1brn: Difference between revisions

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<StructureSection load='1brn' size='340' side='right'caption='[[1brn]], [[Resolution|resolution]] 1.76&Aring;' scene=''>
<StructureSection load='1brn' size='340' side='right'caption='[[1brn]], [[Resolution|resolution]] 1.76&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1brn]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_amyloliquifaciens"_(sic)_fukumoto_1943 "bacillus amyloliquifaciens" (sic) fukumoto 1943]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BRN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BRN FirstGlance]. <br>
<table><tr><td colspan='2'>[[1brn]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_amyloliquefaciens Bacillus amyloliquefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BRN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BRN FirstGlance]. <br>
</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=1brn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1brn OCA], [https://pdbe.org/1brn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1brn RCSB], [https://www.ebi.ac.uk/pdbsum/1brn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1brn ProSAT]</span></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]] 1.76&#8491;</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=1brn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1brn OCA], [https://pdbe.org/1brn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1brn RCSB], [https://www.ebi.ac.uk/pdbsum/1brn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1brn ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/RNBR_BACAM RNBR_BACAM]] Hydrolyzes phosphodiester bonds in RNA, poly- and oligoribonucleotides resulting in 3'-nucleoside monophosphates via 2',3'-cyclophosphate intermediates.  
[https://www.uniprot.org/uniprot/RNBR_BACAM RNBR_BACAM] Hydrolyzes phosphodiester bonds in RNA, poly- and oligoribonucleotides resulting in 3'-nucleoside monophosphates via 2',3'-cyclophosphate intermediates.
== 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=1brn 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=1brn ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
A set of subsites in barnase has been proposed from kinetic studies. A specific substrate analog, the tetradeoxynucleotide, CGAC, has been designed from this information. We report the crystal structure of its complex with barnase at 1.76-A resolution. The structure was solved by molecular replacement from a model of free barnase and refined to a crystallographic R factor of 19.0%. The stoichiometry of the asymmetric unit dimeric complex is [barnase:d(CGAC)]2, with 2-fold noncrystallographic symmetry. Each barnase molecule binds one oligonucleotide whereby the recognition site is occupied by guanine, and all three phosphate groups of the nucleotide make electrostatic interactions with basic residues in a strongly electropositive region at the bottom of the active site. The active-site His 102 packs against the adenine base of the nucleotide in an almost identical manner to the guanine base in the barnase-d(GpC) complex and defines a possible subsite in the Michaelis complex. The overall protein structure is unchanged on forming the complex with d(CGAC), but there are small differences in the active site and in crystal packing regions. The protein coordinates will be useful for theoretical calculations since some disorder induced by packing constraints in the crystals of the free enzyme are absent in the crystals of the complex. The interface of the dimer is formed by a His 102-adenine-adenine-His 102 face-to-face ring stack directly on the 2-fold axis. The edge of the adenine-adenine stack packs closely onto the face of a 3'-cytosine-3'-cytosine interaction, which has a "base-pair"-like conformation but too great a separation of the bases to form hydrogen bonds. This unusual arrangement is the major stabilizing interaction within the dimeric complex, since there are no direct protein-protein interactions. Using the structure of the complex as a starting point for model building, the nature of the enzyme-substrate and enzyme-transition state complexes is investigated.
Subsite binding in an RNase: structure of a barnase-tetranucleotide complex at 1.76-A resolution.,Buckle AM, Fersht AR Biochemistry. 1994 Feb 22;33(7):1644-53. PMID:8110767<ref>PMID:8110767</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1brn" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
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*[[Barnase 3D structures|Barnase 3D structures]]
*[[Barnase 3D structures|Barnase 3D structures]]
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus amyloliquefaciens]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Buckle, A M]]
[[Category: Buckle AM]]
[[Category: Fersht, A R]]
[[Category: Fersht AR]]
[[Category: Hydrolase-dna complex]]
[[Category: Protein-dna complex]]

Latest revision as of 09:38, 7 February 2024

SUBSITE BINDING IN AN RNASE: STRUCTURE OF A BARNASE-TETRANUCLEOTIDE COMPLEX AT 1.76 ANGSTROMS RESOLUTIONSUBSITE BINDING IN AN RNASE: STRUCTURE OF A BARNASE-TETRANUCLEOTIDE COMPLEX AT 1.76 ANGSTROMS RESOLUTION

Structural highlights

1brn is a 4 chain structure with sequence from Bacillus amyloliquefaciens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.76Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RNBR_BACAM Hydrolyzes phosphodiester bonds in RNA, poly- and oligoribonucleotides resulting in 3'-nucleoside monophosphates via 2',3'-cyclophosphate intermediates.

Evolutionary Conservation

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

See Also

1brn, resolution 1.76Å

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