Pup--protein ligase - Mycobacterium tuberculosis

Contribute

Send feedback

Read comments (?) or add your own

P64943 (PAFA_MYCTU) Reviewed, UniProtKB/Swiss-Prot

Last modified May 29, 2013. Version 52. History...

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

Documents (3) |

Third-party data

text xml rdf/xml gff fasta

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

Names and origin

Protein names

Recommended name:
Pup--protein ligase
EC=6.3.2.n2

Alternative name(s):
Proteasome accessory factor A
Pup-conjugating enzyme

Gene names

Name:	pafA
Synonyms:	paf
Ordered Locus Names:	Rv2097c, MT2158
ORF Names:	MTCY49.37c

Organism

Mycobacterium tuberculosis [Reference proteome] [HAMAP]

Taxonomic identifier

1773 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	452 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the covalent attachment of the prokaryotic ubiquitin-like protein modifier Pup to the proteasomal substrate proteins, thereby targeting them for proteasomal degradation. This tagging system is termed pupylation. The ligation reaction involves the side-chain carboxylate of the C-terminal glutamate of Pup and the side-chain amino group of a substrate lysine. PafA is required to confer resistance against the lethal effects of reactive nitrogen intermediates (RNI), antimicrobial molecules produced by activated macrophages and other cell types. Ref.4 Ref.5 Ref.7 Ref.8
Catalytic activity	ATP + [Pup] + [protein]-lysine = ADP + phosphate + [protein]-N-pupyllysine. Ref.7 Ref.8
Pathway	Protein degradation; proteasomal pup-dependent pathway. HAMAP-Rule MF_02111 Protein modification; protein pupylation. HAMAP-Rule MF_02111
Subunit structure	Interacts with the prokaryotic ubiquitin-like protein Pup. Ref.7
Disruption phenotype	Cells lacking this gene have no detectable pupylated proteins and substrate proteins accumulate. These cells also become hypersensitive to reactive nitrogen intermediates (RNI) and fail to grow in both wild-type and nitric oxide synthase 2 deficient macrophages. Moreover, they display increased resistance to hydrogen peroxide. Ref.4 Ref.6
Miscellaneous	The reaction mechanism probably proceeds via the activation of Pup by phosphorylation of its C-terminal glutamate, which is then subject to nucleophilic attack by the substrate lysine, resulting in an isopeptide bond and the release of phosphate as a good leaving group. HAMAP-Rule MF_02111
Sequence similarities	Belongs to the Pup ligase/Pup deamidase family. Pup-conjugating enzyme subfamily.

Ontologies

Keywords
Biological process	Ubl conjugation pathway Virulence
Ligand	ATP-binding Nucleotide-binding
Molecular function	Ligase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	cellular response to nitric oxide Inferred from mutant phenotype Ref.4. Source: UniProtKB modification-dependent protein catabolic process Inferred from mutant phenotype Ref.6. Source: UniProtKB pathogenesis Inferred from mutant phenotype Ref.4. Source: UniProtKB proteasomal protein catabolic process Inferred from mutant phenotype Ref.5 Ref.6. Source: UniProtKB protein pupylation Inferred from direct assay Ref.7. Source: UniProtKB response to nitrosative stress Inferred from mutant phenotype Ref.4. Source: MTBBASE
Cellular_component	cell wall Inferred from direct assay PubMed 15525680. Source: MTBBASE plasma membrane Inferred from direct assay PubMed 14532352 PubMed 15525680. Source: MTBBASE
Molecular_function	ATP binding Inferred from direct assay Ref.7 Ref.8. Source: UniProtKB small conjugating protein ligase activity Inferred from direct assay Ref.7 Ref.8. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 452

452

Pup--protein ligase HAMAP-Rule MF_02111

PRO_0000103966

Regions

Nucleotide binding

7 – 11

ATP By similarity

Experimental info

Mutagenesis

E → A: Abolishes pupylation. Ref.9

Mutagenesis

E → A: Abolishes pupylation. Ref.9

Mutagenesis

R → E: Abolishes pupylation. Ref.9

Mutagenesis

Y → K: Abolishes pupylation. Ref.9

Mutagenesis

D → N: Abolishes pupylation. Ref.9

Mutagenesis

E → A: Abolishes pupylation. Ref.9

Mutagenesis

123

H → A: Abolishes pupylation. Ref.9

Mutagenesis

171

R → A: Abolishes pupylation. Ref.9

Mutagenesis

187

R → A: Abolishes pupylation. Ref.9

Mutagenesis

207

H → E: Abolishes pupylation. Ref.9

Sequences

Sequence

Length

Mass (Da)

Tools

P64943 [UniParc].

Last modified October 11, 2004. Version 1.
Checksum: 12AF8B7872D2F5EA
Show »

FASTA

452

51,384

        10         20         30         40         50         60 
MQRRIMGIET EFGVTCTFHG HRRLSPDEVA RYLFRRVVSW GRSSNVFLRN GARLYLDVGS 

        70         80         90        100        110        120 
HPEYATAECD SLVQLVTHDR AGEWVLEDLL VDAEQRLADE GIGGDIYLFK NNTDSAGNSY 

       130        140        150        160        170        180 
GCHENYLIVR AGEFSRISDV LLPFLVTRQL ICGAGKVLQT PKAATYCLSQ RAEHIWEGVS 

       190        200        210        220        230        240 
SATTRSRPII NTRDEPHADA EKYRRLHVIV GDSNMSETTT MLKVGTAALV LEMIESGVAF 

       250        260        270        280        290        300 
RDFSLDNPIR AIREVSHDVT GRRPVRLAGG RQASALDIQR EYYTRAVEHL QTREPNAQIE 

       310        320        330        340        350        360 
QVVDLWGRQL DAVESQDFAK VDTEIDWVIK RKLFQRYQDR YDMELSHPKI AQLDLAYHDI 

       370        380        390        400        410        420 
KRGRGIFDLL QRKGLAARVT TDEEIAEAVD QPPQTTRARL RGEFISAAQE AGRDFTVDWV 

       430        440        450 
HLKLNDQAQR TVLCKDPFRA VDERVKRLIA SM

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Characterization of the proteasome accessory factor (paf) operon in Mycobacterium tuberculosis." Festa R.A., Pearce M.J., Darwin K.H. J. Bacteriol. 189:3044-3050(2007) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 25618 / H37Rv.
[2]	"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. Barrell B.G. Nature 393:537-544(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 25618 / H37Rv.
[3]	"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. Fraser C.M. J. Bacteriol. 184:5479-5490(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: CDC 1551 / Oshkosh.
[4]	"The proteasome of Mycobacterium tuberculosis is required for resistance to nitric oxide." Darwin K.H., Ehrt S., Gutierrez-Ramos J.-C., Weich N., Nathan C.F. Science 302:1963-1966(2003) [PubMed] [Europe PMC] [Abstract] Cited for: ROLE IN RESISTANCE TO RNI, DISRUPTION PHENOTYPE. Strain: ATCC 25618 / H37Rv.
[5]	"Identification of substrates of the Mycobacterium tuberculosis proteasome." Pearce M.J., Arora P., Festa R.A., Butler-Wu S.M., Gokhale R.S., Darwin K.H. EMBO J. 25:5423-5432(2006) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN THE PROTEASOME DEGRADATION PATHWAY. Strain: ATCC 25618 / H37Rv.
[6]	"Ubiquitin-like protein involved in the proteasome pathway of Mycobacterium tuberculosis." Pearce M.J., Mintseris J., Ferreyra J., Gygi S.P., Darwin K.H. Science 322:1104-1107(2008) [PubMed] [Europe PMC] [Abstract] Cited for: DISRUPTION PHENOTYPE. Strain: ATCC 25618 / H37Rv.
[7]	"Bacterial ubiquitin-like modifier Pup is deamidated and conjugated to substrates by distinct but homologous enzymes." Striebel F., Imkamp F., Sutter M., Steiner M., Mamedov A., Weber-Ban E. Nat. Struct. Mol. Biol. 16:647-651(2009) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY, INTERACTION WITH PUP, MASS SPECTROMETRY, REACTION MECHANISM. Strain: ATCC 25618 / H37Rv.
[8]	"Prokaryotic ubiquitin-like protein (Pup) is coupled to substrates via the side chain of its C-terminal glutamate." Sutter M., Damberger F.F., Imkamp F., Allain F.H., Weber-Ban E. J. Am. Chem. Soc. 132:5610-5612(2010) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY, LIGATION REACTION. Strain: ATCC 25618 / H37Rv.
[9]	"Molecular analysis of the prokaryotic ubiquitin-like protein (Pup) conjugation pathway in Mycobacterium tuberculosis." Cerda-Maira F.A., Pearce M.J., Fuortes M., Bishai W.R., Hubbard S.R., Darwin K.H. Mol. Microbiol. 77:1123-1135(2010) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF GLU-9; GLU-11; ARG-53; TYR-55; ASP-57; GLU-63; HIS-123; ARG-171; ARG-187 AND HIS-207.

Cross-references

Sequence databases
EMBL GenBank DDBJ	DQ990836 Genomic DNA. Translation: ABJ90140.1. AE000516 Genomic DNA. Translation: AAK46439.1. AL123456 Genomic DNA. Translation: CCP44872.1.
PIR	D70768.
RefSeq	NP_216613.1. NC_000962.3. NP_336625.1. NC_002755.2. YP_006515512.1. NC_018143.1.
3D structure databases
ProteinModelPortal	P64943.
SMR	P64943. Positions 1-452.
ModBase	Search...
Protein-protein interaction databases
STRING	83332.Rv2097c.
Proteomic databases
PRIDE	P64943.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAK46439; AAK46439; MT2158.
GeneID	13316903. 888460. 923121.
KEGG	mtc:MT2158. mtu:Rv2097c.
PATRIC	18126506. VBIMycTub22151_2366.
Organism-specific databases
TubercuList	Rv2097c.
Phylogenomic databases
eggNOG	NOG04175.
HOGENOM	HOG000264267.
KO	K13571.
OMA	HDKAGER.
ProtClustDB	CLSK872004.
Enzyme and pathway databases
UniPathway	UPA00997. UPA00998.
Family and domain databases
HAMAP	MF_02111. Pup_ligase.
InterPro	IPR022279. Pup_ligase. IPR004347. Pup_ligase/deamidase. [Graphical view]
Pfam	PF03136. Pup_ligase. 1 hit. [Graphical view]
PIRSF	PIRSF018077. UCP018077. 1 hit.
TIGRFAMs	TIGR03686. pupylate_PafA. 1 hit.
ProtoNet	Search...

Entry information

Entry name

PAFA_MYCTU

Accession

Primary (citable) accession number: P64943
Secondary accession number(s): A0A111, L0T8N5, Q10706

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 11, 2004
Last sequence update:	October 11, 2004
Last modified:	May 29, 2013
This is version 52 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

Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh

Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh: entries and gene names

PATHWAY comments

Index of metabolic and biosynthesis pathways

SIMILARITY comments

Index of protein domains and families

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

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Experimental info

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

Family and domain databases

Entry information

Relevant documents