2dut

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of a M-loop deletion variant of MENT in the native conformation

Structural highlights

2dut is a 4 chain structure with sequence from Gallus gallus. This structure supersedes the now removed PDB entry 2h4s. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SPB10_CHICK DNA-binding protein that promotes DNA condensation into transcriptionally inactive heterochromatin in terminally differentiated avian blood cells. Promotes tight packing of nucleosomes into spherical clusters by binding to linker DNA and subsequent oligomerization. Acts as a cysteine protease inhibitor towards CTSL (cathepsin L1) and CTSV (cathepsin L2), but does not inhibit serine proteases.^[1] ^[2] ^[3] ^[4] ^[5]

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

Most serpins are associated with protease inhibition, and their ability to form loop-sheet polymers is linked to conformational disease and the human serpinopathies. Here we describe the structural and functional dissection of how a unique serpin, the non-histone architectural protein, MENT (Myeloid and Erythroid Nuclear Termination stage-specific protein), participates in DNA and chromatin condensation. Our data suggest that MENT contains at least two distinct DNA-binding sites, consistent with its simultaneous binding to the two closely juxtaposed linker DNA segments on a nucleosome. Remarkably, our studies suggest that the reactive centre loop, a region of the MENT molecule essential for chromatin bridging in vivo and in vitro, is able to mediate formation of a loop-sheet oligomer. These data provide mechanistic insight into chromatin compaction by a non-histone architectural protein and suggest how the structural plasticity of serpins has adapted to mediate physiological, rather than pathogenic, loop-sheet linkages.

X-ray crystal structure of MENT: evidence for functional loop-sheet polymers in chromatin condensation.,McGowan S, Buckle AM, Irving JA, Ong PC, Bashtannyk-Puhalovich TA, Kan WT, Henderson KN, Bulynko YA, Popova EY, Smith AI, Bottomley SP, Rossjohn J, Grigoryev SA, Pike RN, Whisstock JC EMBO J. 2006 Jul 12;25(13):3144-55. Epub 2006 Jun 29. PMID:16810322^[6]

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

References

↑ Grigoryev SA, Bednar J, Woodcock CL. MENT, a heterochromatin protein that mediates higher order chromatin folding, is a new serpin family member. J Biol Chem. 1999 Feb 26;274(9):5626-36. PMID:10026180
↑ Irving JA, Shushanov SS, Pike RN, Popova EY, Bromme D, Coetzer TH, Bottomley SP, Boulynko IA, Grigoryev SA, Whisstock JC. Inhibitory activity of a heterochromatin-associated serpin (MENT) against papain-like cysteine proteinases affects chromatin structure and blocks cell proliferation. J Biol Chem. 2002 Apr 12;277(15):13192-201. Epub 2002 Jan 30. PMID:11821386 doi:http://dx.doi.org/10.1074/jbc.M108460200
↑ Springhetti EM, Istomina NE, Whisstock JC, Nikitina T, Woodcock CL, Grigoryev SA. Role of the M-loop and reactive center loop domains in the folding and bridging of nucleosome arrays by MENT. J Biol Chem. 2003 Oct 31;278(44):43384-93. Epub 2003 Aug 19. PMID:12930828 doi:http://dx.doi.org/10.1074/jbc.M307635200
↑ McGowan S, Buckle AM, Irving JA, Ong PC, Bashtannyk-Puhalovich TA, Kan WT, Henderson KN, Bulynko YA, Popova EY, Smith AI, Bottomley SP, Rossjohn J, Grigoryev SA, Pike RN, Whisstock JC. X-ray crystal structure of MENT: evidence for functional loop-sheet polymers in chromatin condensation. EMBO J. 2006 Jul 12;25(13):3144-55. Epub 2006 Jun 29. PMID:16810322
↑ Grigoryev SA, Woodcock CL. Chromatin structure in granulocytes. A link between tight compaction and accumulation of a heterochromatin-associated protein (MENT). J Biol Chem. 1998 Jan 30;273(5):3082-9. PMID:9446625
↑ McGowan S, Buckle AM, Irving JA, Ong PC, Bashtannyk-Puhalovich TA, Kan WT, Henderson KN, Bulynko YA, Popova EY, Smith AI, Bottomley SP, Rossjohn J, Grigoryev SA, Pike RN, Whisstock JC. X-ray crystal structure of MENT: evidence for functional loop-sheet polymers in chromatin condensation. EMBO J. 2006 Jul 12;25(13):3144-55. Epub 2006 Jun 29. PMID:16810322

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/2dut"

@@ Line 1: / Line 1: @@
 ==Crystal structure of a M-loop deletion variant of MENT in the native conformation==
-<StructureSection load='2dut' size='340' side='right' caption='[[2dut]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+<StructureSection load='2dut' size='340' side='right'caption='[[2dut]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2dut]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2h4s 2h4s]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DUT FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2dut]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2h4s 2h4s]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DUT FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2h4p|2h4p]], [[2h4r|2h4r]], [[2h4q|2h4q]]</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]] 3&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MENT-1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9031 Gallus gallus])</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=2dut FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dut OCA], [https://pdbe.org/2dut PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dut RCSB], [https://www.ebi.ac.uk/pdbsum/2dut PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dut ProSAT]</span></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=2dut FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dut OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dut RCSB], [http://www.ebi.ac.uk/pdbsum/2dut PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/SPB10_CHICK SPB10_CHICK] DNA-binding protein that promotes DNA condensation into transcriptionally inactive heterochromatin in terminally differentiated avian blood cells. Promotes tight packing of nucleosomes into spherical clusters by binding to linker DNA and subsequent oligomerization. Acts as a cysteine protease inhibitor towards CTSL (cathepsin L1) and CTSV (cathepsin L2), but does not inhibit serine proteases.<ref>PMID:10026180</ref> <ref>PMID:11821386</ref> <ref>PMID:12930828</ref> <ref>PMID:16810322</ref> <ref>PMID:9446625</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/du/2dut_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/du/2dut_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2dut ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 25: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2dut" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 30: / Line 33: @@
 </StructureSection>
 [[Category: Gallus gallus]]
-[[Category: Buckle, A M]]
+[[Category: Large Structures]]
-[[Category: Irving, J A]]
+[[Category: Buckle AM]]
-[[Category: McGowan, S]]
+[[Category: Irving JA]]
-[[Category: Whisstock, J C]]
+[[Category: McGowan S]]
-[[Category: Hydrolase inhibitor]]
+[[Category: Whisstock JC]]
-[[Category: Serine protease inhibitor]]
-[[Category: Serpin]]

2dut

From Proteopedia

Current revision

Crystal structure of a M-loop deletion variant of MENT in the native conformation

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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