P17109 (MEND_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	556 AA.
Sequence status	Complete.
Protein existence	Evidence 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.

Ontologies

Keywords
Biological process	Menaquinone biosynthesis
Ligand	Magnesium Manganese Metal-binding Thiamine pyrophosphate
Molecular function	Transferase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	menaquinone biosynthetic process Inferred from mutant phenotype PubMed 6337125. Source: EcoCyc
Molecular_function	2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity Inferred from direct assay Ref.10. Source: EcoCyc magnesium ion binding Inferred from electronic annotation. Source: HAMAP manganese ion binding Inferred from electronic annotation. Source: HAMAP thiamine pyrophosphate binding Inferred from direct assay Ref.10. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 556

556

2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase HAMAP-Rule MF_01659

PRO_0000090829

Experimental info

Mutagenesis

55

1

E → Q: Loss of activity. Ref.8

Sequence conflict

42

1

Missing in AAA24153. Ref.5

Sequence conflict

163 – 183

21

GVHIN…DDTGL → ESISTARLLNRCMAKWTIPG F in AAA24153. Ref.5

Sequence conflict

398

1

Missing in AAA24153. Ref.5

Sequence conflict

543 – 556

14

AQTLQ…QVSHL → RKRSSNFWRR in AAB59060. Ref.6

Secondary structure

1

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556

Helix Strand Turn

Details...

Helix

3 – 19

17

Turn

20 – 22

3

Beta strand

25 – 28

4

Turn

32 – 34

3

Helix

35 – 43

9

Beta strand

48 – 51

4

Helix

55 – 69

15

Beta strand

73 – 77

5

Helix

81 – 84

4

Helix

87 – 96

10

Beta strand

100 – 106

7

Helix

109 – 111

3

Beta strand

112 – 115

4

Turn

123 – 128

6

Beta strand

130 – 135

6

Helix

145 – 157

13

Beta strand

164 – 169

6

Helix

183 – 187

5

Helix

188 – 194

7

Beta strand

199 – 201

3

Beta strand

205 – 207

3

Helix

214 – 217

4

Beta strand

222 – 226

5

Helix

231 – 244

14

Beta strand

248 – 250

3

Turn

252 – 254

3

Helix

263 – 266

4

Helix

270 – 276

7

Beta strand

280 – 287

8

Helix

292 – 300

9

Beta strand

304 – 312

9

Beta strand

322 – 328

7

Helix

330 – 336

7

Helix

349 – 361

13

Turn

362 – 365

4

Beta strand

366 – 368

3

Helix

369 – 374

6

Helix

376 – 378

3

Beta strand

385 – 388

4

Helix

392 – 400

9

Beta strand

409 – 411

3

Beta strand

418 – 420

3

Helix

421 – 432

12

Beta strand

436 – 441

6

Helix

442 – 447

6

Helix

449 – 451

3

Helix

452 – 455

4

Beta strand

462 – 469

8

Helix

474 – 477

4

Helix

482 – 488

7

Helix

498 – 503

6

Beta strand

507 – 509

3

Helix

514 – 524

11

Beta strand

527 – 536

10

Helix

541 – 554

14

Sequences

	Sequence		Length	Mass (Da)
	P17109 [UniParc]. Last modified November 1, 1997. Version 4. Checksum: 278201D02243E76D	FASTA	556	61,367
	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

References

	« Hide 'large scale' referencesShow '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. , 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 277:1453-1474(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.

PIR

F64997.

RefSeq

NP_416767.1. NC_000913.2.
YP_490504.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P17109.

SMR

P17109. Positions 1-556.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-10185N.

MINT

MINT-1246688.

STRING

511145.b2264.

Proteomic databases

PaxDb

P17109.

PRIDE

P17109.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC75324; AAC75324; b2264.
BAA16089; BAA16089; BAA16089.

GeneID

12931512.
946720.

KEGG

ecj:Y75_p2228.
eco:b2264.

PATRIC

32119895. VBIEscCol129921_2357.

Organism-specific databases

EchoBASE

EB0574.

EcoGene

EG10579. menD.

Phylogenomic databases

eggNOG

COG1165.

HOGENOM

HOG000218360.

KO

K02551.

OMA

DGGGIFH.

ProtClustDB

PRK07449.

Enzyme and pathway databases

BioCyc

EcoCyc:MEND-MONOMER.
ECOL316407:JW5374-MONOMER.
MetaCyc:MEND-MONOMER.

SABIO-RK

P17109.

UniPathway

UPA00079; UER00164.

Gene expression databases

Genevestigator

P17109.

Family and domain databases

HAMAP

MF_01659. MenD.

InterPro

IPR004433. MenaQ_synth_MenD.
IPR012001. Thiamin_PyroP_enz_TPP-bd_dom.
IPR011766. TPP_enzyme-bd_C.
[Graphical view]

PANTHER

PTHR18968:SF3. PTHR18968:SF3. 1 hit.

Pfam

PF02775. TPP_enzyme_C. 1 hit.
PF02776. TPP_enzyme_N. 1 hit.
[Graphical view]

PIRSF

PIRSF004983. MenD. 1 hit.

TIGRFAMs

TIGR00173. menD. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P17109.

Entry information

Entry name

MEND_ECOLI

Accession

Primary (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:	May 1, 2013
This is version 122 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program