P63345 (ARC_MYCTU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Proteasome-associated ATPase

Alternative name(s):
AAA ATPase forming ring-shaped complexes
Short name=ARC
Mycobacterial proteasome ATPase

Gene names

Name:	mpa
Ordered Locus Names:	Rv2115c, MT2175
ORF Names:	MTCY261.11c

Organism

Mycobacterium tuberculosis [Reference proteome] [HAMAP]

Taxonomic identifier

1773 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	609 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	ATPase which is responsible for recognizing, binding, unfolding and translocation of pupylated proteins into the bacterial 20S proteasome core particle. May be essential for opening the gate of the 20S proteasome via an interaction with its C-terminus, thereby allowing substrate entry and access to the site of proteolysis. Thus, the C-termini of the proteasomal ATPase may function like a 'key in a lock' to induce gate opening and therefore regulate proteolysis. Is required but not sufficient to confer resistance against the lethal effects of reactive nitrogen intermediates (RNI), antimicrobial molecules produced by activated macrophages and other cell types. Ref.1 Ref.4 Ref.6 Ref.13 Ref.15
Enzyme regulation	ATPase activity is inhibited by EDTA, N-ethylmaleimide (NEM) and sodium azide. Ref.1
Pathway	Protein degradation; proteasomal pup-dependent pathway. Ref.13
Subunit structure	Homohexamer. Assembles into a hexameric ring structure that caps the 20S proteasome core. Strongly interacts with the prokaryotic ubiquitin-like protein Pup through a hydrophobic interface; the interacting region of Mpa lies in its N-terminal coiled-coil domain. There is one Pup binding site per Mpa hexamer ring; the K(D) measured is about 3.8 µM. Upon ATP-binding, the C-terminus of Mpa interacts with the alpha-rings of the proteasome core, possibly by binding to the intersubunit pockets. Ref.1 Ref.8 Ref.9 Ref.10 Ref.11 Ref.12 Ref.15
Domain	Consists of three main regions, an N-terminal coiled-coil domain (residues 1-96) that binds to protein Pup and functions as a docking station, an interdomain (residues 97-245) involved in Mpa hexamerization, and a C-terminal ATPase domain of the AAA type (residues 246-609). Ref.10 Ref.13 Ref.15
Post-translational modification	Pupylated at Lys-591 by the prokaryotic ubiquitin-like protein Pup, which leads to its degradation by the proteasome. Mpa thus promotes its own turnover. Ref.14 Mpa is a target of RNI, thereby is S-nitrosylated in the phagosome of immunologically activated host macrophages, which causes enzyme inhibition. HAMAP-Rule MF_02112
Disruption phenotype	Cells lacking this gene accumulate pupylated proteins. These cells also become hypersensitive to reactive nitrogen intermediates (RNI) and are severely attenuated in both wild-type and nitric oxide synthase 2 deficient mice. Moreover, they display increased resistance to hydrogen peroxide. They also show a reduction in the in vivo growth rate, but still persist in mouse lungs, and elicit reduced levels of interferon-gamma production in the lungs. Expression of the genes lat and MT3159 are highly up-regulated. Ref.4 Ref.7 Ref.8
Biotechnological use	When used as an immunizing agent, the mpa deletion mutant provides significant protection against challenge with a virulent strain of M.tuberculosis. It shows interesting properties as a live attenuated vaccine for tuberculosis and could play a role in generating a safe and effective M.tuberculosis-derived vaccine. Ref.7
Miscellaneous	Was identified as a natural substrate of the M.tuberculosis proteasome. HAMAP-Rule MF_02112
Sequence similarities	Belongs to the AAA ATPase family.
Biophysicochemical properties	Kinetic parameters: KM=330 µM for ATP Ref.1 Vmax=62 pmol/min/µg enzyme pH dependence: Optimum pH is 7.4-7.5.

Ontologies

Keywords
Biological process	Virulence
Cellular component	Proteasome
Domain	Coiled coil
Ligand	ATP-binding Nucleotide-binding
Molecular function	Chaperone
PTM	Isopeptide bond S-nitrosylation Ubl conjugation
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	cellular response to nitric oxide Inferred from mutant phenotype Ref.4Ref.6. Source: UniProtKB modification-dependent protein catabolic process Inferred from direct assay Ref.13. Source: UniProtKB pathogenesis Inferred from mutant phenotype Ref.4Ref.1Ref.6. Source: UniProtKB proteasomal ubiquitin-independent protein catabolic process Inferred from direct assay Ref.15. Source: MTBBASE protein homooligomerization Inferred from physical interaction Ref.1. Source: MTBBASE protein unfolding Inferred from direct assay Ref.13. Source: UniProtKB response to nitrosative stress Inferred from mutant phenotype Ref.4Ref.1. Source: MTBBASE
Cellular_component	cell wall Inferred from direct assay PubMed 20825248. Source: MTBBASE plasma membrane Inferred from direct assay PubMed 14532352PubMed 15525680. Source: MTBBASE proteasome-activating nucleotidase complex Inferred from direct assay Ref.15Ref.13. Source: UniProtKB
Molecular_function	ATP binding Inferred from electronic annotation. Source: HAMAP ATPase activity Inferred from direct assay Ref.1Ref.13. Source: UniProtKB small conjugating protein binding Inferred from direct assay Ref.8Ref.12. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 609

609

Proteasome-associated ATPase HAMAP-Rule MF_02112

PRO_0000084778

Regions

Nucleotide binding

296 – 301

6

ATP By similarity

Region

608 – 609

2

Docks into pockets in the proteasome alpha-ring By similarity

Coiled coil

20 – 96

77

Potential

Amino acid modifications

Cross-link

591

Isoglutamyl lysine isopeptide (Lys-Gln) (interchain with Q-Cter in protein Pup) HAMAP-Rule MF_02112

Experimental info

Mutagenesis

120

1

R → A: Does not dramatically affects proteasome substrate degradation. Ref.15

Mutagenesis

173

1

R → E: Impairs Mpa hexamerization; when associated with A-187 and E-235. Ref.15

Mutagenesis

187

1

W → A: Impairs Mpa hexamerization; when associated with E-173 and E-235. Ref.15

Mutagenesis

225

1

K → A: Does not dramatically affects proteasome substrate degradation. Ref.15

Mutagenesis

235

1

K → E: Impairs Mpa hexamerization; when associated with E-173 and A-187. Ref.15

Mutagenesis

299

1

K → Q: Reduces both ATPase activity and ATP affinity. Abolishes proteasome substrate degradation and protection against RNI. Ref.1 Ref.15

Mutagenesis

341

1

F → A: Abolishes unfolding capacity. Ref.13

Mutagenesis

341

1

F → Y: No effect on unfolding capacity. Ref.13

Mutagenesis

342

1

V → A: Abolishes proteasome substrate degradation. Ref.15

Mutagenesis

371

1

D → A: Severely reduces ATPase activity. Abolishes proteasome substrate degradation and protection against RNI. Ref.1 Ref.15

Mutagenesis

372

1

E → A: Severely reduces ATPase activity. Abolishes protection against RNI. Ref.1

Mutagenesis

372

1

E → Q: Abolishes protection against RNI. Ref.1

Mutagenesis

608 – 609

2

Missing: Retains ATPase and unfolding activities, yet abolishes proteasome substrate degradation and protection against RNI. Is also highly attenuated in mice. Ref.6 Ref.15

Mutagenesis

608

1

Y → E or F: Abolishes proteasome substrate degradation and protection against RNI. Ref.6 Ref.15

Secondary structure

1

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609

Helix Strand Turn

Details...

Helix

53 – 94

42

Beta strand

99 – 107

9

Beta strand

109 – 117

9

Beta strand

120 – 126

7

Beta strand

140 – 143

4

Beta strand

149 – 152

4

Beta strand

158 – 167

10

Beta strand

171 – 177

7

Beta strand

183 – 188

6

Helix

190 – 193

4

Helix

203 – 205

3

Beta strand

219 – 223

5

Turn

224 – 227

4

Beta strand

228 – 233

6

Helix

238 – 245

8

Sequences

	Sequence		Length	Mass (Da)
	P63345 [UniParc]. Last modified October 11, 2004. Version 1. Checksum: 4D5F4E630614C58D	FASTA	609	67,401
	10 20 30 40 50 60 MGESERSEAF GIPRDSPLSS GDAAELEQLR REAAVLREQL ENAVGSHAPT RSARDIHQLE 70 80 90 100 110 120 ARIDSLAARN SKLMETLKEA RQQLLALREE VDRLGQPPSG YGVLLATHDD DTVDVFTSGR 130 140 150 160 170 180 KMRLTCSPNI DAASLKKGQT VRLNEALTVV EAGTFEAVGE ISTLREILAD GHRALVVGHA 190 200 210 220 230 240 DEERVVWLAD PLIAEDLPDG LPEALNDDTR PRKLRPGDSL LVDTKAGYAF ERIPKAEVED 250 260 270 280 290 300 LVLEEVPDVS YADIGGLSRQ IEQIRDAVEL PFLHKELYRE YSLRPPKGVL LYGPPGCGKT 310 320 330 340 350 360 LIAKAVANSL AKKMAEVRGD DAHEAKSYFL NIKGPELLNK FVGETERHIR LIFQRAREKA 370 380 390 400 410 420 SEGTPVIVFF DEMDSIFRTR GTGVSSDVET TVVPQLLSEI DGVEGLENVI VIGASNREDM 430 440 450 460 470 480 IDPAILRPGR LDVKIKIERP DAEAAQDIYS KYLTEFLPVH ADDLAEFDGD RSACIKAMIE 490 500 510 520 530 540 KVVDRMYAEI DDNRFLEVTY ANGDKEVMYF KDFNSGAMIQ NVVDRAKKNA IKSVLETGQP 550 560 570 580 590 600 GLRIQHLLDS IVDEFAENED LPNTTNPDDW ARISGKKGER IVYIRTLVTG KSSSASRAID TESNLGQYL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Characterization of a Mycobacterium tuberculosis proteasomal ATPase homologue." Darwin K.H., Lin G., Chen Z., Li H., Nathan C.F. Mol. Microbiol. 55:561-571(2005) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION AS AN ATPASE, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, SUBUNIT, MUTAGENESIS OF LYS-299; ASP-371; GLU-372 AND 608-TYR-GLU-609. 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. , 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. , 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: GENE NAME, ROLE IN RESISTANCE TO RNI, DISRUPTION PHENOTYPE. Strain: ATCC 25618 / H37Rv.
[5]	"S-nitroso proteome of Mycobacterium tuberculosis: enzymes of intermediary metabolism and antioxidant defense." Rhee K.Y., Erdjument-Bromage H., Tempst P., Nathan C.F. Proc. Natl. Acad. Sci. U.S.A. 102:467-472(2005) [PubMed] [Europe PMC] [Abstract] Cited for: TARGET OF RNI, S-NITROSYLATION. Strain: ATCC 25618 / H37Rv.
[6]	"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, REGULATION OF MPA LEVELS, PROTEASOME SUBSTRATE, MUTAGENESIS OF TYR-608 AND 608-TYR-GLU-609. Strain: ATCC 25618 / H37Rv.
[7]	"Deletion of a Mycobacterium tuberculosis proteasomal ATPase homologue gene produces a slow-growing strain that persists in host tissues." Lamichhane G., Raghunand T.R., Morrison N.E., Woolwine S.C., Tyagi S., Kandavelou K., Bishai W.R. J. Infect. Dis. 194:1233-1240(2006) [PubMed] [Europe PMC] [Abstract] Cited for: BIOTECHNOLOGY, DISRUPTION PHENOTYPE. Strain: CDC 1551 / Oshkosh.
[8]	"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: INTERACTION WITH PUP, DISRUPTION PHENOTYPE. Strain: ATCC 25618 / H37Rv.
[9]	"Pup, a prokaryotic ubiquitin-like protein, is an intrinsically disordered protein." Liao S., Shang Q., Zhang X., Zhang J., Xu C., Tu X. Biochem. J. 422:207-215(2009) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH PUP.
[10]	"A distinct structural region of the prokaryotic ubiquitin-like protein (Pup) is recognized by the N-terminal domain of the proteasomal ATPase Mpa." Sutter M., Striebel F., Damberger F.F., Allain F.H., Weber-Ban E. FEBS Lett. 583:3151-3157(2009) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH PUP, STOICHIOMETRY OF THE PUP-MPA COMPLEX, DOMAIN. Strain: ATCC 25618 / H37Rv.
[11]	"Prokaryotic ubiquitin-like protein Pup is intrinsically disordered." Chen X., Solomon W.C., Kang Y., Cerda-Maira F., Darwin K.H., Walters K.J. J. Mol. Biol. 392:208-217(2009) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH PUP, STOICHIOMETRY OF THE PUP-MPA COMPLEX.
[12]	"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: INTERACTION WITH PUP, MASS SPECTROMETRY. Strain: ATCC 25618 / H37Rv.
[13]	"The mycobacterial Mpa-proteasome unfolds and degrades pupylated substrates by engaging Pup's N-terminus." Striebel F., Hunkeler M., Summer H., Weber-Ban E. EMBO J. 29:1262-1271(2010) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION AS UNFOLDASE AND TRANSLOCASE, DOMAIN, MUTAGENESIS OF PHE-341 AND 608-TYR-GLU-609, RECONSTITUTION OF THE PROTEASOME DEGRADATION PATHWAY. Strain: ATCC 25618 / H37Rv.
[14]	"Prokayrotic ubiquitin-like protein (Pup) proteome of Mycobacterium tuberculosis." Festa R.A., McAllister F., Pearce M.J., Mintseris J., Burns K.E., Gygi S.P., Darwin K.H. PLoS ONE 5:E8589-E8589(2010) [PubMed] [Europe PMC] [Abstract] Cited for: PUPYLATION AT LYS-591, IDENTIFICATION BY MASS SPECTROMETRY. Strain: ATCC 25618 / H37Rv.
[15]	"Structural insights on the Mycobacterium tuberculosis proteasomal ATPase Mpa." Wang T., Li H., Lin G., Tang C., Li D., Nathan C., Darwin K.H., Li H. Structure 17:1377-1385(2009) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 98-245, FUNCTION, INTERACTION WITH PROTEASOME, DOMAIN, MUTAGENESIS OF ARG-120; ARG-173; TRP-187; LYS-225; LYS-235; LYS-299; VAL-342; ASP-371 AND TYR-608. Strain: ATCC 25618 / H37Rv.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

DQ888314 Genomic DNA. Translation: ABI36485.1.
BX842578 Genomic DNA. Translation: CAB10706.1.
AE000516 Genomic DNA. Translation: AAK46458.1.
AL123456 Genomic DNA. Translation: CCP44890.1.

PIR

F70512.

RefSeq

NP_216631.1. NC_000962.3.
NP_336644.1. NC_002755.2.
YP_006515531.1. NC_018143.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3FP9	X-ray	2.00	A/B/C/D/E/F/G/H/I/J/K/L	98-245	[»]
3M91	X-ray	1.80	A/C	46-96	[»]
3M9B	X-ray	3.94	A/B/C/D/E/F/G/H/I/J/K/L	1-234	[»]
3M9D	X-ray	4.50	A/B/C/D/E/F/J/K/L/M/N/O	1-234	[»]
3M9H	X-ray	2.00	A/B/C/D/E/F	46-96	[»]

ProteinModelPortal

P63345.

SMR

P63345. Positions 52-234, 243-605.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-48292N.

MINT

MINT-7262409.

STRING

83332.Rv2115c.

Proteomic databases

PRIDE

P63345.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAK46458; AAK46458; MT2175.

GeneID

13316922.
887297.
923659.

KEGG

mtc:MT2175.
mtu:Rv2115c.
mtv:RVBD_2115c.

PATRIC

18126540. VBIMycTub22151_2383.

Organism-specific databases

TubercuList

Rv2115c.

Phylogenomic databases

eggNOG

COG0464.

HOGENOM

HOG000245286.

KO

K13527.

OMA

VFFDEME.

ProtClustDB

CLSK872012.

Enzyme and pathway databases

UniPathway

UPA00997.

Family and domain databases

HAMAP

MF_02112. ARC_ATPase.

InterPro

IPR003593. AAA+_ATPase.
IPR003959. ATPase_AAA_core.
IPR003960. ATPase_AAA_CS.
IPR022482. Proteasome_ATPase.
[Graphical view]

PANTHER

PTHR23073:SF4. PTHR23073:SF4. 1 hit.

Pfam

PF00004. AAA. 1 hit.
[Graphical view]

SMART

SM00382. AAA. 1 hit.
[Graphical view]

TIGRFAMs

TIGR03689. pup_AAA. 1 hit.

PROSITE

PS00674. AAA. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P63345.

Entry information

Entry name

ARC_MYCTU

Accession

Primary (citable) accession number: P63345
Secondary accession number(s): L0T8W3, O33250, Q0G9Y7

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 11, 2004
Last sequence update:	October 11, 2004
Last modified:	May 1, 2013
This is version 58 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program