5e27

From Proteopedia

(Difference between revisions)

Current revision

The structure of Resuscitation Promoting Factor B from M. tuberculosis reveals unexpected ubiquitin-like domains

Structural highlights

5e27 is a 2 chain structure with sequence from Mycobacterium tuberculosis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.6Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RPFB_MYCTU 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.^[1] ^[2] ^[3] ^[4] 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.^[5] ^[6] ^[7] ^[8]

Publication Abstract from PubMed

BACKGROUND: RpfB is a key factor in resuscitation from dormancy of Mycobacterium tuberculosis. This protein is a cell-wall glycosidase, which cleaves cell-wall peptidoglycan. RpfB is structurally complex and is composed of three types of domains, including a catalytic, a G5 and three DUF348 domains. Structural information is currently limited to a portion of the protein including only the catalytic and G5 domains. To gain insights into the structure and function of all domains we have undertaken structural investigations on a large protein fragment containing all three types of domains that constitute RpfB (RpfB3D). METHODS: The structural features of RpfB3D have been investigated combining x-ray crystallography and biophysical studies. RESULTS AND CONCLUSIONS: The crystal structure of RpfB3D provides the first structural characterization of a DUF348 domain and revealed an unexpected structural relationship with ubiquitin. The crystal structure also provides specific structural features of these domains explaining their frequent association with G5 domains. GENERAL SIGNIFICANCE: Results provided novel insights into the mechanism of peptidoglycan degradation necessary to the resuscitation of M. tuberculosis. Features of the DUF348 domain add structural data to a large set of proteins embedding this domain. Based on its structural similarity to ubiquitin and frequent association to the G5 domain, we propose to name this domain as G5-linked-Ubiquitin-like domain, UBLG5.

The structure of Resuscitation promoting factor B from M. tuberculosis reveals unexpected ubiquitin-like domains.,Ruggiero A, Squeglia F, Romano M, Vitagliano L, De Simone A, Berisio R Biochim Biophys Acta. 2015 Nov 5. pii: S0304-4165(15)00300-1. doi:, 10.1016/j.bbagen.2015.11.001. PMID:26549874^[9]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Mukamolova GV, Turapov OA, Young DI, Kaprelyants AS, Kell DB, Young M. A family of autocrine growth factors in Mycobacterium tuberculosis. Mol Microbiol. 2002 Nov;46(3):623-35. PMID:12410821
↑ Zhu W, Plikaytis BB, Shinnick TM. Resuscitation factors from mycobacteria: homologs of Micrococcus luteus proteins. Tuberculosis (Edinb). 2003;83(4):261-9. PMID:12906837
↑ Hett EC, Chao MC, Deng LL, Rubin EJ. A mycobacterial enzyme essential for cell division synergizes with resuscitation-promoting factor. PLoS Pathog. 2008 Feb 29;4(2):e1000001. doi: 10.1371/journal.ppat.1000001. PMID:18463693 doi:10.1371/journal.ppat.1000001
↑ Demina GR, Makarov VA, Nikitushkin VD, Ryabova OB, Vostroknutova GN, Salina EG, Shleeva MO, Goncharenko AV, Kaprelyants AS. Finding of the low molecular weight inhibitors of resuscitation promoting factor enzymatic and resuscitation activity. PLoS One. 2009 Dec 16;4(12):e8174. doi: 10.1371/journal.pone.0008174. PMID:20016836 doi:10.1371/journal.pone.0008174
↑ Mukamolova GV, Turapov OA, Young DI, Kaprelyants AS, Kell DB, Young M. A family of autocrine growth factors in Mycobacterium tuberculosis. Mol Microbiol. 2002 Nov;46(3):623-35. PMID:12410821
↑ Zhu W, Plikaytis BB, Shinnick TM. Resuscitation factors from mycobacteria: homologs of Micrococcus luteus proteins. Tuberculosis (Edinb). 2003;83(4):261-9. PMID:12906837
↑ Hett EC, Chao MC, Deng LL, Rubin EJ. A mycobacterial enzyme essential for cell division synergizes with resuscitation-promoting factor. PLoS Pathog. 2008 Feb 29;4(2):e1000001. doi: 10.1371/journal.ppat.1000001. PMID:18463693 doi:10.1371/journal.ppat.1000001
↑ Demina GR, Makarov VA, Nikitushkin VD, Ryabova OB, Vostroknutova GN, Salina EG, Shleeva MO, Goncharenko AV, Kaprelyants AS. Finding of the low molecular weight inhibitors of resuscitation promoting factor enzymatic and resuscitation activity. PLoS One. 2009 Dec 16;4(12):e8174. doi: 10.1371/journal.pone.0008174. PMID:20016836 doi:10.1371/journal.pone.0008174
↑ Ruggiero A, Squeglia F, Romano M, Vitagliano L, De Simone A, Berisio R. The structure of Resuscitation promoting factor B from M. tuberculosis reveals unexpected ubiquitin-like domains. Biochim Biophys Acta. 2015 Nov 5. pii: S0304-4165(15)00300-1. doi:, 10.1016/j.bbagen.2015.11.001. PMID:26549874 doi:http://dx.doi.org/10.1016/j.bbagen.2015.11.001

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5e27"

@@ Line 1: / Line 1: @@
 ==The structure of Resuscitation Promoting Factor B from M. tuberculosis reveals unexpected ubiquitin-like domains==
-<StructureSection load='5e27' size='340' side='right' caption='[[5e27]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+<StructureSection load='5e27' size='340' side='right'caption='[[5e27]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5e27]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E27 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5E27 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5e27]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E27 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5E27 FirstGlance]. <br>
-</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5e27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e27 OCA], [http://pdbe.org/5e27 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e27 RCSB], [http://www.ebi.ac.uk/pdbsum/5e27 PDBsum]</span></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5e27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e27 OCA], [https://pdbe.org/5e27 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5e27 RCSB], [https://www.ebi.ac.uk/pdbsum/5e27 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5e27 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/RPFB_MYCTU RPFB_MYCTU] 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>PMID:12410821</ref> <ref>PMID:12906837</ref> <ref>PMID:18463693</ref> <ref>PMID:20016836</ref>   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>PMID:12410821</ref> <ref>PMID:12906837</ref> <ref>PMID:18463693</ref> <ref>PMID:20016836</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 18: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Berisio, R]]
+[[Category: Large Structures]]
-[[Category: Romano, M]]
+[[Category: Mycobacterium tuberculosis]]
-[[Category: Ruggiero, A]]
+[[Category: Berisio R]]
-[[Category: Simone, A De]]
+[[Category: De Simone A]]
-[[Category: Squeglia, F]]
+[[Category: Romano M]]
-[[Category: Vitagliano, L]]
+[[Category: Ruggiero A]]
-[[Category: Cell adhesion]]
+[[Category: Squeglia F]]
-[[Category: Cell wall]]
+[[Category: Vitagliano L]]
-[[Category: Peptidoglycan]]
-[[Category: Tuberculosis]]

5e27

From Proteopedia

Current revision

The structure of Resuscitation Promoting Factor B from M. tuberculosis reveals unexpected ubiquitin-like domains

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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