O06414 (MENB_MYCTU) Reviewed, UniProtKB/Swiss-Prot

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:	Rv0548c, MT0573

Organism

Mycobacterium tuberculosis

Taxonomic identifier

1773 [NCBI]

Taxonomic lineage

Bacteria › Actinobacteria › Actinobacteridae › Actinomycetales › Corynebacterineae › Mycobacteriaceae › Mycobacterium › Mycobacterium tuberculosis complex

Protein attributes

Sequence length	314 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.3
Catalytic activity	4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-naphthoyl-CoA + H2O. Ref.3 Ref.5
Pathway	Cofactor biosynthesis; menaquinone biosynthesis; menaquinone-2 from chorismate: step 6/8.
Subunit structure	Homohexamer. Dimer of a homotrimer. Ref.3 Ref.4
Sequence similarities	Belongs to the enoyl-CoA hydratase/isomerase family.
Biophysicochemical properties	Kinetic parameters: KM=7.3 µM for O-succinylbenzoyl-CoA (at 25 degrees Celsius an pH 5.9) Ref.3

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 direct assay Ref.3. Source: UniProtKB protein hexamerization Inferred from direct assay Ref.4. Source: MTBBASE protein homooligomerization Inferred from physical interaction Ref.3. Source: MTBBASE
Cellular component	plasma membrane Inferred from direct assay. Source: MTBBASE
Molecular function	1,4-dihydroxy-2-naphthoyl-CoA synthase activity Inferred from direct assay Ref.3. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 314

314

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

PRO_0000399471

Regions

Region

57 – 58

2

Substrate binding

Region

103 – 107

5

Substrate binding

Region

157 – 161

5

Substrate binding

Sites

Active site

185

1

Proton acceptor Ref.5

Binding site

95

1

Substrate

Binding site

184

1

Substrate

Binding site

190

1

Substrate By similarity

Site

192

1

Important for catalysis Potential

Site

287

1

Important for catalysis Potential

Experimental info

Mutagenesis

133

1

R → A: Loss of DHNA-CoA synthase activity. Ref.3

Mutagenesis

185

1

D → G or N: Loss of DHNA-CoA synthase activity. Ref.3 Ref.5

Mutagenesis

192

1

D → N: Loss of DHNA-CoA synthase activity. Ref.3

Mutagenesis

287

1

Y → F: Loss of DHNA-CoA synthase activity. Ref.3

Secondary structure

1

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314

Helix Strand Turn

Details...

Helix

22 – 24

3

Beta strand

25 – 27

3

Beta strand

35 – 46

12

Beta strand

48 – 52

5

Helix

55 – 57

3

Helix

63 – 78

16

Beta strand

85 – 88

4

Helix

136 – 145

10

Beta strand

146 – 148

3

Beta strand

150 – 154

5

Helix

164 – 168

5

Beta strand

169 – 175

7

Turn

176 – 178

3

Helix

185 – 187

3

Helix

198 – 201

4

Helix

207 – 214

8

Helix

221 – 226

6

Beta strand

231 – 234

4

Helix

236 – 238

3

Turn

239 – 241

3

Helix

245 – 251

7

Helix

255 – 267

13

Turn

276 – 278

3

Helix

282 – 287

6

Helix

290 – 293

4

Helix

297 – 300

4

Sequences

	Sequence		Length	Mass (Da)
	O06414 [UniParc]. Last modified July 1, 1997. Version 1. Checksum: AF2D192A9F607DC7	FASTA	314	34,689
	10 20 30 40 50 60 MVAPAGEQGR SSTALSDNPF DAKAWRLVDG FDDLTDITYH RHVDDATVRV AFNRPEVRNA 70 80 90 100 110 120 FRPHTVDELY RVLDHARMSP DVGVVLLTGN GPSPKDGGWA FCSGGDQRIR GRSGYQYASG 130 140 150 160 170 180 DTADTVDVAR AGRLHILEVQ RLIRFMPKVV ICLVNGWAAG GGHSLHVVCD LTLASREYAR 190 200 210 220 230 240 FKQTDADVGS FDGGYGSAYL ARQVGQKFAR EIFFLGRTYT AEQMHQMGAV NAVAEHAELE 250 260 270 280 290 300 TVGLQWAAEI NAKSPQAQRM LKFAFNLLDD GLVGQQLFAG EATRLAYMTD EAVEGRDAFL 310 QKRPPDWSPF PRYF

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence." Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E., Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K. , Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K., Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J., Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S., Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S., Barrell B.G. Nature 393:537-544(1998) [PubMed: 9634230] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 25618 / H37Rv.
[2]	"Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains." Fleischmann R.D., Alland D., Eisen J.A., Carpenter L., White O., Peterson J.D., DeBoy R.T., Dodson R.J., Gwinn M.L., Haft D.H., Hickey E.K., Kolonay J.F., Nelson W.C., Umayam L.A., Ermolaeva M.D., Salzberg S.L., Delcher A., Utterback T.R. , Weidman J.F., Khouri H.M., Gill J., Mikula A., Bishai W., Jacobs W.R. Jr., Venter J.C., Fraser C.M. J. Bacteriol. 184:5479-5490(2002) [PubMed: 12218036] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: CDC 1551 / Oshkosh.
[3]	"Crystal structure of Mycobacterium tuberculosis MenB, a key enzyme in vitamin K2 biosynthesis." Truglio J.J., Theis K., Feng Y., Gajda R., Machutta C., Tonge P.J., Kisker C. J. Biol. Chem. 278:42352-42360(2003) [PubMed: 12909628] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS, FUNCTION AS A DHNA-COA SYNTHASE, CATALYTIC ACTIVITY, MUTAGENESIS OF ARG-133; ASP-185; ASP-192 AND TYR-287, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
[4]	"Structure of naphthoate synthase (MenB) from Mycobacterium tuberculosis in both native and product-bound forms." Johnston J.M., Arcus V.L., Baker E.N. Acta Crystallogr. D 61:1199-1206(2005) [PubMed: 16131752] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS, SUBUNIT.
[5]	"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: 20643650] [Abstract] Cited for: ACTIVE SITE, CATALYTIC ACTIVITY, MUTAGENESIS OF ASP-185.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

BX842573 Genomic DNA. Translation: CAB08959.1.
AE000516 Genomic DNA. Translation: AAK44795.1.

PIR

G70547.

RefSeq

NP_215062.1. NC_000962.2.
NP_334981.1. NC_002755.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1Q51	X-ray	2.30	A/B/C/D/E/F/G/H/I/J/K/L	1-314	[»]
1Q52	X-ray	1.80	A/B/C/D/E/F/G/H/I/J/K/L	1-314	[»]
1RJM	X-ray	2.15	A/B/C	1-314	[»]
1RJN	X-ray	2.30	A/B/C	1-314	[»]
3T8A	X-ray	2.24	A/B/C	1-314	[»]
3T8B	X-ray	1.65	A/B	1-314	[»]

ProteinModelPortal

O06414.

SMR

O06414. Positions 18-314.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBMYCT00000001170; EBMYCP00000001170; EBMYCG00000001170.
EBMYCT00000072625; EBMYCP00000070684; EBMYCG00000072620.

GeneID

887529.
924909.

GenomeReviews

Gene locus MT0573 in contig AE000516_GR.
Gene locus Rv0548c in contig AL123456_GR.

KEGG

mtc:MT0573.
mtu:Rv0548c.

PATRIC

18122962. VBIMycTub22151_0615.

TIGR

MT0573.

Organism-specific databases

TubercuList

Rv0548c.

Phylogenomic databases

GeneTree

EBGT00050000015513.

HOGENOM

HBG748731.

OMA

FDFTDIT.

PhylomeDB

O06414.

ProtClustDB

PRK08321.

Enzyme and pathway databases

BioCyc

MetaCyc:MONOMER-13810.

Family and domain databases

InterPro

IPR014748. Crontonase_C.
IPR001753. Crotonase_core.
IPR010198. Naphthoate_synthase.
[Graphical view]

Gene3D

G3DSA:1.10.12.10. Crontonase_C. 1 hit.

KO

K01661.

Pfam

PF00378. ECH. 1 hit.
[Graphical view]

TIGRFAMs

TIGR01929. MenB. 1 hit.

PROSITE

PS00166. ENOYL_COA_HYDRATASE. False negative.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

MENB_MYCTU

Accession

Primary (citable) accession number: O06414
Secondary accession number(s): Q7D9N7

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 5, 2010
Last sequence update:	July 1, 1997
Last modified:	January 25, 2012
This is version 79 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program