1zbi

From Proteopedia

(Difference between revisions)

Current revision

Bacillus halodurans RNase H catalytic domain mutant D132N in complex with 12-mer RNA/DNA hybrid

Structural highlights

1zbi is a 4 chain structure with sequence from Alkalihalobacillus halodurans C-125. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.85Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RNH1_HALH5 Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.^[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

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.

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:15989951^[2]

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

References

↑ Nowotny M, Gaidamakov SA, Crouch RJ, Yang W. Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis. Cell. 2005 Jul 1;121(7):1005-16. PMID:15989951 doi:http://dx.doi.org/10.1016/j.cell.2005.04.024
↑ Nowotny M, Gaidamakov SA, Crouch RJ, Yang W. Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis. Cell. 2005 Jul 1;121(7):1005-16. PMID:15989951 doi:http://dx.doi.org/10.1016/j.cell.2005.04.024

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/1zbi"

@@ Line 3: / Line 3: @@
 <StructureSection load='1zbi' size='340' side='right'caption='[[1zbi]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1zbi]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Alkhc Alkhc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZBI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZBI FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1zbi]] is a 4 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=1ZBI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZBI FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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]] 1.85&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1zbf|1zbf]], [[1zbl|1zbl]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </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=1zbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zbi OCA], [https://pdbe.org/1zbi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zbi RCSB], [https://www.ebi.ac.uk/pdbsum/1zbi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zbi ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/RNH1_BACHD RNH1_BACHD]] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.
+[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]]
@@ Line 37: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Alkhc]]
+[[Category: Alkalihalobacillus halodurans C-125]]
 [[Category: Large Structures]]
-[[Category: Ribonuclease H]]
+[[Category: Crouch RJ]]
-[[Category: Crouch, R J]]
+[[Category: Gaidamakov SA]]
-[[Category: Gaidamakov, S A]]
+[[Category: Nowotny M]]
-[[Category: Nowotny, M]]
+[[Category: Yang W]]
-[[Category: Yang, W]]
-[[Category: Dde motif]]
-[[Category: Hydrolase-rna-dna complex]]
-[[Category: Rna/dna hybrid]]
-[[Category: Rnase h]]

1zbi

From Proteopedia

Current revision

Bacillus halodurans RNase H catalytic domain mutant D132N in complex with 12-mer RNA/DNA hybrid

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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