Reviewed, UniProtKB/Swiss-Prot P26602 (UBIC_ECOLI)

Names and origin

Protein names

Recommended name:
    Chorismate--pyruvate lyase
      Short name=CL
      Short name=CPL
    EC=4.1.3.40

Gene names

Name:	ubiC
Ordered Locus Names:	b4039, JW5713

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	165 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	Removes the pyruvyl group from chorismate, with concomitant aromatization of the ring, to provide 4-hydroxybenzoate (4HB) for the ubiquinone pathway. HAMAP MF_01632
Catalytic activity	Chorismate = 4-hydroxybenzoate + pyruvate. HAMAP MF_01632
Enzyme regulation	Inhibited by 4-hydroxybenzoate, vanillate, 4-hydroxybenzaldehyde and 3-carboxymethylaminomethyl-4-hydroxybenzoic acid. Ref.10 Ref.13
Pathway	Cofactor biosynthesis; ubiquinone biosynthesis. HAMAP MF_01632
Subunit structure	Monomer. HAMAP MF_01632
Subcellular location	Cytoplasm. HAMAP MF_01632
Sequence similarities	Belongs to the ubiC family.
biophysicochemical properties	Kinetic parameters: KM=29 µM for chorismate HAMAP MF_01632 pH dependence: Optimum pH is 7.5.

Ontologies

Keywords
Biological process	Ubiquinone biosynthesis
Cellular component	Cytoplasm
Molecular function	Lyase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	pyruvate biosynthetic process Inferred from electronic annotation. Source: HAMAP ubiquinone biosynthetic process Inferred from electronic annotation. Source: HAMAP
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	chorismate lyase activity Inferred from electronic annotation. Source: HAMAP protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
aceE	P0AFG8	1	EBI-559360,EBI-542683

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.2

Chain

2 – 165

164

Chorismate--pyruvate lyase HAMAP MF_01632

PRO_0000065711

Sites

Binding site

35

1

Substrate; via amide nitrogen HAMAP MF_01632

Binding site

77

1

Substrate HAMAP MF_01632

Binding site

115

1

Substrate; via amide nitrogen HAMAP MF_01632

Experimental info

Mutagenesis

91

1

G → A: Increases the inhibition by product by about 40%. No effect on substrate affinity. Ref.13

Mutagenesis

156

1

E → K: Loss of activity. Ref.9

Secondary structure

1

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165

Helix Strand Turn

Details...

Helix

4 – 11

8

Helix

23 – 30

8

Helix

36 – 40

5

Turn

41 – 43

3

Beta strand

46 – 56

11

Helix

58 – 60

3

Turn

62 – 64

3

Helix

65 – 67

3

Beta strand

74 – 83

10

Beta strand

86 – 96

11

Helix

97 – 99

3

Helix

102 – 108

7

Helix

117 – 119

3

Beta strand

125 – 135

11

Beta strand

138 – 147

10

Beta strand

150 – 158

9

Sequences

	Sequence		Length	Mass (Da)
	P26602-1 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: 6DAACD25BC338F09	FASTA	165	18,777
	10 20 30 40 50 60 MSHPALTQLR ALRYCKEIPA LDPQLLDWLL LEDSMTKRFE QQGKTVSVTM IREGFVEQNE 70 80 90 100 110 120 IPEELPLLPK ESRYWLREIL LCADGEPWLA GRTVVPVSTL SGPELALQKL GKTPLGRYLF 130 140 150 160 TSSTLTRDFI EIGRDAGLWG RRSRLRLSGK PLLLTELFLP ASPLY

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Ubiquinone biosynthesis. Cloning of the genes coding for chorismate pyruvate-lyase and 4-hydroxybenzoate octaprenyl transferase from Escherichia coli." Siebert M., Bechthold A., Melzer M., May U., Berger U., Schroeder G., Schroeder J., Severin K., Heide L. FEBS Lett. 307:347-350(1992) [PubMed: 1644192] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12 / MC4100 / ATCC 35695 / DSM 6574.
[2]	"Cloning and sequencing of Escherichia coli ubiC and purification of chorismate lyase." Nichols B.P., Green J.M. J. Bacteriol. 174:5309-5316(1992) [PubMed: 1644758] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-21. Strain: K12.
[3]	"Location of the ubiA gene on the physical map of Escherichia coli." Nishimura K., Nakahigashi K., Inokuchi H. J. Bacteriol. 174:5762-5762(1992) [PubMed: 1512213] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"Mutants of Escherichia coli affected in respiration: the cloning and nucleotide sequence of ubiA, encoding the membrane-bound p-hydroxybenzoate:octaprenyltransferase." Wu G., Williams H.D., Gibson F., Poole R.K. J. Gen. Microbiol. 139:1795-1805(1993) [PubMed: 8409922] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[5]	Zhang D., Shrestha B., Tan T. Submitted (JUN-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: BL21.
[6]	"Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes." Blattner F.R., Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L. Nucleic Acids Res. 21:5408-5417(1993) [PubMed: 8265357] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[7]	"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.
[8]	"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.
[9]	"Formation of 4-hydroxybenzoate in Escherichia coli: characterization of the ubiC gene and its encoded enzyme chorismate pyruvate-lyase." Siebert M., Severin K., Heide L. Microbiology 140:897-904(1994) [PubMed: 8012607] [Abstract] Cited for: CHARACTERIZATION, MUTAGENESIS OF GLU-156.
[10]	"Chorismate lyase: kinetics and engineering for stability." Holden M.J., Mayhew M.P., Gallagher D.T., Vilker V.L. Biochim. Biophys. Acta 1594:160-167(2002) [PubMed: 11825618] [Abstract] Cited for: BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION. Strain: K12 / MG1655 / ATCC 47076.
[11]	"Crystallization and 1.1-A diffraction of chorismate lyase from Escherichia coli." Stover C., Mayhew M.P., Holden M.J., Howard A., Gallagher D.T. J. Struct. Biol. 129:96-99(2000) [PubMed: 10675300] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.1 ANGSTROMS).
[12]	"The crystal structure of chorismate lyase shows a new fold and a tightly retained product." Gallagher D.T., Mayhew M., Holden M.J., Howard A., Kim K.-J., Vilker V.L. Proteins 44:304-311(2001) [PubMed: 11455603] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS) IN COMPLEX WITH PRODUCT; MUTANT SER-15/SER-82 IN COMPLEX WITH PRODUCT; MUTANT SER-15 IN COMPLEX WITH PRODUCT.
[13]	"Structural analysis of ligand binding and catalysis in chorismate lyase." Smith N., Roitberg A.E., Rivera E., Howard A., Holden M.J., Mayhew M., Kaistha S., Gallagher D.T. Arch. Biochem. Biophys. 445:72-80(2006) [PubMed: 16343413] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.0 ANGSTROMS) OF MUTANT SER-15/SER-82 IN COMPLEXES WITH PRODUCT AND SUBSTRATE ANALOG; MUTANT SER-15/SER-82/ALA-91 IN COMPLEXES WITH PRODUCT AND SUBSTRATE ANALOG, MUTAGENESIS OF GLY-91, ENZYME REGULATION.

Cross-references

Sequence databases

EMBLGenBankDDBJ

X66619 Genomic DNA. Translation: CAA47181.1.
M93136 Genomic DNA. Translation: AAA24711.1.
M93413 Genomic DNA. Translation: AAA24716.1.
X57434 Genomic DNA. Translation: CAA40681.1. Different initiation.
M96268 Unassigned DNA. Translation: AAA17027.1.
DQ087228 Genomic DNA. Translation: AAY88959.1.
U00006 Genomic DNA. Translation: AAC43133.1. Different initiation.
U00096 Genomic DNA. Translation: AAC77009.1. Different initiation.
AP009048 Genomic DNA. Translation: BAE78041.1.

PIR

S25660.

RefSeq

AP_004540.1.
NP_418463.4.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1FW9	X-ray	1.40	A	2-165	[»]
1G1B	X-ray	1.99	A/B	2-165	[»]
1G81	X-ray	1.71	A	2-165	[»]
1JD3	X-ray	2.03	A	2-165	[»]
1TT8	X-ray	1.00	A	2-165	[»]
1XLR	X-ray	1.94	A	2-165	[»]
2AHC	X-ray	2.40	A/B/C/D	2-165	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:11066N.

IntAct

P26602. 3 interactions.

Genome annotation databases

GeneID

948545.

GenomeReviews

Gene locus JW5713 in contig AP009048_GR.
Gene locus b4039 in contig U00096_GR.

KEGG

ecj:JW5713.
eco:b4039.

Organism-specific databases

EchoBASE

EB1343.

EcoGene

EG11369. ubiC.

CMR

Search...

Phylogenomic databases

HOGENOM

P26602.

OMA

P26602. WGRRSRF.

Enzyme and pathway databases

BioCyc

EcoCyc:CHORPYRLY-MON.
MetaCyc:CHORPYRLY-MON.

BRENDA

4.1.3.40. 246.

Family and domain databases

HAMAP

MF_01632.
[Tree]

InterPro

IPR007440. Chorismate_lyase.
[Graphical view]

Pfam

PF04345. Chor_lyase. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

UBIC_ECOLI

Accession

Primary (citable) accession number: P26602
Secondary accession number(s): P76783, Q2M6R5, Q4JHR8

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1992
Last sequence update:	January 23, 2007
Last modified:	June 16, 2009
This is version 89 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)