3aa3: Difference between revisions

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<StructureSection load='3aa3' size='340' side='right'caption='[[3aa3]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='3aa3' size='340' side='right'caption='[[3aa3]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3aa3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AA3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3AA3 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3aa3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AA3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AA3 FirstGlance]. <br>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3aa2|3aa2]], [[3aa4|3aa4]], [[3aa5|3aa5]]</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]] 2.2&#8491;</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3aa3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3aa3 OCA], [https://pdbe.org/3aa3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3aa3 RCSB], [https://www.ebi.ac.uk/pdbsum/3aa3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3aa3 ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3aa3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3aa3 OCA], [http://pdbe.org/3aa3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3aa3 RCSB], [http://www.ebi.ac.uk/pdbsum/3aa3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3aa3 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://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]  
[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]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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=3aa3 ConSurf].
</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=3aa3 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
It has generally been accepted that an increase in protein stability is proportional to the increase in hydrophobicity. When a cavity is created by large-to-small substitutions of amino acid residues in protein cores, protein stability decreases 5.3 kJ/mol per single methyl(ene) group removal. In contrast, many reported cavity-filling mutations either failed to increase stability or produced marginal increases in stability; even in successful cases, the increase in stability was much lower than expected from the cost of single methyl(ene) group removal in cavity-creating mutations. Previously it was found that some cavity-filling mutant proteins at Ala52 in E. coli RNase HI increased stability, but decreased activity and they did not increase the stability to the degree expected by the hydrophobic effect alone. The present study attempted to structurally analyze these variant proteins, and it was found that substitutions have little effect on the overall fold but cause conformational strains with the neighboring residues. The present results and literature on cavity-creating/-filling variants provide insight into protein architecture, indicating that natural protein cores are able to accommodate larger side-chain residue by substitution; in other words, excess-packing may not be chosen in natural selection.
Protein core adaptability: crystal structures of the cavity-filling variants of Escherichia coli RNase HI.,Tanaka M, Chon H, Angkawidjaja C, Koga Y, Takano K, Kanaya S Protein Pept Lett. 2010 Sep;17(9):1163-9. PMID:20423323<ref>PMID:20423323</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3aa3" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
*[[Temp|Temp]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Ecoli]]
[[Category: Escherichia coli K-12]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Ribonuclease H]]
[[Category: Takano K]]
[[Category: Takano, K]]
[[Category: Cavity]]
[[Category: Endonuclease]]
[[Category: Hydrolase]]
[[Category: Magnesium]]
[[Category: Metal-binding]]
[[Category: Nuclease]]
[[Category: Stability]]

Latest revision as of 17:00, 13 March 2024

A52L E. coli RNase HIA52L E. coli RNase HI

Structural highlights

3aa3 is a 1 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.2Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

3aa3, resolution 2.20Å

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