Lipoate-protein ligase A - Escherichia coli (strain K12)

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Reviewed, UniProtKB/Swiss-Prot P32099 (LPLA_ECOLI)

Last modified June 16, 2009. Version 84. History...

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

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    Lipoate-protein ligase A
    EC=2.7.7.63
Alternative name(s):
    Lipoate--protein ligase

Gene names

Name:	lplA
Synonyms:	yjjF
Ordered Locus Names:	b4386, JW4349

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

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Protein attributes

Sequence length	338 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	Catalyzes both the ATP-dependent activation of exogenously supplied lipoate to lipoyl-AMP and the transfer of the activated lipoyl onto the lipoyl domains of lipoate-dependent enzymes. Is also able to catalyze very poorly the transfer of lipoyl and octanoyl moiety from their acyl carrier protein. Ref.6
Catalytic activity	ATP + lipoate = diphosphate + lipoyl-AMP. HAMAP MF_01602 Lipoyl-AMP + protein = protein N(6)-(lipoyl)lysine + AMP. HAMAP MF_01602
Enzyme regulation	6-seleno-octanoate, 8-thio-octanoate and 8-seleno-octanoate caused 100%, 50% and 63% inhibition respectively. Inhibited by Cu²⁺. HAMAP MF_01602
Pathway	Protein modification; protein lipoylation via exogenous pathway; protein N(6)-(lipoyl)lysine from lipoic acid: step 1/2. HAMAP MF_01602 Protein modification; protein lipoylation via exogenous pathway; protein N(6)-(lipoyl)lysine from lipoic acid: step 2/2.
Subunit structure	Monomer. Ref.6
Subcellular location	Cytoplasm. HAMAP MF_01602
Miscellaneous	In the transfer reaction, the free carboxyl group of lipoic acid is attached via an amide linkage to the epsilon-amino group of a specific lysine residue of lipoyl domains of lipoate-dependent enzymes. HAMAP MF_01602
Sequence similarities	Belongs to the lplA family.
Biophysicochemical properties	Kinetic parameters: K_M=1.9 µM for ATP HAMAP MF_01602 K_M=1.7 µM for D,L-lipoic acid K_M=152 µM for magnesium ion V_max=40 nmol/min/mg enzyme toward ATP V_max=24 nmol/min/mg enzyme toward D,L-lipoic acid pH dependence: Most active from pH 5.5 to 8.0. Inactive below pH 4.3.

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Ontologies

Keywords
Cellular component	Cytoplasm
Ligand	ATP-binding Nucleotide-binding
Molecular function	Transferase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	peptidyl-lysine lipoylation Inferred from electronic annotation. Source: HAMAP
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW lipoate-protein ligase activity Inferred from electronic annotation. Source: HAMAP protein binding Inferred from physical interaction. Source: IntAct transferase activity Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

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Binary interactions

With	Entry	#Exp.	IntAct	Notes
yncE	P76116	1	EBI-553559,EBI-562173

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed Ref.1

Chain

2 – 338

337

Lipoate-protein ligase A HAMAP MF_01602

PRO_0000209564

Regions

Nucleotide binding

76 – 79

ATP By similarity

Sites

Binding site

ATP By similarity

Binding site

134

ATP By similarity

Binding site

134

Lipoate By similarity

Natural variations

Natural variant

G → S in lplA1 or slr1; selenolipoate resistance mutation. Ref.7

Experimental info

Mutagenesis

S → A: 20-fold decrease in affinity for ATP. Ref.9

Mutagenesis

141

R → A: More than 10-fold reduction in Vmax. Ref.9

Secondary structure

338

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P32099-1 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: 102788082E182A6F
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FASTA

338

37,926

        10         20         30         40         50         60 
MSTLRLLISD SYDPWFNLAV EECIFRQMPA TQRVLFLWRN ADTVVIGRAQ NPWKECNTRR 

        70         80         90        100        110        120 
MEEDNVRLAR RSSGGGAVFH DLGNTCFTFM AGKPEYDKTI STSIVLNALN ALGVSAEASG 

       130        140        150        160        170        180 
RNDLVVKTVE GDRKVSGSAY RETKDRGFHH GTLLLNADLS RLANYLNPDK KKLAAKGITS 

       190        200        210        220        230        240 
VRSRVTNLTE LLPGITHEQV CEAITEAFFA HYGERVEAEI ISPNKTPDLP NFAETFARQS 

       250        260        270        280        290        300 
SWEWNFGQAP AFSHLLDERF TWGGVELHFD VEKGHITRAQ VFTDSLNPAP LEALAGRLQG 

       310        320        330 
CLYRADMLQQ ECEALLVDFP EQEKELRELS AWMAGAVR

« Hide

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Identification of the gene encoding lipoate-protein ligase A of Escherichia coli. Molecular cloning and characterization of the lplA gene and gene product." Morris T.W., Reed K.E., Cronan J.E. Jr. J. Biol. Chem. 269:16091-16100(1994) [PubMed: 8206909] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-26, CHARACTERIZATION. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[2]	"Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes." Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R. Nucleic Acids Res. 23:2105-2119(1995) [PubMed: 7610040] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[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: 9278503] [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: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"An Escherichia coli membrane protein with a unique signal sequence." Neuwald A.F., Stauffer G.V. Gene 82:219-228(1989) [PubMed: 2684780] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-68. Strain: K12.
[6]	"Purification and properties of the lipoate protein ligase of Escherichia coli." Green D.E., Morris T.W., Green J., Cronan J.E. Jr., Guest J.R. Biochem. J. 309:853-862(1995) [PubMed: 7639702] [Abstract] Cited for: PARTIAL PROTEIN SEQUENCE, FUNCTION, SUBSTRATE SPECIFICITY, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[7]	"Lipoic acid metabolism in Escherichia coli: the lplA and lipB genes define redundant pathways for ligation of lipoyl groups to apoprotein." Morris T.W., Reed K.E., Cronan J.E. Jr. J. Bacteriol. 177:1-10(1995) [PubMed: 8002607] [Abstract] Cited for: VARIANT SER-74.
[8]	"The Escherichia coli lipB gene encodes lipoyl (octanoyl)-acyl carrier protein:protein transferase." Jordan S.W., Cronan J.E. Jr. J. Bacteriol. 185:1582-1589(2003) [PubMed: 12591875] [Abstract] Cited for: CHARACTERIZATION. Strain: K12 / JK1.
[9]	"Crystal structure of lipoate-protein ligase A from Escherichia coli. Determination of the lipoic acid-binding site." Fujiwara K., Toma S., Okamura-Ikeda K., Motokawa Y., Nakagawa A., Taniguchi H. J. Biol. Chem. 280:33645-33651(2005) [PubMed: 16043486] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS), MUTAGENESIS OF SER-73 AND ARG-141.

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Cross-references

Sequence databases

L27665 Genomic DNA. Translation: AAA21740.1.
U14003 Genomic DNA. Translation: AAA97282.1.
U00096 Genomic DNA. Translation: AAC77339.1.
AP009048 Genomic DNA. Translation: BAE78375.1.
X03046 Genomic DNA. Translation: CAA26854.1.

PIR

A54035.

RefSeq

AP_004874.1.
NP_418803.1.

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1X2G	X-ray	2.40	A/B/C	2-338	[»]
1X2H	X-ray	2.91	A/B/C	2-338	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:10119N.

IntAct

P32099. 3 interactions.

Genome annotation databases

GeneID

944865.

GenomeReviews

Gene locus JW4349 in contig AP009048_GR.
Gene locus b4386 in contig U00096_GR.

KEGG

ecj:JW4349.
eco:b4386.

Organism-specific databases

EchoBASE

EB1744.

EcoGene

EG11796. lplA.

CMR

Search...

Phylogenomic databases

HOGENOM

P32099.

OMA

P32099. YEQSHLE.

Enzyme and pathway databases

BioCyc

EcoCyc:EG11796-MON.
MetaCyc:EG11796-MON.

Family and domain databases

HAMAP

MF_01602.
[Tree]

InterPro

IPR004143. BPL_LipA_LipB.
IPR005107. CO_DH_flav_C.
IPR019491. Lipoate_protein_ligase_C.
IPR004562. LipoylTrfase_LipoateP_Ligase.
[Graphical view]

Gene3D

G3DSA:3.30.390.50. CO_DH_flav_C. 1 hit.

Pfam

PF03099. BPL_LipA_LipB. 1 hit.
PF10437. Lip_prot_lig_C. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00545. lipoyltrans. 1 hit.

ProtoNet

Search...

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Entry information

Entry name

LPLA_ECOLI

Accession

Primary (citable) accession number: P32099
Secondary accession number(s): Q2M5T1

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1993
Last sequence update:	January 23, 2007
Last modified:	June 16, 2009
This is version 84 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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

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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 and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Sites

Natural variations

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents