P0ABQ0 (COABC_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Coenzyme A biosynthesis bifunctional protein CoaBC

Alternative name(s):
DNA/pantothenate metabolism flavoprotein

Including the following 2 domains:

1. Phosphopantothenoylcysteine decarboxylase
   Short name=PPCDC
   EC=4.1.1.36
   Alternative name(s):
   CoaC
2. Phosphopantothenate--cysteine ligase
   EC=6.3.2.5
   Alternative name(s):
   CoaB
   PPC synthetase
   Short name=PPCS
   Phosphopantothenoylcysteine synthase

Gene names

Name:	coaBC
Synonyms:	dfp
Ordered Locus Names:	b3639, JW5642

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	406 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes two steps in the biosynthesis of coenzyme A. In the first step cysteine is conjugated to 4'-phosphopantothenate to form 4-phosphopantothenoylcysteine, in the latter compound is decarboxylated to form 4'-phosphopantotheine.
Catalytic activity	N-((R)-4'-phosphopantothenoyl)-L-cysteine = pantotheine 4'-phosphate + CO2. CTP + (R)-4'-phosphopantothenate + L-cysteine = CMP + PPi + N-((R)-4'-phosphopantothenoyl)-L-cysteine.
Cofactor	Magnesium. Binds 1 FMN per subunit.
Pathway	Cofactor biosynthesis; coenzyme A biosynthesis; CoA from (R)-pantothenate: step 2/5. Cofactor biosynthesis; coenzyme A biosynthesis; CoA from (R)-pantothenate: step 3/5.
Subunit structure	Homododecamer, the CoaB domains form homodimers.
Sequence similarities	In the N-terminal section; belongs to the HFCD (homo-oligomeric flavin containing Cys decarboxylase) superfamily. In the C-terminal section; belongs to the PPC synthetase family.
Sequence caution	The sequence AAA61992.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Ontologies

Keywords
Ligand	FMN Flavoprotein Magnesium Metal-binding
Molecular function	Decarboxylase Ligase Lyase
Technical term	3D-structure Complete proteome Direct protein sequencing Multifunctional enzyme Reference proteome
Gene Ontology (GO)
Biological process	coenzyme A biosynthetic process Inferred from electronic annotation. Source: InterPro pantothenate catabolic process Inferred from electronic annotation. Source: InterPro
Molecular function	FMN binding Inferred from electronic annotation. Source: InterPro metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW phosphopantothenate--cysteine ligase activity Inferred from electronic annotation. Source: EC phosphopantothenoylcysteine decarboxylase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.4

Chain

2 – 406

405

Coenzyme A biosynthesis bifunctional protein CoaBC

PRO_0000182022

Regions

Region

2 – 188

187

Phosphopantothenoylcysteine decarboxylase

Region

189 – 406

218

Phosphopantothenate--cysteine ligase

Sites

Active site

158

1

Proton donor Probable

Binding site

125

1

Substrate By similarity

Binding site

279

1

CTP

Binding site

289

1

CTP

Binding site

341

1

CTP

Binding site

345

1

CTP

Experimental info

Mutagenesis

11

1

G → D in Dfp-707; temperature-sensitive, impairs folding. Ref.7

Mutagenesis

14

1

G → S: No FMN binding. Ref.7

Mutagenesis

15

1

G → A: Less than 5% of wild-type activity. Ref.7

Mutagenesis

16

1

I → L: Severely reduced activity. Ref.7

Mutagenesis

16

1

I → V: Slightly reduced activity. Ref.7

Mutagenesis

17

1

A → D: Less than 5% of wild-type activity. Ref.7

Mutagenesis

17

1

A → G or S: Almost wild-type activity. Ref.7

Mutagenesis

19

1

Y → F: Almost wild-type activity. Ref.7

Mutagenesis

19

1

Y → L: Reduced activity. Ref.7

Mutagenesis

20

1

K → N or Q: Reduced activity. Ref.7

Mutagenesis

20

1

K → R: Almost wild-type activity. Ref.7

Mutagenesis

46

1

F → L: Reduced activity. Ref.4

Mutagenesis

75

1

H → N: Loss of activity. Ref.4

Mutagenesis

89

1

P → A: Binds FMN, but more loosely than wild-type. Ref.4

Mutagenesis

89

1

P → D: No FMN binding. Ref.4

Mutagenesis

91

1

T → V: Binds FMN. Ref.4

Mutagenesis

124

1

M → L: No effect. Ref.4

Mutagenesis

125

1

N → D or Q: Loss of activity. Ref.4 Ref.7

Mutagenesis

128

1

M → L: Severely reduced activity. Ref.4

Mutagenesis

158

1

C → A or S: Loss of activity.

Mutagenesis

194

1

T → V: Loss of dimerization. Ref.8

Mutagenesis

198

1

T → V: Loss of dimerization. Ref.8

Mutagenesis

203

1

D → N: Loss of dimerization. Ref.8

Mutagenesis

210

1

N → D: Loss of activity, reaction intermediate detectable. Ref.8 Ref.9

Mutagenesis

210

1

N → H or K: Loss of activity, reaction intermediate not detectable. Ref.8 Ref.9

Mutagenesis

212

1

S → A: Small effect on activity. Ref.8

Mutagenesis

215

1

K → Q: No effect. Ref.8

Mutagenesis

275

1

A → V: Loss of dimerization. Ref.8 Ref.9

Mutagenesis

289

1

K → Q: Loss of activity. Ref.8

Mutagenesis

291

1

K → Q: Reduced activity. Ref.8

Mutagenesis

292

1

K → Q: Small effect on activity. Ref.8

Secondary structure

1

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406

Helix Strand Turn

Details...

Turn

185 – 188

4

Beta strand

190 – 197

8

Beta strand

200 – 203

4

Beta strand

206 – 208

3

Helix

215 – 225

11

Turn

226 – 228

3

Beta strand

230 – 235

6

Beta strand

247 – 250

4

Helix

254 – 264

11

Helix

265 – 267

3

Beta strand

269 – 273

5

Beta strand

301 – 303

3

Helix

310 – 315

6

Beta strand

318 – 320

3

Beta strand

323 – 328

6

Beta strand

331 – 333

3

Helix

334 – 344

11

Beta strand

348 – 352

5

Beta strand

366 – 373

8

Beta strand

376 – 384

9

Helix

385 – 404

20

Sequences

	Sequence		Length	Mass (Da)
	P0ABQ0 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: CBD11B9347E8C6AB	FASTA	406	43,438
	10 20 30 40 50 60 MSLAGKKIVL GVSGGIAAYK TPELVRRLRD RGADVRVAMT EAAKAFITPL SLQAVSGYPV 70 80 90 100 110 120 SDSLLDPAAE AAMGHIELGK WADLVILAPA TADLIARVAA GMANDLVSTI CLATPAPVAV 130 140 150 160 170 180 LPAMNQQMYR AAATQHNLEV LASRGLLIWG PDSGSQACGD IGPGRMLDPL TIVDMAVAHF 190 200 210 220 230 240 SPVNDLKHLN IMITAGPTRE PLDPVRYISN HSSGKMGFAI AAAAARRGAN VTLVSGPVSL 250 260 270 280 290 300 PTPPFVKRVD VMTALEMEAA VNASVQQQNI FIGCAAVADY RAATVAPEKI KKQATQGDEL 310 320 330 340 350 360 TIKMVKNPDI VAGVAALKDH RPYVVGFAAE TNNVEEYARQ KRIRKNLDLI CANDVSQPTQ 370 380 390 400 GFNSDNNALH LFWQDGDKVL PLERKELLGQ LLLDEIVTRY DEKNRR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication." Burland V.D., Plunkett G. III, Daniels D.L., Blattner F.R. Genomics 16:551-561(1993) [PubMed: 7686882] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[2]	"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: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"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: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"Molecular characterization of lantibiotic-synthesizing enzyme EpiD reveals a function for bacterial Dfp proteins in coenzyme A biosynthesis." Kupke T., Uebele M., Schmid D., Jung G., Blaesse M., Steinbacher S. J. Biol. Chem. 275:31838-31846(2000) [PubMed: 10922366] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-11, CHARACTERIZATION OF COAC ACTIVITY, MUTAGENESIS OF PHE-46; HIS-75; PRO-89; THR-91; MET-124; ASN-125 AND MET-128.
[5]	"Nucleotide sequence of the structural gene for dUTPase of Escherichia coli K-12." Lundberg L.G., Thoresson H.-O., Karlstroem O.H., Nyman P.O. EMBO J. 2:967-971(1983) [PubMed: 6139280] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 288-406. Strain: K12.
[6]	"Phosphopantothenoylcysteine synthetase from Escherichia coli. Identification and characterization of the last unidentified coenzyme A biosynthetic enzyme in bacteria." Strauss E., Kinsland C., Ge Y., McLafferty F.W., Begley T.P. J. Biol. Chem. 276:13513-13516(2001) [PubMed: 11278255] [Abstract] Cited for: CHARACTERIZATION OF COAB ACTIVITY.
[7]	"Molecular characterization of the 4'-phosphopantothenoylcysteine decarboxylase domain of bacterial Dfp flavoproteins." Kupke T. J. Biol. Chem. 276:27597-27604(2001) [PubMed: 11358972] [Abstract] Cited for: CHARACTERIZATION OF COAC ACTIVITY, MUTAGENESIS OF GLY-11; GLY-14; GLY-15; ILE-16; ALA-17; TYR-19; LYS-20 AND ASN-125.
[8]	"Molecular characterization of the 4'-phosphopantothenoylcysteine synthetase domain of bacterial dfp flavoproteins." Kupke T. J. Biol. Chem. 277:36137-36145(2002) [PubMed: 12140293] [Abstract] Cited for: CHARACTERIZATION OF COAB ACTIVITY, MUTAGENESIS OF THR-194; THR-198; ASP-203; ASN-210; SER-212; LYS-215; ALA-275; LYS-289; LYS-291 AND LYS-292.
[9]	"Active-site residues and amino acid specificity of the bacterial 4'-phosphopantothenoylcysteine synthetase CoaB." Kupke T. Eur. J. Biochem. 271:163-172(2004) [PubMed: 14686929] [Abstract] Cited for: CHARACTERIZATION OF COAB ACTIVITY, MUTAGENESIS OF ASN-210 AND ALA-275.
[10]	"Structural basis of CTP-dependent peptide bond formation in coenzyme A biosynthesis catalyzed by Escherichia coli PPC synthetase." Stanitzek S., Augustin M.A., Huber R., Kupke T., Steinbacher S. Structure 12:1977-1988(2004) [PubMed: 15530362] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 181-406 OF MUTANT ASP-210 APOENZYME AND OF COMPLEX WITH SUBSTRATE; CTP AND CALCIUM IONS.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

L10328 Genomic DNA. Translation: AAA61992.1. Different initiation.
U00096 Genomic DNA. Translation: AAC76663.2.
AP009048 Genomic DNA. Translation: BAE77653.1.
V01578 Genomic DNA. No translation available.

RefSeq

NP_418096.4. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1U7U	X-ray	2.40	A	181-406	[»]
1U7W	X-ray	2.50	A/B/C	181-406	[»]
1U7Z	X-ray	2.30	A/B/C	181-406	[»]
1U80	X-ray	2.85	A/B/C	181-406	[»]

ProteinModelPortal

P0ABQ0.

SMR

P0ABQ0. Positions 1-405.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-48472N.

IntAct

P0ABQ0. 2 interactions.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000005034; EBESCP00000005034; EBESCG00000004108.
EBESCT00000016777; EBESCP00000016068; EBESCG00000015836.

GeneID

949047.

GenomeReviews

Gene locus JW5642 in contig AP009048_GR.
Gene locus b3639 in contig U00096_GR.

KEGG

ecj:JW5642.
eco:b3639.

PATRIC

32122765. VBIEscCol129921_3759.

Organism-specific databases

EchoBASE

EB0004.

EcoGene

EG10004. dfp.

Phylogenomic databases

eggNOG

COG0452.

GeneTree

EBGT00050000011616.

HOGENOM

HBG523890.

OMA

VTSGPTH.

PhylomeDB

P0ABQ0.

ProtClustDB

PRK05579.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10004-MONOMER.
MetaCyc:EG10004-MONOMER.

Gene expression databases

Genevestigator

P0ABQ0.

Family and domain databases

InterPro

IPR005252. Bifunc_COABC.
IPR007085. DNA/pantothenate-metab_flavo_C.
IPR003382. Flavoprotein.
[Graphical view]

Gene3D

G3DSA:3.40.50.10300. DNA/pantothenate-metab_flavo_C. 1 hit.
G3DSA:3.40.50.1950. Flavoprotein. 1 hit.

KO

K13038.

Pfam

PF04127. DFP. 1 hit.
PF02441. Flavoprotein. 1 hit.
[Graphical view]

SUPFAM

SSF102645. DNA/pantothenate-metab_flavo_C. 1 hit.
SSF52507. Flavoprotein. 1 hit.

TIGRFAMs

TIGR00521. CoaBC_dfp. 1 hit.

ProtoNet

Search...

Entry information

Entry name

COABC_ECOLI

Accession

Primary (citable) accession number: P0ABQ0
Secondary accession number(s): P24285, P76718, Q2M7V3

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 8, 2005
Last sequence update:	January 23, 2007
Last modified:	January 25, 2012
This is version 60 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program