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1ytd

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(New page: 200px<br /><applet load="1ytd" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ytd, resolution 2.80&Aring;" /> '''Crystal structure of...)
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[[Image:1ytd.gif|left|200px]]<br /><applet load="1ytd" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1ytd, resolution 2.80&Aring;" />
 
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'''Crystal structure of a nicotinate phosphoribosyltransferase from Thermoplasma acidophilum, Native Structure'''<br />
 
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==Overview==
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==Crystal structure of a nicotinate phosphoribosyltransferase from Thermoplasma acidophilum, Native Structure==
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We have determined the crystal structure of nicotinate, phosphoribosyltransferase from Themoplasma acidophilum (TaNAPRTase). The, TaNAPRTase has three domains, an N-terminal domain, a central functional, domain, and a unique C-terminal domain. The crystal structure revealed, that the functional domain has a type II phosphoribosyltransferase fold, that may be a common architecture for both nicotinic acid and quinolinic, acid (QA) phosphoribosyltransferases (PRTase) despite low sequence, similarity between them. Unlike QAPRTase, TaNAPRTase has a unique extra, C-terminal domain containing a zinc knuckle-like motif containing 4, cysteines. The TaNAPRTase forms a trimer of dimers in the crystal. The, active site pocket is formed at dimer interfaces. The complex structures, with phosphoribosylpyrophosphate (PRPP) and nicotinate mononucleotide, (NAMN) showed, surprisingly, that functional residues lining on the active, site of TaNAPRTase are quite different from those of QAPRTase, although, their substrates are quite similar to each other. The phosphate moiety of, PRPP and NAMN is anchored to the phosphate-binding loops formed by, backbone amides, as found in many alpha/beta barrel enzymes. The, pyrophosphate moiety of PRPP is located at the entrance of the active site, pocket, whereas the nicotinate moiety of NAMN is located deep inside., Interestingly, the nicotinate moiety of NAMN is intercalated between, highly conserved aromatic residues Tyr(21) and Phe(138). Careful, structural analyses combined with other NAPRTase sequence subfamilies, reveal that TaNAPRTase represents a unique sequence subfamily of NAPRTase., The structures of TaNAPRTase also provide valuable insight for other, sequence subfamilies such as pre-B cell colony-enhancing factor, known to, have nicotinamide phosphoribosyltransferase activity.
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<StructureSection load='1ytd' size='340' side='right'caption='[[1ytd]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1ytd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoplasma_acidophilum_DSM_1728 Thermoplasma acidophilum DSM 1728]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YTD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YTD FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ytd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ytd OCA], [https://pdbe.org/1ytd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ytd RCSB], [https://www.ebi.ac.uk/pdbsum/1ytd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ytd ProSAT], [https://www.topsan.org/Proteins/BSGC/1ytd TOPSAN]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PNCB_THEAC PNCB_THEAC] Catalyzes the transfer of the phosphoribosyl moiety of phosphoribosylpyrophosphate (PRPP) onto nicotinate (NA) to yield nicotinate mononucleotide (NAMN), an intermediate in the biosynthesis of NAD. Catalyzes the synthesis of beta-nicotinate D-ribonucleotide from nicotinate and 5-phospho-D-ribose 1-phosphate at the expense of ATP.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yt/1ytd_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1ytd ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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We have determined the crystal structure of nicotinate phosphoribosyltransferase from Themoplasma acidophilum (TaNAPRTase). The TaNAPRTase has three domains, an N-terminal domain, a central functional domain, and a unique C-terminal domain. The crystal structure revealed that the functional domain has a type II phosphoribosyltransferase fold that may be a common architecture for both nicotinic acid and quinolinic acid (QA) phosphoribosyltransferases (PRTase) despite low sequence similarity between them. Unlike QAPRTase, TaNAPRTase has a unique extra C-terminal domain containing a zinc knuckle-like motif containing 4 cysteines. The TaNAPRTase forms a trimer of dimers in the crystal. The active site pocket is formed at dimer interfaces. The complex structures with phosphoribosylpyrophosphate (PRPP) and nicotinate mononucleotide (NAMN) showed, surprisingly, that functional residues lining on the active site of TaNAPRTase are quite different from those of QAPRTase, although their substrates are quite similar to each other. The phosphate moiety of PRPP and NAMN is anchored to the phosphate-binding loops formed by backbone amides, as found in many alpha/beta barrel enzymes. The pyrophosphate moiety of PRPP is located at the entrance of the active site pocket, whereas the nicotinate moiety of NAMN is located deep inside. Interestingly, the nicotinate moiety of NAMN is intercalated between highly conserved aromatic residues Tyr(21) and Phe(138). Careful structural analyses combined with other NAPRTase sequence subfamilies reveal that TaNAPRTase represents a unique sequence subfamily of NAPRTase. The structures of TaNAPRTase also provide valuable insight for other sequence subfamilies such as pre-B cell colony-enhancing factor, known to have nicotinamide phosphoribosyltransferase activity.
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==About this Structure==
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Crystal structure of a nicotinate phosphoribosyltransferase from Thermoplasma acidophilum.,Shin DH, Oganesyan N, Jancarik J, Yokota H, Kim R, Kim SH J Biol Chem. 2005 May 6;280(18):18326-35. Epub 2005 Mar 6. PMID:15753098<ref>PMID:15753098</ref>
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1YTD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermoplasma_acidophilum_dsm_1728 Thermoplasma acidophilum dsm 1728]. Active as [http://en.wikipedia.org/wiki/Nicotinate_phosphoribosyltransferase Nicotinate phosphoribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.11 2.4.2.11] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1YTD OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Crystal structure of a nicotinate phosphoribosyltransferase from Thermoplasma acidophilum., Shin DH, Oganesyan N, Jancarik J, Yokota H, Kim R, Kim SH, J Biol Chem. 2005 May 6;280(18):18326-35. Epub 2005 Mar 6. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15753098 15753098]
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</div>
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[[Category: Nicotinate phosphoribosyltransferase]]
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<div class="pdbe-citations 1ytd" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Thermoplasma acidophilum dsm 1728]]
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[[Category: BSGC, Berkeley.Structural.Genomics.Center.]]
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[[Category: Shin, D.H.]]
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[[Category: berkeley structural genomics center]]
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[[Category: bsgc]]
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[[Category: crystal structure]]
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[[Category: nicotinate phosphoribosyltransferase]]
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[[Category: protein structure initiative]]
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[[Category: psi]]
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[[Category: structural genomics]]
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[[Category: type ii phosphoribosyltransferase]]
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[[Category: zinc-knuckle motif]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 04:34:01 2007''
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==See Also==
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*[[Phosphoribosyltransferase 3D structures|Phosphoribosyltransferase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Thermoplasma acidophilum DSM 1728]]
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[[Category: Shin DH]]

Current revision

Crystal structure of a nicotinate phosphoribosyltransferase from Thermoplasma acidophilum, Native Structure

PDB ID 1ytd

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