1zbl
From Proteopedia
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|PDB= 1zbl |SIZE=350|CAPTION= <scene name='initialview01'>1zbl</scene>, resolution 2.20Å | |PDB= 1zbl |SIZE=350|CAPTION= <scene name='initialview01'>1zbl</scene>, resolution 2.20Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=MG:MAGNESIUM ION'>MG</scene> | + | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene> |
| - | |ACTIVITY= [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] | + | |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> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1zbf|1ZBF]], [[1zbi|1ZBI]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1zbl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zbl OCA], [http://www.ebi.ac.uk/pdbsum/1zbl PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1zbl RCSB]</span> | ||
}} | }} | ||
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[[Category: Nowotny, M.]] | [[Category: Nowotny, M.]] | ||
[[Category: Yang, W.]] | [[Category: Yang, W.]] | ||
| - | [[Category: MG]] | ||
[[Category: dde motif]] | [[Category: dde motif]] | ||
[[Category: rna/dna hybrid]] | [[Category: rna/dna hybrid]] | ||
[[Category: rnase h]] | [[Category: rnase h]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:33:38 2008'' |
Revision as of 22:33, 30 March 2008
| |||||||
| , resolution 2.20Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , , , | ||||||
| Activity: | Ribonuclease H, with EC number 3.1.26.4 | ||||||
| Related: | 1ZBF, 1ZBI
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Bacillus halodurans RNase H catalytic domain mutant D192N in complex with 12-mer RNA/DNA hybrid
Overview
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.
About this Structure
1ZBL is a Single protein structure of sequence from Bacillus halodurans. Full crystallographic information is available from OCA.
Reference
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
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