324; b2264 BAA16089; BAA16089; BAA16089 |
GeneIDi | 946720 |
KEGGi | ecj:JW5374 eco:b2264 |
PATRICi | fig|511145.12.peg.2357 |
Organism-specific databases
EchoBASEi | EB0574 |
Phylogenomic databases
eggNOGi | COG1165, Bacteria |
HOGENOMi | CLU_006051_3_0_6 |
InParanoidi | P17109 |
PhylomeDBi | P17109 |
Enzyme and pathway databases
UniPathwayi | UPA00079 UPA01057;UER00164 |
BioCyci | EcoCyc:MEND-MONOMER MetaCyc:MEND-MONOMER |
BRENDAi | 2.2.1.9, 2165 |
SABIO-RKi | P17109 |
Miscellaneous databases
EvolutionaryTracei | P17109 |
PROi | PR:P17109 |
Family and domain databases
HAMAPi | MF_01659, MenD, 1 hit |
InterProi | View protein in InterPro IPR004433, MenaQ_synth_MenD IPR032264, MenD_middle IPR029061, THDP-binding IPR012001, Thiamin_PyroP_enz_TPP-bd_dom IPR011766, TPP_enzyme-bd_C |
PANTHERi | PTHR42916, PTHR42916, 1 hit |
Pfami | View protein in Pfam PF02775, TPP_enzyme_C, 1 hit PF16582, TPP_enzyme_M_2, 1 hit PF02776, TPP_enzyme_N, 1 hit |
PIRSFi | PIRSF004983, MenD, 1 hit |
SUPFAMi | SSF52518, SSF52518, 2 hits |
TIGRFAMsi | TIGR00173, menD, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | MEND_ECOLI | |
Accessioni | P17109Primary (citable) accession number: P17109 Secondary accession number(s): P76478, P78180, P78181 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | August 1, 1990 |
Last sequence update: | November 1, 1997 | |
Last modified: | December 2, 2020 | |
This is version 171 of the entry and version 4 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Prokaryotic Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Reference proteomeDocuments
- PATHWAY comments
Index of metabolic and biosynthesis pathways - PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families