1zbf

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:03, 14 February 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1zbf.gif|left|200px]]
 
-
{{Structure
+
==Crystal structure of B. halodurans RNase H catalytic domain mutant D132N==
-
|PDB= 1zbf |SIZE=350|CAPTION= <scene name='initialview01'>1zbf</scene>, resolution 1.50&Aring;
+
<StructureSection load='1zbf' size='340' side='right'caption='[[1zbf]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
+
<table><tr><td colspan='2'>[[1zbf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Alkalihalobacillus_halodurans_C-125 Alkalihalobacillus halodurans C-125]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZBF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZBF FirstGlance]. <br>
-
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </span>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-
|DOMAIN=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1zbf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zbf OCA], [https://pdbe.org/1zbf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zbf RCSB], [https://www.ebi.ac.uk/pdbsum/1zbf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zbf ProSAT]</span></td></tr>
-
|RELATEDENTRY=[[1zbi|1ZBI]], [[1zbl|1ZBL]]
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1zbf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zbf OCA], [http://www.ebi.ac.uk/pdbsum/1zbf PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1zbf RCSB]</span>
+
== Function ==
-
}}
+
[https://www.uniprot.org/uniprot/RNH1_HALH5 RNH1_HALH5] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.<ref>PMID:15989951</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/zb/1zbf_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/main_output.php?pdb_ID=1zbf ConSurf].
 +
<div style="clear:both"></div>
-
'''Crystal structure of B. halodurans RNase H catalytic domain mutant D132N'''
+
==See Also==
-
 
+
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
-
 
+
== References ==
-
==Overview==
+
<references/>
-
RNase H belongs to a nucleotidyl-transferase superfamily, which includes transposase, retroviral integrase, Holliday junction resolvase, and RISC nuclease Argonaute. We report the crystal structures of RNase H complexed with an RNA/DNA hybrid and a mechanism for substrate recognition and two-metal-ion-dependent catalysis. RNase H specifically recognizes the A form RNA strand and the B form DNA strand. Structure comparisons lead us to predict the catalytic residues of Argonaute and conclude that two-metal-ion catalysis is a general feature of the superfamily. In nucleases, the two metal ions are asymmetrically coordinated and have distinct roles in activating the nucleophile and stabilizing the transition state. In transposases, they are symmetrically coordinated and exchange roles to alternately activate a water and a 3'-OH for successive strand cleavage and transfer by a ping-pong mechanism.
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Alkalihalobacillus halodurans C-125]]
-
1ZBF is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_halodurans Bacillus halodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZBF OCA].
+
[[Category: Large Structures]]
-
 
+
[[Category: Crouch RJ]]
-
==Reference==
+
[[Category: Gaidamakov SA]]
-
Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis., Nowotny M, Gaidamakov SA, Crouch RJ, Yang W, Cell. 2005 Jul 1;121(7):1005-16. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15989951 15989951]
+
[[Category: Nowotny M]]
-
[[Category: Bacillus halodurans]]
+
[[Category: Yang W]]
-
[[Category: Ribonuclease H]]
+
-
[[Category: Single protein]]
+
-
[[Category: Crouch, R J.]]
+
-
[[Category: Gaidamakov, S A.]]
+
-
[[Category: Nowotny, M.]]
+
-
[[Category: Yang, W.]]
+
-
[[Category: dde motif]]
+
-
[[Category: rna/dna hybrid]]
+
-
[[Category: rnase h]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:33:34 2008''
+

Current revision

Crystal structure of B. halodurans RNase H catalytic domain mutant D132N

PDB ID 1zbf

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1zbf"
Personal tools