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New page: left|200px<br /><applet load="1mi8" size="450" color="white" frame="true" align="right" spinBox="true" caption="1mi8, resolution 2.0Å" /> '''2.0 Angstrom crystal ... |
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== | ==2.0 Angstrom crystal structure of a DnaB intein from Synechocystis sp. PCC 6803== | ||
We have determined the crystal structure of a 154-residue intein derived | <StructureSection load='1mi8' size='340' side='right'caption='[[1mi8]], [[Resolution|resolution]] 2.00Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1mi8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechocystis_sp._PCC_6803 Synechocystis sp. PCC 6803]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MI8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MI8 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</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=1mi8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mi8 OCA], [https://pdbe.org/1mi8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mi8 RCSB], [https://www.ebi.ac.uk/pdbsum/1mi8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mi8 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/DNAB_SYNY3 DNAB_SYNY3] Participates in initiation and elongation during chromosome replication; it exhibits DNA-dependent ATPase activity (By similarity). | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mi/1mi8_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</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=1mi8 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
We have determined the crystal structure of a 154-residue intein derived from the dnaB gene of Synechocystis sp. strain PCC6803 and refined it to a 2.0-A resolution. The x-ray structure suggests that this intein possesses two catalytic sites that appear to be separately responsible for splicing and cleavage of the N- and C-terminal scissile bonds. The conserved intein block F residues are the important components of a catalytic site for side chain cyclization of the last intein residue, Asn-154. The data suggest that the imidazole ring of His-143 is involved in the activation of the side chain Ndelta atom of Asn-154, leading to a nucleophilic attack on the carbonyl carbon of Asn-154. Substitution of His-143 with Ala or Gln resulted in the inhibition of C-terminal cleavage. His-153, Asp-136, and a water molecule appear to constitute an oxyanion binding site by contacting the carbonyl oxygen of Asn-154 to stabilize the transition state. The structure and mutagenesis data also support that the close contact between the hydroxyl groups of Thr-138 and Ser-155, whose side chain participates in an S --> O acyl shift, plays an important role in the nucleophile orientation. Our structural modeling suggests that this catalytic module is conserved in the C-terminal subdomains of inteins from diverse organisms. | |||
Crystal structure of a mini-intein reveals a conserved catalytic module involved in side chain cyclization of asparagine during protein splicing.,Ding Y, Xu MQ, Ghosh I, Chen X, Ferrandon S, Lesage G, Rao Z J Biol Chem. 2003 Oct 3;278(40):39133-42. Epub 2003 Jul 23. PMID:12878593<ref>PMID:12878593</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1mi8" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Helicase 3D structures|Helicase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Synechocystis sp. PCC 6803]] | |||
[[Category: Chen X]] | |||
[[Category: Ding Y]] | |||
[[Category: Ferrandon S]] | |||
[[Category: Rao Z]] | |||
[[Category: Xu M]] | |||
Latest revision as of 21:14, 29 May 2024
2.0 Angstrom crystal structure of a DnaB intein from Synechocystis sp. PCC 68032.0 Angstrom crystal structure of a DnaB intein from Synechocystis sp. PCC 6803
Structural highlights
FunctionDNAB_SYNY3 Participates in initiation and elongation during chromosome replication; it exhibits DNA-dependent ATPase activity (By similarity). 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 PubMedWe have determined the crystal structure of a 154-residue intein derived from the dnaB gene of Synechocystis sp. strain PCC6803 and refined it to a 2.0-A resolution. The x-ray structure suggests that this intein possesses two catalytic sites that appear to be separately responsible for splicing and cleavage of the N- and C-terminal scissile bonds. The conserved intein block F residues are the important components of a catalytic site for side chain cyclization of the last intein residue, Asn-154. The data suggest that the imidazole ring of His-143 is involved in the activation of the side chain Ndelta atom of Asn-154, leading to a nucleophilic attack on the carbonyl carbon of Asn-154. Substitution of His-143 with Ala or Gln resulted in the inhibition of C-terminal cleavage. His-153, Asp-136, and a water molecule appear to constitute an oxyanion binding site by contacting the carbonyl oxygen of Asn-154 to stabilize the transition state. The structure and mutagenesis data also support that the close contact between the hydroxyl groups of Thr-138 and Ser-155, whose side chain participates in an S --> O acyl shift, plays an important role in the nucleophile orientation. Our structural modeling suggests that this catalytic module is conserved in the C-terminal subdomains of inteins from diverse organisms. Crystal structure of a mini-intein reveals a conserved catalytic module involved in side chain cyclization of asparagine during protein splicing.,Ding Y, Xu MQ, Ghosh I, Chen X, Ferrandon S, Lesage G, Rao Z J Biol Chem. 2003 Oct 3;278(40):39133-42. Epub 2003 Jul 23. PMID:12878593[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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