4kpm

From Proteopedia

(Difference between revisions)

Revision as of 09:05, 7 December 2022

Crystal structure of the catalytic domain of RpfB from Mycobacterium tuberculosis in complex with triNAG

Structural highlights

4kpm is a 4 chain structure with sequence from Mycobacterium tuberculosis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
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

Resuscitation of Mtb is crucial to the etiology of Tuberculosis, because latent tuberculosis is estimated to affect one-third of the world population. The resuscitation-promoting factor RpfB is mainly responsible for Mtb resuscitation from dormancy. Given the impact of latent Tuberculosis, RpfB represents an interesting target for tuberculosis drug discovery. However, no molecular models of substrate binding and catalysis are hitherto available for this enzyme. Here, we identified key interactions involved in substrate binding to RpfB by combining x-ray diffraction studies and computational approaches. The crystal structure of RpfB catalytic domain in complex with N,N',N-triacetyl-chitotriose, as described here, provides the first, to our knowledge, atomic representation of ligand recognition by RpfB and demonstrates that the strongest interactions are established by the N-acetylglucosamine moiety in the central region of the enzyme binding cleft. Molecular dynamics analyses provided information on the dynamic behavior of protein-substrate interactions and on the role played by the solvent in RpfB function. These data combined with sequence conservation analysis suggest that Glu-292 is the sole residue crucial for catalysis, implying that RpfB acts via the formation of an oxocarbenium ion rather than a covalent intermediate. Present data represent a solid base for the design of effective drug inhibitors of RpfB. Moreover, homology models were generated for the catalytic domains of all members of the Mtb Rpf family (RpfA-E). The analysis of these models unveiled analogies and differences among the different members of the Rpf protein family.

Carbohydrate Recognition by RpfB from Mycobacterium tuberculosis Unveiled by Crystallographic and Molecular Dynamics Analyses.,Squeglia F, Romano M, Ruggiero A, Vitagliano L, De Simone A, Berisio R Biophys J. 2013 Jun 4;104(11):2530-9. doi: 10.1016/j.bpj.2013.04.040. PMID:23746526^[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
↑ Squeglia F, Romano M, Ruggiero A, Vitagliano L, De Simone A, Berisio R. Carbohydrate Recognition by RpfB from Mycobacterium tuberculosis Unveiled by Crystallographic and Molecular Dynamics Analyses. Biophys J. 2013 Jun 4;104(11):2530-9. doi: 10.1016/j.bpj.2013.04.040. PMID:23746526 doi:10.1016/j.bpj.2013.04.040

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/4kpm"

Categories: Large Structures | Mycobacterium tuberculosis | Berisio R | Ruggiero A | Squeglia F

@@ Line 1: / Line 1: @@
 ==Crystal structure of the catalytic domain of RpfB from Mycobacterium tuberculosis in complex with triNAG==
-<StructureSection load='4kpm' size='340' side='right' caption='[[4kpm]], [[Resolution|resolution]] 1.33&Aring;' scene=''>
+<StructureSection load='4kpm' size='340' side='right'caption='[[4kpm]], [[Resolution|resolution]] 1.33&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4kpm]] is a 4 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=4KPM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KPM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4kpm]] is a 4 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=4KPM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KPM FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PRD_900017:triacetyl-beta-chitotriose'>PRD_900017</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4kl7|4kl7]]</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=4kpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kpm OCA], [https://pdbe.org/4kpm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kpm RCSB], [https://www.ebi.ac.uk/pdbsum/4kpm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kpm ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">h37rv, MT1038, MTC1237.26, rpfB, Rv1009 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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=4kpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kpm OCA], [http://pdbe.org/4kpm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4kpm RCSB], [http://www.ebi.ac.uk/pdbsum/4kpm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4kpm ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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>
+[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 24: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Berisio, R]]
+[[Category: Large Structures]]
-[[Category: Ruggiero, A]]
+[[Category: Mycobacterium tuberculosis]]
-[[Category: Squeglia, F]]
+[[Category: Berisio R]]
-[[Category: Alpha-beta]]
+[[Category: Ruggiero A]]
-[[Category: Cell wall hydrolase]]
+[[Category: Squeglia F]]
-[[Category: Hydrolase]]

4kpm

From Proteopedia

Revision as of 09:05, 7 December 2022

Crystal structure of the catalytic domain of RpfB from Mycobacterium tuberculosis in complex with triNAG

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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