Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

P64943 (PAFA_MYCTU) Reviewed, UniProtKB/Swiss-Prot

Last modified February 19, 2014. Version 56. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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
OrganismMycobacterium tuberculosis [Reference proteome] [HAMAP]
Taxonomic identifier1773 [NCBI]
Taxonomic lineageBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeMycobacteriaceaeMycobacteriumMycobacterium tuberculosis complex

Protein attributes

Sequence length452 AA.
Sequence statusComplete.
Protein existenceEvidence 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.

Sequence similarities

Belongs to the Pup ligase/Pup deamidase family. Pup-conjugating enzyme subfamily.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 452452Pup--protein ligase HAMAP-Rule MF_02111
PRO_0000103966

Sites

Active site571Proton acceptor By similarity
Metal binding91Magnesium By similarity
Metal binding551Magnesium By similarity
Metal binding631Magnesium By similarity
Binding site531ATP By similarity
Binding site661ATP; via carbonyl oxygen By similarity
Binding site4191ATP By similarity

Experimental info

Mutagenesis91E → A: Abolishes pupylation. Ref.9
Mutagenesis111E → A: Abolishes pupylation. Ref.9
Mutagenesis531R → E: Abolishes pupylation. Ref.9
Mutagenesis551Y → K: Abolishes pupylation. Ref.9
Mutagenesis571D → N: Abolishes pupylation. Ref.9
Mutagenesis631E → A: Abolishes pupylation. Ref.9
Mutagenesis1231H → A: Abolishes pupylation. Ref.9
Mutagenesis1711R → A: Abolishes pupylation. Ref.9
Mutagenesis1871R → A: Abolishes pupylation. Ref.9
Mutagenesis2071H → E: Abolishes pupylation. Ref.9

Sequences

Sequence LengthMass (Da)Tools
P64943 [UniParc].

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

FASTA45251,384
        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' 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. expand/collapse author list , 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] [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. expand/collapse author list , 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] [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.
PIRD70768.
RefSeqNP_216613.1. NC_000962.3.
NP_336625.1. NC_002755.2.
YP_006515512.1. NC_018143.2.

3D structure databases

ProteinModelPortalP64943.
SMRP64943. Positions 1-452.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING83332.Rv2097c.

Proteomic databases

PRIDEP64943.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAK46439; AAK46439; MT2158.
CCP44872; CCP44872; Rv2097c.
GeneID13316903.
888460.
923121.
KEGGmtc:MT2158.
mtu:Rv2097c.
mtv:RVBD_2097c.
PATRIC18126506. VBIMycTub22151_2366.

Organism-specific databases

TubercuListRv2097c.

Phylogenomic databases

eggNOGNOG04175.
HOGENOMHOG000264267.
KOK13571.
OMAHDKAGER.
OrthoDBEOG6PS5V6.
ProtClustDBCLSK872004.

Enzyme and pathway databases

BioCycMTBCDC:MT2158-MONOMER.
MTBRV:RV2097C-MONOMER.
UniPathwayUPA00997.
UPA00998.

Family and domain databases

HAMAPMF_02111. Pup_ligase.
InterProIPR022279. Pup_ligase.
IPR004347. Pup_ligase/deamidase.
[Graphical view]
PfamPF03136. Pup_ligase. 1 hit.
[Graphical view]
PIRSFPIRSF018077. UCP018077. 1 hit.
TIGRFAMsTIGR03686. pupylate_PafA. 1 hit.
ProtoNetSearch...

Entry information

Entry namePAFA_MYCTU
AccessionPrimary (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: February 19, 2014
This is version 56 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PATHWAY comments

Index of metabolic and biosynthesis pathways

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

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