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P17109

- MEND_ECOLI

UniProt

P17109 - MEND_ECOLI

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Protein

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

Gene

menD

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 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).1 PublicationUniRule annotation

Catalytic activityi

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

Kineticsi

  1. KM=53 nM for isochorismate (at 22.5 degrees Celsius and pH 7.8)2 Publications
  2. KM=1.5 µM for 2-oxoglutarate (at 22.5 degrees Celsius and pH 7.8)2 Publications
  3. KM=2.4 µM for thiamine diphosphate (at 22.5 degrees Celsius and pH 7.8)2 Publications
  4. 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

Pathwayi

GO - Molecular functioni

  1. 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity Source: EcoCyc
  2. metal ion binding Source: UniProtKB-KW
  3. thiamine pyrophosphate binding Source: EcoCyc

GO - Biological processi

  1. menaquinone biosynthetic process Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Menaquinone biosynthesis

Keywords - Ligandi

Magnesium, Manganese, Metal-binding, Thiamine pyrophosphate

Enzyme and pathway databases

BioCyciEcoCyc:MEND-MONOMER.
ECOL316407:JW5374-MONOMER.
MetaCyc:MEND-MONOMER.
SABIO-RKP17109.
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:b2264, JW5374
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10579. menD.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi55 – 551E → Q: Loss of activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 5565562-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthasePRO_0000090829Add
BLAST

Proteomic databases

PaxDbiP17109.
PRIDEiP17109.

Expressioni

Inductioni

By isopropyl-beta-D-thiogalactoside (IPTG).1 Publication

Gene expression databases

GenevestigatoriP17109.

Interactioni

Subunit structurei

Homodimer.2 PublicationsUniRule annotation

Protein-protein interaction databases

DIPiDIP-10185N.
IntActiP17109. 1 interaction.
MINTiMINT-1246688.
STRINGi511145.b2264.

Structurei

Secondary structure

1
556
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 1917Combined sources
Turni20 – 223Combined sources
Beta strandi25 – 284Combined sources
Turni32 – 343Combined sources
Helixi35 – 439Combined sources
Beta strandi48 – 514Combined sources
Helixi55 – 6915Combined sources
Beta strandi73 – 775Combined sources
Helixi81 – 844Combined sources
Helixi87 – 9610Combined sources
Beta strandi100 – 1067Combined sources
Helixi109 – 1113Combined sources
Beta strandi112 – 1154Combined sources
Turni123 – 1286Combined sources
Beta strandi130 – 1356Combined sources
Helixi145 – 15713Combined sources
Beta strandi164 – 1696Combined sources
Helixi183 – 1875Combined sources
Helixi188 – 1947Combined sources
Beta strandi199 – 2013Combined sources
Beta strandi205 – 2073Combined sources
Helixi214 – 2174Combined sources
Beta strandi222 – 2265Combined sources
Helixi231 – 24414Combined sources
Beta strandi248 – 2503Combined sources
Turni252 – 2543Combined sources
Helixi263 – 2664Combined sources
Helixi270 – 2767Combined sources
Beta strandi280 – 2878Combined sources
Helixi292 – 3009Combined sources
Beta strandi304 – 3129Combined sources
Beta strandi322 – 3287Combined sources
Helixi330 – 3367Combined sources
Helixi349 – 36113Combined sources
Turni362 – 3654Combined sources
Beta strandi366 – 3683Combined sources
Helixi369 – 3746Combined sources
Helixi376 – 3783Combined sources
Beta strandi385 – 3884Combined sources
Helixi392 – 4009Combined sources
Beta strandi409 – 4113Combined sources
Beta strandi418 – 4203Combined sources
Helixi421 – 43212Combined sources
Beta strandi436 – 4416Combined sources
Helixi442 – 4476Combined sources
Helixi449 – 4513Combined sources
Helixi452 – 4554Combined sources
Beta strandi462 – 4698Combined sources
Helixi474 – 4774Combined sources
Helixi482 – 4887Combined sources
Helixi498 – 5036Combined sources
Beta strandi507 – 5093Combined sources
Helixi514 – 52411Combined sources
Beta strandi527 – 53610Combined sources
Helixi541 – 55414Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2JLAX-ray2.81A/B/C/D1-556[»]
2JLCX-ray2.50A/B1-556[»]
3FLMX-ray2.70A/B1-556[»]
3HWWX-ray1.95A/D1-556[»]
3HWXX-ray2.601/A/B/I/J/R/S/Z1-556[»]
ProteinModelPortaliP17109.
SMRiP17109. Positions 1-556.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP17109.

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG1165.
HOGENOMiHOG000218360.
InParanoidiP17109.
KOiK02551.
OMAiQKPWLLE.
OrthoDBiEOG6NWBQW.
PhylomeDBiP17109.

Family and domain databases

Gene3Di3.40.50.970. 2 hits.
HAMAPiMF_01659. MenD.
InterProiIPR004433. MenaQ_synth_MenD.
IPR029061. THDP-binding.
IPR012001. Thiamin_PyroP_enz_TPP-bd_dom.
IPR011766. TPP_enzyme-bd_C.
[Graphical view]
PfamiPF02775. TPP_enzyme_C. 1 hit.
PF02776. TPP_enzyme_N. 1 hit.
[Graphical view]
PIRSFiPIRSF004983. MenD. 1 hit.
SUPFAMiSSF52518. SSF52518. 2 hits.
TIGRFAMsiTIGR00173. menD. 1 hit.

Sequencei

Sequence statusi: Complete.

P17109-1 [UniParc]FASTAAdd to Basket

« Hide

        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
Length:556
Mass (Da):61,367
Last modified:November 1, 1997 - v4
Checksum:i278201D02243E76D
GO

Sequence cautioni

The sequence AAA24153.1 differs from that shown. Reason: Frameshift at position 370. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti42 – 421Missing in AAA24153. (PubMed:2666397)Curated
Sequence conflicti163 – 18321GVHIN…DDTGL → ESISTARLLNRCMAKWTIPG F in AAA24153. (PubMed:2666397)CuratedAdd
BLAST
Sequence conflicti398 – 3981Missing in AAA24153. (PubMed:2666397)Curated
Sequence conflicti543 – 55614AQTLQ…QVSHL → RKRSSNFWRR in AAB59060. 1 PublicationCuratedAdd
BLAST

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.
PIRiF64997.
RefSeqiNP_416767.1. NC_000913.3.
YP_490504.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC75324; AAC75324; b2264.
BAA16089; BAA16089; BAA16089.
GeneIDi12931512.
946720.
KEGGiecj:Y75_p2228.
eco:b2264.
PATRICi32119895. VBIEscCol129921_2357.

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.
YP_490504.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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 [» ]
ProteinModelPortali P17109.
SMRi P17109. Positions 1-556.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-10185N.
IntActi P17109. 1 interaction.
MINTi MINT-1246688.
STRINGi 511145.b2264.

Proteomic databases

PaxDbi P17109.
PRIDEi P17109.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC75324 ; AAC75324 ; b2264 .
BAA16089 ; BAA16089 ; BAA16089 .
GeneIDi 12931512.
946720.
KEGGi ecj:Y75_p2228.
eco:b2264.
PATRICi 32119895. VBIEscCol129921_2357.

Organism-specific databases

EchoBASEi EB0574.
EcoGenei EG10579. menD.

Phylogenomic databases

eggNOGi COG1165.
HOGENOMi HOG000218360.
InParanoidi P17109.
KOi K02551.
OMAi QKPWLLE.
OrthoDBi EOG6NWBQW.
PhylomeDBi P17109.

Enzyme and pathway databases

UniPathwayi UPA00079 .
UPA01057 ; UER00164 .
BioCyci EcoCyc:MEND-MONOMER.
ECOL316407:JW5374-MONOMER.
MetaCyc:MEND-MONOMER.
SABIO-RK P17109.

Miscellaneous databases

EvolutionaryTracei P17109.
PROi P17109.

Gene expression databases

Genevestigatori P17109.

Family and domain databases

Gene3Di 3.40.50.970. 2 hits.
HAMAPi MF_01659. MenD.
InterProi IPR004433. MenaQ_synth_MenD.
IPR029061. THDP-binding.
IPR012001. Thiamin_PyroP_enz_TPP-bd_dom.
IPR011766. TPP_enzyme-bd_C.
[Graphical view ]
Pfami PF02775. TPP_enzyme_C. 1 hit.
PF02776. TPP_enzyme_N. 1 hit.
[Graphical view ]
PIRSFi PIRSF004983. MenD. 1 hit.
SUPFAMi SSF52518. SSF52518. 2 hits.
TIGRFAMsi TIGR00173. menD. 1 hit.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "A new isochorismate synthase specifically involved in menaquinone (vitamin K2) biosynthesis encoded by the menF gene."
    Daruwala R., Kwon O., Meganathan R., Hudspeth M.E.S.
    FEMS Microbiol. Lett. 140:159-163(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features."
    Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T.
    , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.
    DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "Sequence and overexpression of the menD gene from Escherichia coli."
    Popp J.L.
    J. Bacteriol. 171:4349-4354(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-507.
  6. Sharma V., Hudspeth M.E., Meganathan R.
    Submitted (JUL-1994) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 536-556.
    Strain: K12.
  7. "Menaquinone (vitamin K2) biosynthesis: evidence that the Escherichia coli menD gene encodes both 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic acid synthase and alpha-ketoglutarate decarboxylase activities."
    Palaniappan C., Sharma V., Hudspeth M.E., Meganathan R.
    J. Bacteriol. 174:8111-8118(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION, PRELIMINARY FUNCTION.
    Strain: K12.
  8. "Steady-state kinetics and molecular evolution of Escherichia coli MenD [(1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase], an anomalous thiamin diphosphate-dependent decarboxylase-carboligase."
    Bhasin M., Billinsky J.L., Palmer D.R.J.
    Biochemistry 42:13496-13504(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBUNIT, COFACTOR, MUTAGENESIS OF GLU-55, BIOPHYSICOCHEMICAL PROPERTIES.
  9. "Crystallization and preliminary X-ray analysis of (1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) synthase (MenD) from Escherichia coli."
    Sieminska E.A.L., Macova A., Palmer D.R.J., Sanders D.A.R.
    Acta Crystallogr. F 61:489-492(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: CRYSTALLIZATION, COFACTOR, SUBUNIT.
  10. "Menaquinone biosynthesis in Escherichia coli: identification of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate as a novel intermediate and re-evaluation of MenD activity."
    Jiang M., Cao Y., Guo Z.-F., Chen M., Chen X., Guo Z.
    Biochemistry 46:10979-10989(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A SEPHCHC SYNTHASE, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES.

Entry informationi

Entry nameiMEND_ECOLI
AccessioniPrimary (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: November 26, 2014
This is version 134 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  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

External Data

Dasty 3