1,4-Dihydroxy-2-naphthoyl-CoA synthase - Escherichia coli (strain K12)

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P0ABU0 (MENB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 66. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
1,4-Dihydroxy-2-naphthoyl-CoA synthase
Short name=DHNA-CoA synthase
EC=4.1.3.36

Gene names

Name:	menB
Ordered Locus Names:	b2262, JW2257

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	285 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Converts o-succinylbenzoyl-CoA (OSB-CoA) to 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA). Ref.6 Ref.7
Catalytic activity	4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-naphthoyl-CoA + H₂O. Ref.7
Cofactor	Bicarbonate ion. The bicarbonate anion plays the same catalytic role (proton acceptor) as the side-chain carboxylate group of the essential 'Asp-185' found in actinobacteria, archaea, bacteroidetes, and deltaproteobacteria. Ref.7
Enzyme regulation	Inhibited by sulfite and nitrate. Ref.7
Pathway	Cofactor biosynthesis; menaquinone biosynthesis; menaquinone-2 from chorismate: step 6/8.
Subunit structure	Homohexamer. Ref.7
Sequence similarities	Belongs to the enoyl-CoA hydratase/isomerase family.

Ontologies

Keywords
Biological process	Menaquinone biosynthesis
Molecular function	Lyase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	menaquinone biosynthetic process Inferred from mutant phenotype Ref.6. Source: EcoCyc
Molecular_function	1,4-dihydroxy-2-naphthoyl-CoA synthase activity Inferred from direct assay Ref.7 PubMed 7045104. Source: EcoCyc bicarbonate binding Inferred from direct assay Ref.7. Source: EcoCyc
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
hldD	P67910	2	EBI-554195,EBI-543760

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 285

285

1,4-Dihydroxy-2-naphthoyl-CoA synthase

PRO_0000109325

Regions

Region

44 – 45

Substrate binding By similarity

Region

84 – 88

Substrate binding By similarity

Region

129 – 133

Substrate binding By similarity

Region

154 – 156

Bicarbonate binding By similarity

Sites

Binding site

Substrate By similarity

Binding site

155

Substrate By similarity

Binding site

161

Substrate By similarity

Site

163

Important for catalysis Potential

Site

258

Important for catalysis Potential

Experimental info

Mutagenesis

154

Q → A: Reduces the specific DHNA-CoA synthase activity by 15-fold, whereas its affinity for bicarbonate is reduced by 36-fold. Ref.7

Mutagenesis

156

G → D: Loss of DHNA-CoA synthase activity. Ref.7

Mutagenesis

184

W → F: Reduces the specific DHNA-CoA synthase activity by 530-fold, whereas its affinity for bicarbonate is reduced by 20-fold. Ref.7

Secondary structure

285

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P0ABU0 [UniParc].

Last modified October 25, 2005. Version 1.
Checksum: C38E7206924408E6
Show »

FASTA

285

31,633

        10         20         30         40         50         60 
MIYPDEAMLY APVEWHDCSE GFEDIRYEKS TDGIAKITIN RPQVRNAFRP LTVKEMIQAL 

        70         80         90        100        110        120 
ADARYDDNIG VIILTGAGDK AFCSGGDQKV RGDYGGYKDD SGVHHLNVLD FQRQIRTCPK 

       130        140        150        160        170        180 
PVVAMVAGYS IGGGHVLHMM CDLTIAADNA IFGQTGPKVG SFDGGWGASY MARIVGQKKA 

       190        200        210        220        230        240 
REIWFLCRQY DAKQALDMGL VNTVVPLADL EKETVRWCRE MLQNSPMALR CLKAALNADC 

       250        260        270        280 
DGQAGLQELA GNATMLFYMT EEGQEGRNAF NQKRQPDFSK FKRNP

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Menaquinone (vitamin K2) biosynthesis: nucleotide sequence and expression of the menB gene from Escherichia coli." Sharma V., Suvarna K., Meganathan R., Hudspeth M.E. J. Bacteriol. 174:5057-5062(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[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. 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]	Sharma V., Hudspeth M.E., Meganathan R. Submitted (JUL-1994) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-6. Strain: K12.
[6]	"Biosynthesis of bacterial menaquinones. Menaquinone mutants of Escherichia coli." Young I.G. Biochemistry 14:399-406(1975) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN MENAQUINONE BIOSYNTHESIS.
[7]	"A bicarbonate cofactor modulates 1,4-dihydroxy-2-naphthoyl-coenzyme a synthase in menaquinone biosynthesis of Escherichia coli." Jiang M., Chen M., Guo Z.F., Guo Z. J. Biol. Chem. 285:30159-30169(2010) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION AS A DHNA-COA SYNTHASE, CATALYTIC ACTIVITY, MUTAGENESIS OF GLN-154; GLY-156 AND TRP-184, COFACTOR, ENZYME REGULATION, SUBUNIT.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M93421 Genomic DNA. Translation: AAA23682.1.
U00096 Genomic DNA. Translation: AAC75322.1.
AP009048 Genomic DNA. Translation: BAA16086.1.
L35030 Genomic DNA. Translation: AAA24152.1.

PIR

D64997. A42714.

RefSeq

NP_416765.1. NC_000913.2.
YP_490502.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3T88	X-ray	2.00	A/B/C/D/E/F	1-285	[»]
3T89	X-ray	1.95	A/B/C/D/E/F	1-285	[»]
4ELS	X-ray	2.30	A/B/C/D/E/F	1-285	[»]
4ELW	X-ray	2.55	A/B/C/D/E/F	1-285	[»]
4ELX	X-ray	2.19	A/B/C/D/E/F	1-285	[»]

ProteinModelPortal

P0ABU0.

SMR

P0ABU0. Positions 5-285.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-47854N.

IntAct

P0ABU0. 6 interactions.

MINT

MINT-1227416.

STRING

511145.b2262.

Proteomic databases

PaxDb

P0ABU0.

PRIDE

P0ABU0.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC75322; AAC75322; b2262.
BAA16086; BAA16086; BAA16086.

GeneID

12931510.
946747.

KEGG

ecj:Y75_p2226.
eco:b2262.

PATRIC

32119891. VBIEscCol129921_2355.

Organism-specific databases

EchoBASE

EB1342.

EcoGene

EG11368. menB.

Phylogenomic databases

eggNOG

COG0447.

HOGENOM

HOG000027942.

K01661.

OMA

EETVQWC.

ProtClustDB

PRK07396.

Enzyme and pathway databases

BioCyc

EcoCyc:NAPHTHOATE-SYN-MONOMER.
ECOL316407:JW2257-MONOMER.
MetaCyc:NAPHTHOATE-SYN-MONOMER.

UniPathway

UPA00079; UER00167.

Gene expression databases

Genevestigator

P0ABU0.

Family and domain databases

Gene3D

1.10.12.10. 1 hit.

InterPro

IPR014748. Crontonase_C.
IPR001753. Crotonase_core_superfam.
IPR018376. Enoyl-CoA_hyd/isom_CS.
IPR010198. Naphthoate_synthase.
[Graphical view]

Pfam

PF00378. ECH. 1 hit.
[Graphical view]

TIGRFAMs

TIGR01929. menB. 1 hit.

PROSITE

PS00166. ENOYL_COA_HYDRATASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

MENB_ECOLI

Accession

Primary (citable) accession number: P0ABU0
Secondary accession number(s): P27290

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 25, 2005
Last sequence update:	October 25, 2005
Last modified:	May 1, 2013
This is version 66 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

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

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

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents