1rdd

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(New page: 200px<br /><applet load="1rdd" size="450" color="white" frame="true" align="right" spinBox="true" caption="1rdd, resolution 2.8&Aring;" /> '''CRYSTAL STRUCTURE OF ...)
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[[Image:1rdd.gif|left|200px]]<br /><applet load="1rdd" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1rdd, resolution 2.8&Aring;" />
 
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'''CRYSTAL STRUCTURE OF ESCHERICHIA COLI RNASE HI IN COMPLEX WITH MG2+ AT 2.8 ANGSTROMS RESOLUTION: PROOF FOR A SINGLE MG2+ SITE'''<br />
 
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==Overview==
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==CRYSTAL STRUCTURE OF ESCHERICHIA COLI RNASE HI IN COMPLEX WITH MG2+ AT 2.8 ANGSTROMS RESOLUTION: PROOF FOR A SINGLE MG2+ SITE==
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To obtain more precise insight into the Mg(2+)-binding site essential for, RNase HI catalytic activity, we have determined the crystal structure of, E. coli RNase HI in complex with Mg2+. The analyzed cocrystal, which is, not isomorphous with the Mg(2+)-free crystal previously refined at 1.48 A, resolution, was grown at a high MgSO4 concentration more than 100 mM so, that even weakly bound Mg2+ sites could be identified. The structure was, solved by the molecular replacement method, using the Mg(2+)-free crystal, structure as a search model, and was refined to give a final R-value of, 0.190 for intensity data from 10 to 2.8 A, using the XPLOR and PROLSQ, programs. The backbone structures are in their entirety very similar to, each other between the Mg(2+)-bound and the metal-free crystals, except, for minor regions in the enzyme interface with the DNA/RNA hybrid. The, active center clearly revealed a single Mg2+ atom located at a position, almost identical to that previously found by the soaking method. Although, the two metal-ion mechanism had been suggested by another group (Yang, W., Hendrickson, W.A., Crouch, R.J., Satow, Y. Science 249:1398-1405, 1990), and partially supported by the crystallographic study of inactive HIV-1 RT, RNase H fragment (Davies, J.F., II, Hostomska, Z., Hostomsky, Z., Jordan, S.R., Matthews, D. Science 252:88-95, 1991), the present result excludes, the possibility that RNase HI requires two metal-binding sites for, activity. In contrast to the features in the metal-free enzyme, the side, chains of Asn-44 and Glu-48 are found to form coordinate bonds with Mg2+, in the metal-bound crystal.
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<StructureSection load='1rdd' size='340' side='right'caption='[[1rdd]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1rdd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RDD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RDD FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
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<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>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rdd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rdd OCA], [https://pdbe.org/1rdd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rdd RCSB], [https://www.ebi.ac.uk/pdbsum/1rdd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rdd ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RNH_ECOLI RNH_ECOLI] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. RNase H participates in DNA replication; it helps to specify the origin of genomic replication by suppressing initiation at origins other than the oriC locus; along with the 5'-3' exonuclease of pol1, it removes RNA primers from the Okazaki fragments of lagging strand synthesis; and it defines the origin of replication for ColE1-type plasmids by specific cleavage of an RNA preprimer.[HAMAP-Rule:MF_00042]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rd/1rdd_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1rdd ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1RDD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with MG as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1RDD OCA].
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*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Crystal structure of Escherichia coli RNase HI in complex with Mg2+ at 2.8 A resolution: proof for a single Mg(2+)-binding site., Katayanagi K, Okumura M, Morikawa K, Proteins. 1993 Dec;17(4):337-46. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8108376 8108376]
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[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Ribonuclease H]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Katayanagi K]]
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[[Category: Katayanagi, K.]]
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[[Category: Morikawa K]]
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[[Category: Morikawa, K.]]
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[[Category: MG]]
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[[Category: hydrolase(endoribonuclease)]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 01:29:23 2007''
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Current revision

CRYSTAL STRUCTURE OF ESCHERICHIA COLI RNASE HI IN COMPLEX WITH MG2+ AT 2.8 ANGSTROMS RESOLUTION: PROOF FOR A SINGLE MG2+ SITE

PDB ID 1rdd

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