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5yrx

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Crystal structure of a hypothetical protein Rv3716c from Mycobacterium tuberculosis

Structural highlights

5yrx is a 1 chain structure with sequence from Mycobacterium tuberculosis H37Rv. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.9Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Y3716_MYCTU Binds to DNA and alters its conformation. May be involved in regulation of gene expression, nucleoid organization and DNA protection.

Publication Abstract from PubMed

Latent tuberculosis (TB) is the main hurdle in reaching the goal of "Stop TB 2050". Tuberculin skin and Interferon-gamma release assay tests used currently for the diagnosis of TB infection cannot distinguish between active disease and latent tuberculosis infection (LTBI) and hence new and sensitive protein markers need to be identified for the diagnosis. A protein Rv3716c from Mycobacterium tuberculosis (MtbRv3716c) has been identified as a potential surrogate marker for the diagnosis of LTBI. Here, we present characterization of MtbRv3716c ( approximately 13 kDa) using both biophysical and X-Ray crystallographic methods. EMSA study showed that MtbRv3716c binds to double stranded DNA. X-ray diffraction data collected on a crystal of MtbRv3716c at 1.9 A resolution was used for structure determination using the molecular replacement method. Significant electron density was not observed for the N-terminal 21 and C-terminal 41 residues in the final electron density map. The C- terminal disordered region is proline rich and displays characteristics of intrinsically disordered proteins. Although the crystal asymmetric unit contained a protomer, a tight dimer could be generated by the application of the crystal two-fold symmetry parallel to the b axis. Packing of dimers in the crystal is mediated by a cadmium ion (Cd(2+)) occurring at the interface of two dimers. Molecular packing analysis reveals large cavities that are probably occupied by the disordered segments of the N- and C-termini. Structural comparison with other homologous hypothetical DNA binding proteins (PDB codes: 1PUG, 1YBX) highlights structural features that might be significant for DNA binding.

Structural and biophysical characterization of Rv3716c, a hypothetical protein from Mycobacterium tuberculosis.,Gopalan A, Deka G, Prabhavathi M, Savithri HS, Murthy MRN, Raja A Biochem Biophys Res Commun. 2018 Jan 1;495(1):982-987. doi:, 10.1016/j.bbrc.2017.11.093. Epub 2017 Nov 15. PMID:29154992^[1]

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

References

↑ Gopalan A, Deka G, Prabhavathi M, Savithri HS, Murthy MRN, Raja A. Structural and biophysical characterization of Rv3716c, a hypothetical protein from Mycobacterium tuberculosis. Biochem Biophys Res Commun. 2018 Jan 1;495(1):982-987. doi:, 10.1016/j.bbrc.2017.11.093. Epub 2017 Nov 15. PMID:29154992 doi:http://dx.doi.org/10.1016/j.bbrc.2017.11.093

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/5yrx"

@@ Line 3: / Line 3: @@
 <StructureSection load='5yrx' size='340' side='right'caption='[[5yrx]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5yrx]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YRX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YRX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5yrx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YRX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YRX FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></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]] 1.9&#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=5yrx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yrx OCA], [http://pdbe.org/5yrx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yrx RCSB], [http://www.ebi.ac.uk/pdbsum/5yrx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yrx ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></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=5yrx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yrx OCA], [https://pdbe.org/5yrx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yrx RCSB], [https://www.ebi.ac.uk/pdbsum/5yrx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yrx ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/Y3716_MYCTU Y3716_MYCTU]] Binds to DNA and alters its conformation. May be involved in regulation of gene expression, nucleoid organization and DNA protection.
+[https://www.uniprot.org/uniprot/Y3716_MYCTU Y3716_MYCTU] Binds to DNA and alters its conformation. May be involved in regulation of gene expression, nucleoid organization and DNA protection.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 24: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Deka, G]]
+[[Category: Mycobacterium tuberculosis H37Rv]]
-[[Category: Gopalan, A]]
+[[Category: Deka G]]
-[[Category: Murthy, M R.N]]
+[[Category: Gopalan A]]
-[[Category: Prabhavathi, M]]
+[[Category: Murthy MRN]]
-[[Category: Raja, A]]
+[[Category: Prabhavathi M]]
-[[Category: Savithri, H S]]
+[[Category: Raja A]]
-[[Category: Dna binding]]
+[[Category: Savithri HS]]
-[[Category: Dna binding protein]]
-[[Category: Metal ion]]
-[[Category: Mtbrv3716]]

5yrx

From Proteopedia

Current revision

Crystal structure of a hypothetical protein Rv3716c from Mycobacterium tuberculosis

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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