3boy: Difference between revisions

Revision as of 20:49, 2 October 2014

Crystal structure of the HutP antitermination complex bound to the HUT mRNA

Structural highlights

3boy is a 4 chain structure with sequence from Bacillus subtilis. This structure supersedes the now removed PDB entry 2gzt. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	HIS, MG
Related:	1vea, 1wpt, 1wmq, 1wpu, 1wrq, 1wpv
Gene:	hutP (Bacillus subtilis)
Resources:	FirstGlance, OCA, RCSB, PDBsum, TOPSAN

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

HutP is an L-histidine-activated RNA binding protein that regulates the expression of the histidine utilization (hut) operon in Bacillus subtilis by binding to cis-acting regulatory sequences on the hut mRNA. The crystal structure of HutP complexed with an L-histidine analog showed a novel fold; there are four antiparallel beta strands in the central region of each monomer, with two alpha helices each on the front and back. Two HutP monomers form a dimer, and three dimers are arranged in crystallographic 3-fold symmetry to form a hexamer. A histidine analog was located in between the two monomers of HutP, with the imidazole group of L-histidine hydrogen bonded to Glu81. An activation mechanism is proposed based on the identification of key residues of HutP. The HutP binding region in hut mRNA was defined: it consists of three UAG trinucleotide motifs separated by four spacer nucleotides. Residues of HutP potentially important for RNA binding were identified.

Crystal structure of activated HutP; an RNA binding protein that regulates transcription of the hut operon in Bacillus subtilis.,Kumarevel T, Fujimoto Z, Karthe P, Oda M, Mizuno H, Kumar PK Structure. 2004 Jul;12(7):1269-80. PMID:15242603^[1]

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

References

↑ Kumarevel T, Fujimoto Z, Karthe P, Oda M, Mizuno H, Kumar PK. Crystal structure of activated HutP; an RNA binding protein that regulates transcription of the hut operon in Bacillus subtilis. Structure. 2004 Jul;12(7):1269-80. PMID:15242603 doi:https://dx.doi.org/10.1016/j.str.2004.05.005

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Kumarevel T, Fujimoto Z, Karthe P, Oda M, Mizuno H, Kumar PK. Crystal structure of activated HutP; an RNA binding protein that regulates transcription of the hut operon in Bacillus subtilis. Structure. 2004 Jul;12(7):1269-80. PMID:15242603 doi:https://dx.doi.org/10.1016/j.str.2004.05.005

[1]

@@ Line 1: / Line 1: @@
-[[Image:3boy.png|left|200px]]
+==Crystal structure of the HutP antitermination complex bound to the HUT mRNA==
+<StructureSection load='3boy' size='340' side='right' caption='[[3boy]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3boy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2gzt 2gzt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BOY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BOY FirstGlance]. <br>
+</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HIS:HISTIDINE'>HIS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
+<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1vea|1vea]], [[1wpt|1wpt]], [[1wmq|1wmq]], [[1wpu|1wpu]], [[1wrq|1wrq]], [[1wpv|1wpv]]</td></tr>
+<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hutP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</td></tr>
+<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3boy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3boy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3boy RCSB], [http://www.ebi.ac.uk/pdbsum/3boy PDBsum], [http://www.topsan.org/Proteins/RSGI/3boy TOPSAN]</span></td></tr>
+<table>
+== 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/bo/3boy_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].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+HutP is an L-histidine-activated RNA binding protein that regulates the expression of the histidine utilization (hut) operon in Bacillus subtilis by binding to cis-acting regulatory sequences on the hut mRNA. The crystal structure of HutP complexed with an L-histidine analog showed a novel fold; there are four antiparallel beta strands in the central region of each monomer, with two alpha helices each on the front and back. Two HutP monomers form a dimer, and three dimers are arranged in crystallographic 3-fold symmetry to form a hexamer. A histidine analog was located in between the two monomers of HutP, with the imidazole group of L-histidine hydrogen bonded to Glu81. An activation mechanism is proposed based on the identification of key residues of HutP. The HutP binding region in hut mRNA was defined: it consists of three UAG trinucleotide motifs separated by four spacer nucleotides. Residues of HutP potentially important for RNA binding were identified.
-{{STRUCTURE_3boy|  PDB=3boy  |  SCENE=  }}
+Crystal structure of activated HutP; an RNA binding protein that regulates transcription of the hut operon in Bacillus subtilis.,Kumarevel T, Fujimoto Z, Karthe P, Oda M, Mizuno H, Kumar PK Structure. 2004 Jul;12(7):1269-80. PMID:15242603<ref>PMID:15242603</ref>
-===Crystal structure of the HutP antitermination complex bound to the HUT mRNA===
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-{{ABSTRACT_PUBMED_15242603}}
+== References ==
+<references/>
-==About this Structure==
+__TOC__
-[[3boy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2gzt 2gzt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BOY OCA].
+</StructureSection>
-==Reference==
-<ref group="xtra">PMID:015242603</ref><ref group="xtra">PMID:015273277</ref><ref group="xtra">PMID:015758992</ref><ref group="xtra">PMID:016192572</ref><references group="xtra"/>
 [[Category: Bacillus subtilis]]
 [[Category: Balasundaresan, D.]]

3boy: Difference between revisions

Revision as of 20:49, 2 October 2014

Crystal structure of the HutP antitermination complex bound to the HUT mRNA

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

References

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