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P17109 (MEND_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 129. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase

Short name=SEPHCHC synthase
EC=2.2.1.9
Alternative name(s):
Menaquinone biosynthesis protein MenD
Gene names
Name:menD
Ordered Locus Names:b2264, JW5374
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length556 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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). Ref.7 Ref.10

Catalytic activity

Isochorismate + 2-oxoglutarate = 5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO2. Ref.10

Cofactor

Magnesium or manganese. Ref.8 Ref.9 Ref.10

Binds 1 thiamine pyrophosphate per subunit. Ref.8 Ref.9 Ref.10

Pathway

Cofactor biosynthesis; menaquinone biosynthesis; menaquinone-2 from chorismate: step 2/8. HAMAP-Rule MF_01659

Subunit structure

Homodimer. Ref.8 Ref.9

Induction

By isopropyl-beta-D-thiogalactoside (IPTG). Ref.7

Sequence similarities

Belongs to the TPP enzyme family. MenD subfamily.

Caution

Was originally thought (Ref.7, Ref.8 and Ref.9) to be a 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) synthase but further protein analysis (Ref.10) clearly suggests that it is a 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC) synthase.

Biophysicochemical properties

Kinetic parameters:

KM=53 nM for isochorismate (at 22.5 degrees Celsius and pH 7.8) Ref.8 Ref.10

KM=1.5 µM for 2-oxoglutarate (at 22.5 degrees Celsius and pH 7.8)

KM=2.4 µM for thiamine diphosphate (at 22.5 degrees Celsius and pH 7.8)

KM=80 µM for magnesium ions (at 22.5 degrees Celsius and pH 7.8)

pH dependence:

Optimum pH is 7-8.

Sequence caution

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 5565562-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase HAMAP-Rule MF_01659
PRO_0000090829

Experimental info

Mutagenesis551E → Q: Loss of activity. Ref.8
Sequence conflict421Missing in AAA24153. Ref.5
Sequence conflict163 – 18321GVHIN…DDTGL → ESISTARLLNRCMAKWTIPG F in AAA24153. Ref.5
Sequence conflict3981Missing in AAA24153. Ref.5
Sequence conflict543 – 55614AQTLQ…QVSHL → RKRSSNFWRR in AAB59060. Ref.6

Secondary structure

..................................................................................................... 556
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P17109 [UniParc].

Last modified November 1, 1997. Version 4.
Checksum: 278201D02243E76D

FASTA55661,367
        10         20         30         40         50         60 
MSVSAFNRRW AAVILEALTR HGVRHICIAP GSRSTPLTLA AAENSAFIHH THFDERGLGH 

        70         80         90        100        110        120 
LALGLAKVSK QPVAVIVTSG TAVANLYPAL IEAGLTGEKL ILLTADRPPE LIDCGANQAI 

       130        140        150        160        170        180 
RQPGMFASHP THSISLPRPT QDIPARWLVS TIDHALGTLH AGGVHINCPF AEPLYGEMDD 

       190        200        210        220        230        240 
TGLSWQQRLG DWWQDDKPWL REAPRLESEK QRDWFFWRQK RGVVVAGRMS AEEGKKVALW 

       250        260        270        280        290        300 
AQTLGWPLIG DVLSQTGQPL PCADLWLGNA KATSELQQAQ IVVQLGSSLT GKRLLQWQAS 

       310        320        330        340        350        360 
CEPEEYWIVD DIEGRLDPAH HRGRRLIANI ADWLELHPAE KRQPWCVEIP RLAEQAMQAV 

       370        380        390        400        410        420 
IARRDAFGEA QLAHRICDYL PEQGQLFVGN SLVVRLIDAL SQLPAGYPVY SNRGASGIDG 

       430        440        450        460        470        480 
LLSTAAGVQR ASGKPTLAIV GDLSALYDLN ALALLRQVSA PLVLIVVNNN GGQIFSLLPT 

       490        500        510        520        530        540 
PQSERERFYL MPQNVHFEHA AAMFELKYHR PQNWQELETA FADAWRTPTT TVIEMVVNDT 

       550 
DGAQTLQQLL AQVSHL 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRF64997.
RefSeqNP_416767.1. NC_000913.3.
YP_490504.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortalP17109.
SMRP17109. Positions 1-556.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-10185N.
IntActP17109. 1 interaction.
MINTMINT-1246688.
STRING511145.b2264.

Proteomic databases

PaxDbP17109.
PRIDEP17109.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC75324; AAC75324; b2264.
BAA16089; BAA16089; BAA16089.
GeneID12931512.
946720.
KEGGecj:Y75_p2228.
eco:b2264.
PATRIC32119895. VBIEscCol129921_2357.

Organism-specific databases

EchoBASEEB0574.
EcoGeneEG10579. menD.

Phylogenomic databases

eggNOGCOG1165.
HOGENOMHOG000218360.
KOK02551.
OMADGGGIFH.
OrthoDBEOG6NWBQW.
PhylomeDBP17109.
ProtClustDBPRK07449.

Enzyme and pathway databases

BioCycEcoCyc:MEND-MONOMER.
ECOL316407:JW5374-MONOMER.
MetaCyc:MEND-MONOMER.
SABIO-RKP17109.
UniPathwayUPA00079; UER00164.

Gene expression databases

GenevestigatorP17109.

Family and domain databases

HAMAPMF_01659. MenD.
InterProIPR004433. MenaQ_synth_MenD.
IPR012001. Thiamin_PyroP_enz_TPP-bd_dom.
IPR011766. TPP_enzyme-bd_C.
[Graphical view]
PfamPF02775. TPP_enzyme_C. 1 hit.
PF02776. TPP_enzyme_N. 1 hit.
[Graphical view]
PIRSFPIRSF004983. MenD. 1 hit.
TIGRFAMsTIGR00173. menD. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP17109.
PROP17109.

Entry information

Entry nameMEND_ECOLI
AccessionPrimary (citable) accession number: P17109
Secondary accession number(s): P76478, P78180, P78181
Entry history
Integrated into UniProtKB/Swiss-Prot: August 1, 1990
Last sequence update: November 1, 1997
Last modified: April 16, 2014
This is version 129 of the entry and version 4 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Escherichia coli

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