Pup deamidase/depupylase - Mycobacterium tuberculosis

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O33247 (DOP_MYCTU) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 69. History...

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

Documents (3) |

Third-party data

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

Names and origin

Protein names

Recommended name:
Pup deamidase/depupylase
EC=3.4.-.-
EC=3.5.1.-

Alternative name(s):
Deamidase of protein Pup

Gene names

Name:	dop
Synonyms:	pafD
Ordered Locus Names:	Rv2112c, MT2172

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	505 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Specifically catalyzes the deamidation of the C-terminal glutamine of the prokaryotic ubiquitin-like protein Pup to glutamate, thereby rendering Pup competent for conjugation. Also displays depupylase (DPUP) activity, removing conjugated Pup from target proteins; is thus involved in the recycling of Pup and may function similarly to deubiquitinases (DUBs) in eukaryotes to prevent or promote proteasomal degradation of certain proteins. Ref.3 Ref.4 Ref.5
Cofactor	ATP. ATP is required for the deamidation and depupylation reactions but is not hydrolyzed during the reactions. Ref.3 Ref.4
Pathway	Protein degradation; proteasomal pup-dependent pathway.
Subunit structure	Interacts with the prokaryotic ubiquitin-like protein Pup. Ref.3 Ref.5
Disruption phenotype	Disruption of dop abolishes pupylation. Cells lacking this gene also become hypersensitive to reactive nitrogen intermediates (RNI) and are severely attenuated for survival and growth in mice. They also cannot depupylate proteasome substrates. Ref.4 Ref.5
Sequence similarities	Belongs to the Pup ligase/Pup deamidase family. Pup deamidase subfamily.
Sequence caution	The sequence CAB10703.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Ontologies

Keywords
Biological process	Virulence
Ligand	ATP-binding Nucleotide-binding
Molecular function	Hydrolase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	modification-dependent protein catabolic process Inferred from direct assay PubMed 20798673. Source: MTBBASE pathogenesis Inferred from electronic annotation. Source: UniProtKB-KW proteasomal protein catabolic process Inferred from direct assay PubMed 20798673. Source: MTBBASE protein pupylation Inferred from direct assay Ref.3. Source: UniProtKB
Molecular_function	ATP binding Inferred from direct assay Ref.3. Source: UniProtKB hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides Inferred from direct assay Ref.3. Source: UniProtKB peptidase activity Inferred from direct assay PubMed 20798673. Source: MTBBASE
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 505

505

Pup deamidase/depupylase

PRO_0000383480

Regions

Nucleotide binding

6 – 10

ATP By similarity

Experimental info

Mutagenesis

E → A: Abolishes pupylation. Ref.5

Mutagenesis

E → A: Abolishes pupylation and depupylase activity. Ref.4 Ref.5

Mutagenesis

D → N: Abolishes pupylation. Ref.5

Mutagenesis

H → V: Abolishes pupylation. Ref.5

Mutagenesis

100

E → A: Abolishes pupylation. Ref.5

Mutagenesis

206

R → A: Abolishes pupylation. Ref.5

Mutagenesis

222

R → A: Abolishes pupylation. Ref.5

Sequences

Sequence

Length

Mass (Da)

Tools

O33247 [UniParc].

Last modified September 22, 2009. Version 2.
Checksum: 963CF8592FC182EB
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FASTA

505

55,179

        10         20         30         40         50         60 
MQRIIGTEVE YGISSPSDPT ANPILTSTQA VLAYAAAAGI QRAKRTRWDY EVESPLRDAR 

        70         80         90        100        110        120 
GFDLSRSAGP PPVVDADEVG AANMILTNGA RLYVDHAHPE YSAPECTDPL DAVIWDKAGE 

       130        140        150        160        170        180 
RVMEAAARHV ASVPGAAKLQ LYKNNVDGKG ASYGSHENYL MSRQTPFSAI ITGLTPFLVS 

       190        200        210        220        230        240 
RQVVTGSGRV GIGPSGDEPG FQLSQRSDYI EVEVGLETTL KRGIINTRDE PHADADRYRR 

       250        260        270        280        290        300 
LHVIIGDANL AETSTYLKLG TTALVLDLIE EGPAHAIDLT DLALARPVHA VHAISRDPSL 

       310        320        330        340        350        360 
RATVALADGR ELTGLALQRI YLDRVAKLVD SRDPDPRAAD IVETWAHVLD QLERDPMDCA 

       370        380        390        400        410        420 
ELLDWPAKLR LLDGFRQREN LSWSAPRLHL VDLQYSDVRL DKGLYNRLVA RGSMKRLVTE 

       430        440        450        460        470        480 
HQVLSAVENP PTDTRAYFRG ECLRRFGADI AAASWDSVIF DLGGDSLVRI PTLEPLRGSK 

       490        500 
AHVGALLDSV DSAVELVEQL TAEPR

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"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.
[2]	"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.
[3]	"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 AS PUP DEAMIDASE, CATALYTIC ACTIVITY, COFACTOR, INTERACTION WITH PUP, MASS SPECTROMETRY. Strain: ATCC 25618 / H37Rv.
[4]	"'Depupylation' of prokaryotic ubiquitin-like protein from mycobacterial proteasome substrates." Burns K.E., Cerda-Maira F.A., Wang T., Li H., Bishai W.R., Darwin K.H. Mol. Cell 39:821-827(2010) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION AS DEPUPYLASE, CATALYTIC ACTIVITY, COFACTOR, DISRUPTION PHENOTYPE, MUTAGENESIS OF GLU-10.
[5]	"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: FUNCTION IN PUP RECYCLING, ROLE IN PUPYLATION; RESISTANCE TO RNI AND VIRULENCE, DISRUPTION PHENOTYPE, INTERACTION WITH PUP, MUTAGENESIS OF GLU-8; GLU-10; ASP-95; HIS-96; GLU-100; ARG-206 AND ARG-222.

Cross-references

Sequence databases
EMBL GenBank DDBJ	BX842578 Genomic DNA. Translation: CAB10703.1. Different initiation. AE000516 Genomic DNA. Translation: AAK46455.1.
PIR	C70512.
RefSeq	NP_216628.1. NC_000962.3. NP_336641.1. NC_002755.2. YP_006515528.1. NC_018143.1.
3D structure databases
ProteinModelPortal	O33247.
SMR	O33247. Positions 1-501.
ModBase	Search...
Protein-protein interaction databases
STRING	83332.Rv2112c.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAK46455; AAK46455; MT2172.
GeneID	13316919. 888290. 924460.
KEGG	mtc:MT2172. mtu:Rv2112c. mtv:RVBD_2112c.
PATRIC	18126534. VBIMycTub22151_2380.
Organism-specific databases
TubercuList	Rv2112c.
Phylogenomic databases
eggNOG	NOG04176.
HOGENOM	HOG000264266.
KO	K13571.
OMA	LKRPIIN.
ProtClustDB	CLSK872004.
Enzyme and pathway databases
UniPathway	UPA00997.
Family and domain databases
InterPro	IPR022366. Pup_deamidase. IPR004347. Pup_ligase/deamidase. [Graphical view]
Pfam	PF03136. Pup_ligase. 1 hit. [Graphical view]
PIRSF	PIRSF018077. UCP018077. 1 hit.
TIGRFAMs	TIGR03688. pupylate_PafA2. 1 hit.
ProtoNet	Search...

Entry information

Entry name

DOP_MYCTU

Accession

Primary (citable) accession number: O33247
Secondary accession number(s): Q8VJQ0

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 22, 2009
Last sequence update:	September 22, 2009
Last modified:	May 1, 2013
This is version 69 of the entry and version 2 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

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents