1by9

From Proteopedia

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Current revision

CRYSTAL STRUCTURE OF THE E2 DNA-BINDING DOMAIN FROM HUMAN PAPILLOMAVIRUS TYPE-16: IMPLICATIONS FOR ITS DNA BINDING-SITE SELECTION MECHANISM

Structural highlights

1by9 is a 1 chain structure with sequence from Human papillomavirus type 16. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.2Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

VE2_HPV16 Plays an accessory role in initiation of DNA replication. A dimer of E2 interacts with a dimer of E1 in order to improve specificity of E1 DNA binding activity. Once the complex recognizes and binds DNA at specific sites, the E2 dimer is removed from DNA. E2 also regulates viral transcription through binding to the E2RE response element (5'-ACCNNNNNNGGT-3') present in multiple copies in the regulatory regions of the viral genome. Activates or represses transcription depending on E2RE's position with regards to proximal promoter elements including the TATA-box. Repression occurs by sterically hindering the assembly of the transcription initiation complex.^[1] ^[2] ^[3]

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

The crystal structure of the E2 DNA-binding domain from the high-risk cervical cancer-associated strain human papillomavirus type 16 (HPV-16) is described here. The papillomavirus E2 proteins regulate transcription from all viral promoters and are required for the initiation of replication in vivo. They belong to a family of viral proteins that form dimeric beta-barrels and use surface alpha-helices for DNA interaction. Although all E2 proteins recognize the same consensus, palindromic DNA sequence, proteins from different viral strains differ in their abilities to discriminate among their specific DNA-binding sites. The structure reported here reveals that while the overall fold of the HPV-16 E2 DNA-binding domain resembles that of its counterpart from the related viral strain bovine papillomavirus type 1, the precise placement of the recognition helices is significantly different. Additionally, the charge distribution on the DNA-binding surfaces of the two proteins varies; HPV-16 E2 has a much less electropositive surface. HPV-16 E2 is thus less able to utilize charge neutralization of the phosphate groups on DNA to induce bending. These results correlate well with previous solution studies that showed decreased affinity between HPV-16 E2 and flexible DNA target sequences, and enhanced affinity towards A-tract-containing, pre-bent sequences. In summary, the crystal structure of the HPV-16 E2 DNA-binding domain shows that the protein presents a stereo-chemically and electrostatically unique surface to DNA, characteristics that can contribute to its mechanism of DNA target discrimination.

Crystal structure of the E2 DNA-binding domain from human papillomavirus type 16: implications for its DNA binding-site selection mechanism.,Hegde RS, Androphy EJ J Mol Biol. 1998 Dec 18;284(5):1479-89. PMID:9878365^[4]

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

References

↑ Phelps WC, Howley PM. Transcriptional trans-activation by the human papillomavirus type 16 E2 gene product. J Virol. 1987 May;61(5):1630-8. PMID:3033289
↑ Del Vecchio AM, Romanczuk H, Howley PM, Baker CC. Transient replication of human papillomavirus DNAs. J Virol. 1992 Oct;66(10):5949-58. PMID:1326651
↑ Okoye A, Cordano P, Taylor ER, Morgan IM, Everett R, Campo MS. Human papillomavirus 16 L2 inhibits the transcriptional activation function, but not the DNA replication function, of HPV-16 E2. Virus Res. 2005 Mar;108(1-2):1-14. PMID:15681049 doi:10.1016/j.virusres.2004.07.004
↑ Hegde RS, Androphy EJ. Crystal structure of the E2 DNA-binding domain from human papillomavirus type 16: implications for its DNA binding-site selection mechanism. J Mol Biol. 1998 Dec 18;284(5):1479-89. PMID:9878365 doi:10.1006/jmbi.1998.2260

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1by9"

Categories: Human papillomavirus type 16 | Large Structures | Androphy EJ | Hegde RS

@@ Line 1: / Line 1: @@
 ==CRYSTAL STRUCTURE OF THE E2 DNA-BINDING DOMAIN FROM HUMAN PAPILLOMAVIRUS TYPE-16: IMPLICATIONS FOR ITS DNA BINDING-SITE SELECTION MECHANISM==
-<StructureSection load='1by9' size='340' side='right' caption='[[1by9]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+<StructureSection load='1by9' size='340' side='right'caption='[[1by9]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1by9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Hpv16 Hpv16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BY9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BY9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1by9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_papillomavirus_type_16 Human papillomavirus type 16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BY9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BY9 FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">E2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=333760 HPV16])</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]] 2.2&#8491;</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=1by9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1by9 OCA], [http://pdbe.org/1by9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1by9 RCSB], [http://www.ebi.ac.uk/pdbsum/1by9 PDBsum]</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=1by9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1by9 OCA], [https://pdbe.org/1by9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1by9 RCSB], [https://www.ebi.ac.uk/pdbsum/1by9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1by9 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/VE2_HPV16 VE2_HPV16]] Plays an accessory role in initiation of DNA replication. A dimer of E2 interacts with a dimer of E1 in order to improve specificity of E1 DNA binding activity. Once the complex recognizes and binds DNA at specific sites, the E2 dimer is removed from DNA. E2 also regulates viral transcription through binding to the E2RE response element (5'-ACCNNNNNNGGT-3') present in multiple copies in the regulatory regions of the viral genome. Activates or represses transcription depending on E2RE's position with regards to proximal promoter elements including the TATA-box. Repression occurs by sterically hindering the assembly of the transcription initiation complex.<ref>PMID:3033289</ref> <ref>PMID:1326651</ref> <ref>PMID:15681049</ref>
+[https://www.uniprot.org/uniprot/VE2_HPV16 VE2_HPV16] Plays an accessory role in initiation of DNA replication. A dimer of E2 interacts with a dimer of E1 in order to improve specificity of E1 DNA binding activity. Once the complex recognizes and binds DNA at specific sites, the E2 dimer is removed from DNA. E2 also regulates viral transcription through binding to the E2RE response element (5'-ACCNNNNNNGGT-3') present in multiple copies in the regulatory regions of the viral genome. Activates or represses transcription depending on E2RE's position with regards to proximal promoter elements including the TATA-box. Repression occurs by sterically hindering the assembly of the transcription initiation complex.<ref>PMID:3033289</ref> <ref>PMID:1326651</ref> <ref>PMID:15681049</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/by/1by9_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/by/1by9_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=1by9 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 28: @@
 </div>
 <div class="pdbe-citations 1by9" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Regulatory protein E2|Regulatory protein E2]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Hpv16]]
+[[Category: Human papillomavirus type 16]]
-[[Category: Androphy, E J]]
+[[Category: Large Structures]]
-[[Category: Hegde, R S]]
+[[Category: Androphy EJ]]
-[[Category: Beta-barrel]]
+[[Category: Hegde RS]]
-[[Category: Papillomavirus]]
-[[Category: Transcription regulation]]

1by9

From Proteopedia

Current revision

CRYSTAL STRUCTURE OF THE E2 DNA-BINDING DOMAIN FROM HUMAN PAPILLOMAVIRUS TYPE-16: IMPLICATIONS FOR ITS DNA BINDING-SITE SELECTION MECHANISM

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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