2dqb: Difference between revisions
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==Crystal structure of dNTP triphosphohydrolase from Thermus thermophilus HB8, which is homologous to dGTP triphosphohydrolase== | ==Crystal structure of dNTP triphosphohydrolase from Thermus thermophilus HB8, which is homologous to dGTP triphosphohydrolase== | ||
<StructureSection load='2dqb' size='340' side='right' caption='[[2dqb]], [[Resolution|resolution]] 2.20Å' scene=''> | <StructureSection load='2dqb' size='340' side='right'caption='[[2dqb]], [[Resolution|resolution]] 2.20Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2dqb]] is a 6 chain structure with sequence from [ | <table><tr><td colspan='2'>[[2dqb]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DQB FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | </td></tr><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> | ||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TTHA0412 ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TTHA0412 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/dGTPase dGTPase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.5.1 3.1.5.1] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dqb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dqb OCA], [https://pdbe.org/2dqb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dqb RCSB], [https://www.ebi.ac.uk/pdbsum/2dqb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dqb ProSAT], [https://www.topsan.org/Proteins/RSGI/2dqb TOPSAN]</span></td></tr> | ||
</table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Thet8]] | [[Category: Thet8]] | ||
[[Category: DGTPase]] | [[Category: DGTPase]] | ||
Revision as of 14:35, 10 February 2021
Crystal structure of dNTP triphosphohydrolase from Thermus thermophilus HB8, which is homologous to dGTP triphosphohydrolaseCrystal structure of dNTP triphosphohydrolase from Thermus thermophilus HB8, which is homologous to dGTP triphosphohydrolase
Structural highlights
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 PubMedDeoxyribonucleoside triphosphate triphosphohydrolase from Thermus thermophilus (Tt-dNTPase) has a unique regulatory mechanism for the degradation of deoxyribonucleoside triphosphates (dNTPs). Whereas the Escherichia coli homologue specifically hydrolyzes dGTP alone, dNTPs act as both substrate and activator for Tt-dNTPase. Here, the crystal structure of Tt-dNTPase has been determined at 2.2 A resolution, representing the first report of the tertiary structure of a dNTPase homologue belonging to the HD superfamily, a diverse group of metal-dependent phosphohydrolases that includes a variety of uncharacterized proteins. This enzyme forms a homohexamer as a double ring of trimers. The subunit is composed of 19 alpha-helices; the inner six helices include the region annotated as the catalytic domain of the HD superfamily. Structural comparison with other HD-superfamily proteins indicates that a pocket at the centre of the inner six helices, formed from highly conserved charged residues clustered around a bound magnesium ion, constitutes the catalytic site. Tt-dNTPase also hydrolyzed noncanonical dNTPs, but hardly hydrolyzed dNDP and dNMP. The broad substrate specificity for different dNTPs might be rationalized by the involvement of a flexible loop during molecular recognition of the base moiety. Recognition of the triphosphate moiety crucial for the activity might be attained by highly conserved positively charged residues. The possible mode of dNTP binding is discussed in light of the structure. Structure of dNTP-inducible dNTP triphosphohydrolase: insight into broad specificity for dNTPs and triphosphohydrolase-type hydrolysis.,Kondo N, Nakagawa N, Ebihara A, Chen L, Liu ZJ, Wang BC, Yokoyama S, Kuramitsu S, Masui R Acta Crystallogr D Biol Crystallogr. 2007 Feb;63(Pt 2):230-9. Epub 2007, Jan 16. PMID:17242516[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)
OCA- Large Structures
- Thet8
- DGTPase
- Chen, L
- Ebihara, A
- Kondo, N
- Kuramitsu, S
- Liu, Z J
- Masui, R
- Nakagawa, N
- Structural genomic
- Wang, B C
- Yokoyama, S
- Dgtpase
- Dna
- Dna binding protein
- Dntp
- Dntpase
- Hd superfamily
- Hydrolase
- National project on protein structural and functional analyse
- Nppsfa
- Rsgi
- Single-stranded dna
- Triphosphohydrolase