O05594 (RPFB_MYCTU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Resuscitation-promoting factor RpfB
EC=3.-.-.-

Gene names

Name:	rpfB
Ordered Locus Names:	Rv1009, MT1038
ORF Names:	MTC1237.26

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

General annotation (Comments)

Function	Factor that stimulates resuscitation of dormant cells. Has peptidoglycan (PG) hydrolytic activity. Active in the pM concentration range. Has little to no effect on actively-growing cells. PG fragments could either directly activate the resuscitation pathway of dormant bacteria or serve as a substrate for endogenous Rpf, resulting in low molecular weight products with resuscitation activity. Ref.3 Ref.5 Ref.9 Ref.10 Reduces lag phase and enhances the growth of quiescent (1 month-old culture) M.tuberculosis; works best between 8 and 128 pM. Increases the number of bacteria that can be recovered from a 3 month-old culture. Stimulates growth of stationary phase M.bovis (a slowly-growing Mycobacterium) as well as M.smegmatis cells (a fast grower). Binds N,N',N''-triacetylchitotriose (tri-NAG). A fragment (residues 194-362) hydrolyzes an artificial lysozyme substrate 4-methylumbelliferyl-beta-D-N,N',N''-triacetylchitotrioside (MUF tri-NAG). By itself has little activity on cell wall, in combination with RipA is active against cell wall extracts from a number of Actinobacteria; this activity is inhibited by PBP1A (ponA1). Sequential gene disruption indicates RpfB and RpfE are higher than RpfD and RpfC in functional hierarchy. Ref.3 Ref.5 Ref.9 Ref.10
Enzyme regulation	Activity on the artifical substrate MUF tri-NAG is inhibited by 2-nitrophenylthiocyanates (NPT) compounds. The synergistic effects on peptidoglycan degradation of RipA plus RpfB are inhibited by addition of PBP1A (ponA1). Ref.10 Ref.12
Subunit structure	Monomer Probable. Interacts with RipA. Ref.7 Ref.15
Subcellular location	Cell membrane; Lipid-anchor Potential. Note: Localizes to the septa upon expression in M.smegmatis. Ref.7
Induction	Expressed in actively growing cells. Ref.3 Ref.10 Ref.12
Domain	An expressed fragment (residues 194-362) hydrolyzes an artificial lysozyme substrate 4-methylumbelliferyl-beta-D-N,N',N''-triacetylchitotrioside (MUF tri-NAG).
Disruption phenotype	Not essential, disruption of rpfB alone has no effect on growth or survival in liquid culture, nor in mouse infection models, colonies plated over a 52-week culture period are visibly drier and more friable. Alterations in gene expression are seen. All 5 genes in this family can be deleted without affecting growth in culture, however triple deletion mutants (rpfA-rpfC-rpfB or rpfA-rpfC-rpfD) are not able to resuscitate spontaneously in the presence or absence of O2, and are attenuated in a mouse infection model. Ref.6 Ref.8
Biotechnological use	A promising vaccine candidate, an rpfB-encoding DNA vaccine induces elevated cellular immune responses, confers modest but significant protection against intra-tracheal tuberculosis challenge in female C57BL/6 and BALB/c mice. Ref.4 Ref.13
Miscellaneous	Was identified as a high-confidence drug target.
Sequence similarities	Belongs to the transglycosylase family. Rpf subfamily. Contains 1 G5 domain.

Ontologies

Keywords
Biological process	Virulence
Cellular component	Cell membrane Membrane
Domain	Signal
Molecular function	Hydrolase
PTM	Disulfide bond Lipoprotein Palmitate
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	dormancy exit of symbiont in host Inferred from mutant phenotype PubMed 16622237. Source: MTBBASE negative regulation of gene expression Inferred from direct assay Ref.6. Source: MTBBASE pathogenesis Inferred from electronic annotation. Source: UniProtKB-KW positive regulation of gene expression Inferred from direct assay Ref.6. Source: MTBBASE positive regulation of growth rate Inferred from direct assay Ref.3. Source: MTBBASE
Cellular_component	extracellular region Inferred from direct assay Ref.3PubMed 21148733. Source: MTBBASE plasma membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	hydrolase activity Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 23

23

Potential

Chain

24 – 362

339

Resuscitation-promoting factor RpfB

PRO_0000421026

Regions

Domain

192 – 272

81

G5

Amino acid modifications

Lipidation

24

1

N-palmitoyl cysteine Potential

Lipidation

24

1

S-diacylglycerol cysteine Potential

Disulfide bond

291 ↔ 355

Ref.14 Ref.15

Secondary structure

1

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362

Helix Strand Turn

Details...

Beta strand

196 – 206

11

Beta strand

210 – 215

6

Beta strand

223 – 227

5

Beta strand

232 – 243

12

Beta strand

246 – 259

14

Beta strand

264 – 269

6

Helix

284 – 293

10

Beta strand

302 – 304

3

Turn

307 – 310

4

Helix

313 – 318

6

Helix

321 – 323

3

Helix

328 – 330

3

Helix

333 – 347

15

Helix

349 – 351

3

Helix

355 – 358

4

Sequences

	Sequence		Length	Mass (Da)
	O05594 [UniParc]. Last modified July 1, 1997. Version 1. Checksum: 02B55D8C70373D10	FASTA	362	38,078
	10 20 30 40 50 60 MLRLVVGALL LVLAFAGGYA VAACKTVTLT VDGTAMRVTT MKSRVIDIVE ENGFSVDDRD 70 80 90 100 110 120 DLYPAAGVQV HDADTIVLRR SRPLQISLDG HDAKQVWTTA STVDEALAQL AMTDTAPAAA 130 140 150 160 170 180 SRASRVPLSG MALPVVSAKT VQLNDGGLVR TVHLPAPNVA GLLSAAGVPL LQSDHVVPAA 190 200 210 220 230 240 TAPIVEGMQI QVTRNRIKKV TERLPLPPNA RRVEDPEMNM SREVVEDPGV PGTQDVTFAV 250 260 270 280 290 300 AEVNGVETGR LPVANVVVTP AHEAVVRVGT KPGTEVPPVI DGSIWDAIAG CEAGGNWAIN 310 320 330 340 350 360 TGNGYYGGVQ FDQGTWEANG GLRYAPRADL ATREEQIAVA EVTRLRQGWG AWPVCAARAG AR

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. , 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.
[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. , 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.
[3]	"A family of autocrine growth factors in Mycobacterium tuberculosis." Mukamolova G.V., Turapov O.A., Young D.I., Kaprelyants A.S., Kell D.B., Young M. Mol. Microbiol. 46:623-635(2002) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INDUCTION. Strain: ATCC 25618 / H37Rv.
[4]	"Proteins of the Rpf family: immune cell reactivity and vaccination efficacy against tuberculosis in mice." Yeremeev V.V., Kondratieva T.K., Rubakova E.I., Petrovskaya S.N., Kazarian K.A., Telkov M.V., Biketov S.F., Kaprelyants A.S., Apt A.S. Infect. Immun. 71:4789-4794(2003) [PubMed] [Europe PMC] [Abstract] Cited for: BIOTECHNOLOGY. Strain: ATCC 25618 / H37Rv.
[5]	"Resuscitation factors from mycobacteria: homologs of Micrococcus luteus proteins." Zhu W., Plikaytis B.B., Shinnick T.M. Tuberculosis 83:261-269(2003) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION. Strain: ATCC 25618 / H37Rv.
[6]	"Global expression profiling of strains harbouring null mutations reveals that the five rpf-like genes of Mycobacterium tuberculosis show functional redundancy." Downing K.J., Betts J.C., Young D.I., McAdam R.A., Kelly F., Young M., Mizrahi V. Tuberculosis 84:167-179(2004) [PubMed] [Europe PMC] [Abstract] Cited for: DISRUPTION PHENOTYPE. Strain: ATCC 25618 / H37Rv.
[7]	"A partner for the resuscitation-promoting factors of Mycobacterium tuberculosis." Hett E.C., Chao M.C., Steyn A.J., Fortune S.M., Deng L.L., Rubin E.J. Mol. Microbiol. 66:658-668(2007) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH RIPA, SUBCELLULAR LOCATION. Strain: ATCC 25618 / H37Rv.
[8]	"The resuscitation-promoting factors of Mycobacterium tuberculosis are required for virulence and resuscitation from dormancy but are collectively dispensable for growth in vitro." Kana B.D., Gordhan B.G., Downing K.J., Sung N., Vostroktunova G., Machowski E.E., Tsenova L., Young M., Kaprelyants A., Kaplan G., Mizrahi V. Mol. Microbiol. 67:672-684(2008) [PubMed] [Europe PMC] [Abstract] Cited for: DISRUPTION PHENOTYPE. Strain: ATCC 25618 / H37Rv.
[9]	"A mycobacterial enzyme essential for cell division synergizes with resuscitation-promoting factor." Hett E.C., Chao M.C., Deng L.L., Rubin E.J. PLoS Pathog. 4:E1000001-E1000001(2008) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN CELL DIVISION. Strain: ATCC 25618 / H37Rv.
[10]	"Finding of the low molecular weight inhibitors of resuscitation promoting factor enzymatic and resuscitation activity." Demina G.R., Makarov V.A., Nikitushkin V.D., Ryabova O.B., Vostroknutova G.N., Salina E.G., Shleeva M.O., Goncharenko A.V., Kaprelyants A.S. PLoS ONE 4:E8174-E8174(2009) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION AS A MURALYTIC ENZYME, ENZYME REGULATION. Strain: ATCC 25618 / H37Rv.
[11]	"targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis." Raman K., Yeturu K., Chandra N. BMC Syst. Biol. 2:109-109(2008) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION AS A DRUG TARGET [LARGE SCALE ANALYSIS].
[12]	"Interaction and modulation of two antagonistic cell wall enzymes of mycobacteria." Hett E.C., Chao M.C., Rubin E.J. PLoS Pathog. 6:E1001020-E1001020(2010) [PubMed] [Europe PMC] [Abstract] Cited for: ENZYME REGULATION. Strain: ATCC 25618 / H37Rv.
[13]	"Potential of Mycobacterium tuberculosis resuscitation-promoting factors as antigens in novel tuberculosis sub-unit vaccines." Romano M., Aryan E., Korf H., Bruffaerts N., Franken C.L., Ottenhoff T.H., Huygen K. Microbes Infect. 14:86-95(2012) [PubMed] [Europe PMC] [Abstract] Cited for: BIOTECHNOLOGY. Strain: ATCC 25618 / H37Rv.
[14]	"The structure of a resuscitation-promoting factor domain from Mycobacterium tuberculosis shows homology to lysozymes." Cohen-Gonsaud M., Barthe P., Bagneris C., Henderson B., Ward J., Roumestand C., Keep N.H. Nat. Struct. Mol. Biol. 12:270-273(2005) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR OF 255-362, DISULFIDE BOND, BINDING TO TRI-NAG. Strain: ATCC 25618 / H37Rv.
[15]	"Crystal structure of the resuscitation-promoting factor (DeltaDUF)RpfB from M. tuberculosis." Ruggiero A., Tizzano B., Pedone E., Pedone C., Wilmanns M., Berisio R. J. Mol. Biol. 385:153-162(2009) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.83 ANGSTROMS) OF 194-362, SUBUNIT, DISULFIDE BOND. Strain: ATCC 25618 / H37Rv.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AE000516 Genomic DNA. Translation: AAK45288.1.
AL123456 Genomic DNA. Translation: CCP43759.1.

PIR

D70603.

RefSeq

NP_215525.1. NC_000962.3.
NP_335474.1. NC_002755.2.
YP_006514370.1. NC_018143.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1XSF	NMR	-	A	255-362	[»]
3EO5	X-ray	1.83	A	194-362	[»]
4EMN	X-ray	1.17	A/B/C/D	282-362	[»]

ProteinModelPortal

O05594.

SMR

O05594. Positions 194-362.

ModBase

Search...

Protein-protein interaction databases

STRING

83332.Rv1009.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAK45288; AAK45288; MT1038.

GeneID

13319571.
886048.
925164.

KEGG

mtc:MT1038.
mtu:Rv1009.

PATRIC

18124026. VBIMycTub22151_1135.

Organism-specific databases

TubercuList

Rv1009.

Phylogenomic databases

HOGENOM

HOG000241450.

OMA

QNTWERQ.

ProtClustDB

CLSK790891.

Family and domain databases

InterPro

IPR007137. DUF348.
IPR011098. G5_dom.
IPR010618. Transglycosylas.
[Graphical view]

Pfam

PF03990. DUF348. 3 hits.
PF07501. G5. 1 hit.
PF06737. Transglycosylas. 1 hit.
[Graphical view]

PROSITE

PS51109. G5. 1 hit.
PS51257. PROKAR_LIPOPROTEIN. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

O05594.

Entry information

Entry name

RPFB_MYCTU

Accession

Primary (citable) accession number: O05594
Secondary accession number(s): F2GHD1, L0T719, Q7D900

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 6, 2013
Last sequence update:	July 1, 1997
Last modified:	May 29, 2013
This is version 84 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program