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Protein

Isochorismate synthase MenF

Gene

menF

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the conversion of chorismate to isochorismate. Can also catalyze the reverse reaction, but with a lower efficiency.4 Publications

Catalytic activityi

Chorismate = isochorismate.UniRule annotation4 Publications

Cofactori

Mg2+UniRule annotation4 PublicationsNote: Binds more tightly in the presence of chorismate.1 Publication

Kineticsi

kcat is 213 min(-1) for mutase activity with chorismate. kcat is 176 min(-1) for mutase activity with chorismate in the presence of 30 mM of beta-mercaptoethanol (BME). kcat is 144.9 min(-1) for mutase activity with chorismate (at pH 7.5 and 37 degrees Celsius). kcat is 80 min(-1) for mutase activity with chorismate in the absence of 30 mM of beta-mercaptoethanol (BME). kcat is 3.8 min(-1) for mutase activity with isochorismate (at pH 7.5 and 37 degrees Celsius.3 Publications

  1. KM=119 µM for isochorismate (at pH 7.5 and 37 degrees Celsius)1 Publication
  2. KM=166.9 µM for chorismate (at pH 7.5 and 37 degrees Celsius)1 Publication
  3. KM=192 µM for chorismate1 Publication
  4. KM=195 µM for chorismate1 Publication
  5. KM=770 µM for magnesium1 Publication
  1. Vmax=91.7 pmol/sec/mg enzyme with chorismate as substrate (at pH 7.5 and 37 degrees Celsius)1 Publication
  2. Vmax=2.4 pmol/sec/mg enzyme with isochorismate as substrate (at pH 7.5 and 37 degrees Celsius)1 Publication

pH dependencei

Optimum pH is between 7.5 and 8. The mutase activity decreases sharply at pH 6.5 and 9 to about 20% of that observed at the optimum pH.2 Publications

Temperature dependencei

Optimum temperature is 37 degrees Celsius. At 60 degrees Celsius the mutase activity is completely lost.2 Publications

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

This protein is involved in step 1 of the subpathway that synthesizes 1,4-dihydroxy-2-naphthoate from chorismate.UniRule annotation2 Publications
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. 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. 1,4-dihydroxy-2-naphthoyl-CoA hydrolase (menI)
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 annotation1 Publication
View all proteins of this organism that are known to be involved in the pathway menaquinone biosynthesis and in Quinol/quinone metabolism.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei190 – 1901Proton acceptorUniRule annotation1 Publication
Active sitei240 – 2401Proton donorUniRule annotation1 Publication
Metal bindingi284 – 2841MagnesiumUniRule annotation1 Publication
Metal bindingi416 – 4161MagnesiumUniRule annotation1 Publication

GO - Molecular functioni

  • isochorismate synthase activity Source: EcoCyc
  • magnesium ion binding Source: EcoCyc

GO - Biological processi

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

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Menaquinone biosynthesis

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:MENF-MONOMER.
ECOL316407:JW2260-MONOMER.
MetaCyc:MENF-MONOMER.
BRENDAi5.4.4.2. 2026.
SABIO-RKP38051.
UniPathwayiUPA00079.
UPA01057; UER00163.

Names & Taxonomyi

Protein namesi
Recommended name:
Isochorismate synthase MenF1 PublicationUniRule annotation (EC:5.4.4.2UniRule annotation4 Publications)
Alternative name(s):
Isochorismate hydroxymutase1 Publication
Isochorismate mutaseUniRule annotation
Gene namesi
Name:menFUniRule annotation
Synonyms:yfbA
Ordered Locus Names:b2265, JW2260
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12362. menF.

Pathology & Biotechi

Disruption phenotypei

Mutant produces only a trace of menaquinone.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi190 – 1901K → A: Lack of activity. 1 Publication
Mutagenesisi240 – 2401E → Q: Lack of activity. 1 Publication
Mutagenesisi255 – 2551L → A: Decrease in activity. 1 Publication
Mutagenesisi344 – 3441A → T: Lack of activity. 1 Publication
Mutagenesisi387 – 3871R → A: Lack of activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 431431Isochorismate synthase MenFPRO_0000154147Add
BLAST

Proteomic databases

PaxDbiP38051.
PRIDEiP38051.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

BioGridi4262080. 6 interactions.
DIPiDIP-10187N.
IntActiP38051. 7 interactions.
MINTiMINT-1275996.
STRINGi511145.b2265.

Structurei

Secondary structure

1
431
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi2 – 1514Combined sources
Beta strandi21 – 3212Combined sources
Helixi40 – 456Combined sources
Beta strandi52 – 565Combined sources
Beta strandi60 – 7516Combined sources
Helixi76 – 849Combined sources
Helixi87 – 893Combined sources
Beta strandi94 – 985Combined sources
Beta strandi105 – 11713Combined sources
Beta strandi120 – 13112Combined sources
Helixi133 – 14614Combined sources
Beta strandi160 – 1678Combined sources
Helixi169 – 18517Combined sources
Beta strandi190 – 20314Combined sources
Helixi207 – 21711Combined sources
Beta strandi221 – 2277Combined sources
Beta strandi229 – 23810Combined sources
Beta strandi241 – 2466Combined sources
Beta strandi249 – 26012Combined sources
Helixi265 – 27511Combined sources
Helixi281 – 29616Combined sources
Helixi297 – 2993Combined sources
Beta strandi309 – 3124Combined sources
Beta strandi314 – 32916Combined sources
Helixi332 – 3398Combined sources
Turni343 – 3453Combined sources
Beta strandi346 – 3494Combined sources
Helixi350 – 36011Combined sources
Turni366 – 3694Combined sources
Beta strandi370 – 3756Combined sources
Beta strandi377 – 3848Combined sources
Beta strandi387 – 3926Combined sources
Beta strandi395 – 40410Combined sources
Helixi410 – 42516Combined sources
Turni426 – 4283Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2EUAX-ray2.50A/B1-431[»]
3BZMX-ray1.95A1-431[»]
3BZNX-ray2.00A1-431[»]
ProteinModelPortaliP38051.
SMRiP38051. Positions 1-429.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP38051.

Family & Domainsi

Sequence similaritiesi

Belongs to the isochorismate synthase family.UniRule annotationCurated

Phylogenomic databases

eggNOGiENOG4105E4F. Bacteria.
COG1169. LUCA.
HOGENOMiHOG000028186.
InParanoidiP38051.
KOiK02552.
OMAiSIESWPE.
OrthoDBiEOG6PGK1Z.
PhylomeDBiP38051.

Family and domain databases

Gene3Di3.60.120.10. 1 hit.
HAMAPiMF_01935. MenF_gammaproteo.
InterProiIPR005801. ADC_synthase.
IPR015890. Chorismate_C.
IPR004561. IsoChor_synthase.
[Graphical view]
PfamiPF00425. Chorismate_bind. 1 hit.
[Graphical view]
SUPFAMiSSF56322. SSF56322. 1 hit.
TIGRFAMsiTIGR00543. isochor_syn. 1 hit.

Sequencei

Sequence statusi: Complete.

P38051-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQSLTTALEN LLRHLSQEIP ATPGIRVIDI PFPLKDAFDA LSWLASQQTY
60 70 80 90 100
PQFYWQQRNG DEEAVVLGAI TRFTSLDQAQ RFLRQHPEHA DLRIWGLNAF
110 120 130 140 150
DPSQGNLLLP RLEWRRCGGK ATLRLTLFSE SSLQHDAIQA KEFIATLVSI
160 170 180 190 200
KPLPGLHLTT TREQHWPDKT GWTQLIELAT KTIAEGELDK VVLARATDLH
210 220 230 240 250
FASPVNAAAM MAASRRLNLN CYHFYMAFDG ENAFLGSSPE RLWRRRDKAL
260 270 280 290 300
RTEALAGTVA NNPDDKQAQQ LGEWLMADDK NQRENMLVVE DICQRLQADT
310 320 330 340 350
QTLDVLPPQV LRLRKVQHLR RCIWTSLNKA DDVICLHQLQ PTAAVAGLPR
360 370 380 390 400
DLARQFIARH EPFTREWYAG SAGYLSLQQS EFCVSLRSAK ISGNVVRLYA
410 420 430
GAGIVRGSDP EQEWQEIDNK AAGLRTLLQM E
Length:431
Mass (Da):48,765
Last modified:November 1, 1997 - v4
Checksum:iD081724F3329FE47
GO

Sequence cautioni

The sequence M21787 differs from that shown. Reason: Frameshift at positions 270, 310 and 341. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti310 – 3123VLR → YC in AAC44303 (PubMed:8764478).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z50849 Genomic DNA. Translation: CAA90702.1.
U54790 Genomic DNA. Translation: AAC44303.1.
U00096 Genomic DNA. Translation: AAC75325.2.
AP009048 Genomic DNA. Translation: BAA16092.1.
U58768 Genomic DNA. Translation: AAB02729.1.
M21787 Genomic DNA. No translation available.
PIRiG64997.
RefSeqiNP_416768.4. NC_000913.3.
WP_001191419.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75325; AAC75325; b2265.
BAA16092; BAA16092; BAA16092.
GeneIDi946712.
KEGGiecj:JW2260.
eco:b2265.
PATRICi32119897. VBIEscCol129921_2358.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z50849 Genomic DNA. Translation: CAA90702.1.
U54790 Genomic DNA. Translation: AAC44303.1.
U00096 Genomic DNA. Translation: AAC75325.2.
AP009048 Genomic DNA. Translation: BAA16092.1.
U58768 Genomic DNA. Translation: AAB02729.1.
M21787 Genomic DNA. No translation available.
PIRiG64997.
RefSeqiNP_416768.4. NC_000913.3.
WP_001191419.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2EUAX-ray2.50A/B1-431[»]
3BZMX-ray1.95A1-431[»]
3BZNX-ray2.00A1-431[»]
ProteinModelPortaliP38051.
SMRiP38051. Positions 1-429.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262080. 6 interactions.
DIPiDIP-10187N.
IntActiP38051. 7 interactions.
MINTiMINT-1275996.
STRINGi511145.b2265.

Proteomic databases

PaxDbiP38051.
PRIDEiP38051.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75325; AAC75325; b2265.
BAA16092; BAA16092; BAA16092.
GeneIDi946712.
KEGGiecj:JW2260.
eco:b2265.
PATRICi32119897. VBIEscCol129921_2358.

Organism-specific databases

EchoBASEiEB2265.
EcoGeneiEG12362. menF.

Phylogenomic databases

eggNOGiENOG4105E4F. Bacteria.
COG1169. LUCA.
HOGENOMiHOG000028186.
InParanoidiP38051.
KOiK02552.
OMAiSIESWPE.
OrthoDBiEOG6PGK1Z.
PhylomeDBiP38051.

Enzyme and pathway databases

UniPathwayiUPA00079.
UPA01057; UER00163.
BioCyciEcoCyc:MENF-MONOMER.
ECOL316407:JW2260-MONOMER.
MetaCyc:MENF-MONOMER.
BRENDAi5.4.4.2. 2026.
SABIO-RKP38051.

Miscellaneous databases

EvolutionaryTraceiP38051.
PROiP38051.

Family and domain databases

Gene3Di3.60.120.10. 1 hit.
HAMAPiMF_01935. MenF_gammaproteo.
InterProiIPR005801. ADC_synthase.
IPR015890. Chorismate_C.
IPR004561. IsoChor_synthase.
[Graphical view]
PfamiPF00425. Chorismate_bind. 1 hit.
[Graphical view]
SUPFAMiSSF56322. SSF56322. 1 hit.
TIGRFAMsiTIGR00543. isochor_syn. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "An isochorismate hydroxymutase isogene in Escherichia coli."
    Mueller R., Dahm C., Schulte G., Leistner E.
    FEBS Lett. 378:131-134(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PATHWAY.
    Strain: K12 / MC4100 / ATCC 35695 / DSM 6574.
  2. Mueller R.
    Submitted (FEB-1998) to the EMBL/GenBank/DDBJ databases
    Cited for: SEQUENCE REVISION.
  3. "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], FUNCTION, CATALYTIC ACTIVITY.
    Strain: K12 / PL2024.
  4. "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.
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  6. "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.
  7. Huisman G.W.
    Submitted (JUN-1996) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-216.
    Strain: K12.
  8. "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 216-431.
  9. "Intrinsic and extrinsic approaches for detecting genes in a bacterial genome."
    Borodovsky M., Rudd K.E., Koonin E.V.
    Nucleic Acids Res. 22:4756-4767(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION.
  10. "Menaquinone (vitamin K2) biosynthesis: overexpression, purification, and characterization of a new isochorismate synthase from Escherichia coli."
    Daruwala R., Bhattacharyya D.K., Kwon O., Meganathan R.
    J. Bacteriol. 179:3133-3138(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, COFACTOR.
  11. "The role of isochorismate hydroxymutase genes entC and menF in enterobactin and menaquinone biosynthesis in Escherichia coli."
    Dahm C., Muller R., Schulte G., Schmidt K., Leistner E.
    Biochim. Biophys. Acta 1425:377-386(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, PATHWAY, DISRUPTION PHENOTYPE.
  12. "Lysine 190 is the catalytic base in MenF, the menaquinone-specific isochorismate synthase from Escherichia coli: implications for an enzyme family."
    Kolappan S., Zwahlen J., Zhou R., Truglio J.J., Tonge P.J., Kisker C.
    Biochemistry 46:946-953(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF LYS-190; GLU-240; LEU-255; ALA-344 AND ARG-387, ACTIVE SITES.
  13. "Structure of isochorismate synthase in complex with magnesium."
    Parsons J.F., Shi K.M., Ladner J.E.
    Acta Crystallogr. D 64:607-610(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) IN COMPLEX WITH MAGNESIUM, COFACTOR.

Entry informationi

Entry nameiMENF_ECOLI
AccessioniPrimary (citable) accession number: P38051
Secondary accession number(s): P76479
, P78297, Q47009, Q47704
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: November 1, 1997
Last modified: January 20, 2016
This is version 144 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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

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.