O05594 (RPFB_MYCTU) Reviewed, UniProtKB/Swiss-Prot
Last modified
May 29, 2013.
Version 84.
History...
Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order
Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize orderNames and origin
| Protein names | Recommended name: Resuscitation-promoting factor RpfB EC=3.-.-.- | ||||||
| Gene names |
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| 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 | 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 | |
| Subcellular location | Cell membrane; Lipid-anchor Potential. Note: Localizes to the septa upon expression in M.smegmatis. Ref.7 |
| Induction | |
| 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 expressionInferred from direct assay Ref.6. Source: MTBBASE pathogenesisInferred from electronic annotation. Source: UniProtKB-KW positive regulation of gene expressionInferred from direct assay Ref.6. Source: MTBBASE positive regulation of growth rateInferred from direct assay Ref.3. Source: MTBBASE |
| Cellular_component | extracellular region Inferred from direct assay Ref.3PubMed 21148733. Source: MTBBASE plasma membraneInferred 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 | |||||||||||||||||||||||||||||||||||||||
Helix Strand Turn | |||||||||||||||||||||||||||||||||||||||
| 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
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References
| « Hide '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] | "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 |
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| 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 |
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| 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 |
| PDB cross-references Index of Protein Data Bank (PDB) cross-references |
| SIMILARITY comments Index of protein domains and families |

Clusters with
