2dqb: Difference between revisions
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|PDB= 2dqb |SIZE=350|CAPTION= <scene name='initialview01'>2dqb</scene>, resolution 2.2Å | |PDB= 2dqb |SIZE=350|CAPTION= <scene name='initialview01'>2dqb</scene>, resolution 2.2Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=MG:MAGNESIUM ION'>MG</scene> | |LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene> | ||
|ACTIVITY= [http://en.wikipedia.org/wiki/dGTPase dGTPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.5.1 3.1.5.1] | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/dGTPase dGTPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.5.1 3.1.5.1] </span> | ||
|GENE= TTHA0412 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus]) | |GENE= TTHA0412 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus]) | ||
|DOMAIN= | |||
|RELATEDENTRY= | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dqb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dqb OCA], [http://www.ebi.ac.uk/pdbsum/2dqb PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2dqb RCSB]</span> | |||
}} | }} | ||
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[[Category: Wang, B C.]] | [[Category: Wang, B C.]] | ||
[[Category: Yokoyama, S.]] | [[Category: Yokoyama, S.]] | ||
[[Category: dgtpase]] | [[Category: dgtpase]] | ||
[[Category: dna]] | [[Category: dna]] | ||
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[[Category: triphosphohydrolase]] | [[Category: triphosphohydrolase]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:38:02 2008'' | ||
Revision as of 02:38, 31 March 2008
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| , resolution 2.2Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Gene: | TTHA0412 (Thermus thermophilus) | ||||||
| Activity: | dGTPase, with EC number 3.1.5.1 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of dNTP triphosphohydrolase from Thermus thermophilus HB8, which is homologous to dGTP triphosphohydrolase
OverviewOverview
Deoxyribonucleoside 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.
About this StructureAbout this Structure
2DQB is a Single protein structure of sequence from Thermus thermophilus. Full crystallographic information is available from OCA.
ReferenceReference
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
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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)
OCA- Pages with broken file links
- Single protein
- Thermus thermophilus
- DGTPase
- Chen, L.
- Ebihara, A.
- Kondo, N.
- Kuramitsu, S.
- Liu, Z J.
- Masui, R.
- Nakagawa, N.
- RSGI, RIKEN Structural Genomics/Proteomics Initiative.
- Wang, B C.
- Yokoyama, S.
- Dgtpase
- Dna
- Dntp
- Dntpase
- Hd superfamily
- National project on protein structural and functional analyse
- Nppsfa
- Riken structural genomics/proteomics initiative
- Rsgi
- Single-stranded dna
- Structural genomic
- Triphosphohydrolase