1k99

From Proteopedia

(Difference between revisions)

Current revision

Solution Structure of the first HMG box in human Upstream binding factor

Structural highlights

1k99 is a 1 chain structure with sequence from Homo sapiens. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

UBF1_HUMAN Recognizes the ribosomal RNA gene promoter and activates transcription mediated by RNA polymerase I through cooperative interactions with the transcription factor SL1/TIF-IB complex. It binds specifically to the upstream control element.^[1]

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

Human upstream binding factor is a nucleolar transcription factor involved in transcription by RNA polymerase I. It contains six HMG box domains; the HMG box is a minor groove DNA-binding domain that has been found in hundreds of proteins with different functions. Among the six HMG box domains in hUBF, the first one can bind to the ribosomal promoter specifically by itself and is essential for the whole protein's DNA binding specificity. Here we report the three-dimensional structure of this first HMG box free in solution determined by multidimensional NMR using (13)C,(15)N-labeled protein. Like the previously determined HMG box structures, hUBF HMG box 1 adopts a twisted L-shape consisting of three alpha-helices: helix 1 (17-30) and helix 2 (38-51) pack onto each other to form the short arm, while helix 3 (57-76) is associated with an extended strand N-terminal to helix 1 and forms the long arm. A cluster of conserved residues, in particular the aromatic residues F21, Y49, and Y60, is important to maintain the fold. The short arm is rigid due to extensive hydrophobic interaction between helix 1 and helix 2, while the long arm is less rigid.

Solution structure of the first HMG box domain in human upstream binding factor.,Xu Y, Yang W, Wu J, Shi Y Biochemistry. 2002 Apr 30;41(17):5415-20. PMID:11969401^[2]

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

References

↑ Kwon H, Green MR. The RNA polymerase I transcription factor, upstream binding factor, interacts directly with the TATA box-binding protein. J Biol Chem. 1994 Dec 2;269(48):30140-6. PMID:7982918
↑ Xu Y, Yang W, Wu J, Shi Y. Solution structure of the first HMG box domain in human upstream binding factor. Biochemistry. 2002 Apr 30;41(17):5415-20. PMID:11969401

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/1k99"

@@ Line 1: / Line 1: @@
 ==Solution Structure of the first HMG box in human Upstream binding factor==
-<StructureSection load='1k99' size='340' side='right' caption='[[1k99]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='1k99' size='340' side='right'caption='[[1k99]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1k99]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K99 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K99 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1k99]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K99 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K99 FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hUBF(103-192) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1k99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k99 OCA], [http://pdbe.org/1k99 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1k99 RCSB], [http://www.ebi.ac.uk/pdbsum/1k99 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=1k99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k99 OCA], [https://pdbe.org/1k99 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k99 RCSB], [https://www.ebi.ac.uk/pdbsum/1k99 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k99 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/UBF1_HUMAN UBF1_HUMAN]] Recognizes the ribosomal RNA gene promoter and activates transcription mediated by RNA polymerase I through cooperative interactions with the transcription factor SL1/TIF-IB complex. It binds specifically to the upstream control element.<ref>PMID:7982918</ref>
+[https://www.uniprot.org/uniprot/UBF1_HUMAN UBF1_HUMAN] Recognizes the ribosomal RNA gene promoter and activates transcription mediated by RNA polymerase I through cooperative interactions with the transcription factor SL1/TIF-IB complex. It binds specifically to the upstream control element.<ref>PMID:7982918</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/k9/1k99_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k9/1k99_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=1k99 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 31: / Line 32: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Shi, Y]]
+[[Category: Large Structures]]
-[[Category: Wu, J]]
+[[Category: Shi Y]]
-[[Category: Xu, Y]]
+[[Category: Wu J]]
-[[Category: Yang, W]]
+[[Category: Xu Y]]
-[[Category: Alpha-helix]]
+[[Category: Yang W]]
-[[Category: Dna binding protein]]
-[[Category: L-shape]]

1k99

From Proteopedia

Current revision

Solution Structure of the first HMG box in human Upstream binding factor

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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