3eo5

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the resuscitation promoting factor RpfB

Structural highlights

3eo5 is a 1 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 1.83Å
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]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Mycobacterium tuberculosis is able to establish a non-replicating state and survive in an intracellular habitat for years. Resuscitation of dormant M. tuberculosis bacteria is promoted by resuscitation-promoting factors (Rpfs), which are secreted from slowly replicating bacteria close to dormant bacteria. Here we report the crystal structure of a truncated form of RpfB (residues 194-362), the sole indispensable Rpf of the five Rpfs encoded in this bacterium genome. The structure, denoted as (DeltaDUF)RpfB, exhibits a comma-like shape formed by a lysozyme-like globular catalytic domain and an elongated G5 domain, which is widespread among cell surface binding proteins. The G5 domain, whose structure was previously uncharacterised, presents some peculiar features. The basic structural motif of this domain, which represents the tail of the comma-like structure, is a novel super-secondary-structure element, made of two beta-sheets interconnected by a pseudo-triple helix. This intricate organisation leads to the exposure of several backbone hydrogen-bond donors/acceptors. Mutagenesis analyses and solution studies indicate that this protein construct as well as the full-length form are elongated monomeric proteins. Although (DeltaDUF)RpfB does not self-associate, the exposure of structural elements (backbone H-bond donors/acceptors and hydrophobic side chains) that are usually buried in globular proteins is typically associated with adhesive properties. This suggests that the RpfB G5 domain has a cell-wall adhesive function, which allows the catalytic domain to be properly oriented for the cleavage reaction. Interestingly, sequence comparisons indicate that these structural features are also shared by G5 domains involved in biofilm formation.

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. 2009 Jan 9;385(1):153-62. Epub 2008 Oct 22. PMID:18992255^[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, Tizzano B, Pedone E, Pedone C, Wilmanns M, Berisio R. Crystal structure of the resuscitation-promoting factor (DeltaDUF)RpfB from M. tuberculosis. J Mol Biol. 2009 Jan 9;385(1):153-62. Epub 2008 Oct 22. PMID:18992255 doi:http://dx.doi.org/S0022-2836(08)01306-5

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3eo5"

@@ Line 3: / Line 3: @@
 <StructureSection load='3eo5' size='340' side='right'caption='[[3eo5]], [[Resolution|resolution]] 1.83&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3eo5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EO5 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3EO5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3eo5]] is a 1 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=3EO5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EO5 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1xsf|1xsf]]</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]] 1.83&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3eo5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eo5 OCA], [http://pdbe.org/3eo5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3eo5 RCSB], [http://www.ebi.ac.uk/pdbsum/3eo5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3eo5 ProSAT]</span></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=3eo5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eo5 OCA], [https://pdbe.org/3eo5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3eo5 RCSB], [https://www.ebi.ac.uk/pdbsum/3eo5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3eo5 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RPFB_MYCTO RPFB_MYCTO]] Factor that stimulates resuscitation of dormant cells. Has peptidoglycan (PG) hydrolytic activity. 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 (By similarity).
+[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>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 14: / Line 14: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/eo/3eo5_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 33: / Line 33: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Berisio, R]]
+[[Category: Mycobacterium tuberculosis]]
-[[Category: Pedone, C]]
+[[Category: Berisio R]]
-[[Category: Pedone, E]]
+[[Category: Pedone C]]
-[[Category: Ruggiero, A]]
+[[Category: Pedone E]]
-[[Category: Tizzano, B]]
+[[Category: Ruggiero A]]
-[[Category: Wilmanns, M]]
+[[Category: Tizzano B]]
-[[Category: Cell adhesion]]
+[[Category: Wilmanns M]]
-[[Category: Crystal]]
-[[Category: Resuscitation]]

3eo5

From Proteopedia

Current revision

Crystal structure of the resuscitation promoting factor RpfB

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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