|
|
| (4 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| | + | |
| | ==Crystal structure of a nicotinate phosphoribosyltransferase from Thermoplasma acidophilum with nicotinate mononucleotide== | | ==Crystal structure of a nicotinate phosphoribosyltransferase from Thermoplasma acidophilum with nicotinate mononucleotide== |
| - | <StructureSection load='1ytk' size='340' side='right' caption='[[1ytk]], [[Resolution|resolution]] 2.65Å' scene=''> | + | <StructureSection load='1ytk' size='340' side='right'caption='[[1ytk]], [[Resolution|resolution]] 2.65Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1ytk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Theac Theac]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YTK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YTK FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1ytk]] 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=1YTK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YTK FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NCN:NICOTINATE+MONONUCLEOTIDE'>NCN</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></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]] 2.65Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ytd|1ytd]], [[1yte|1yte]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NCN:NICOTINATE+MONONUCLEOTIDE'>NCN</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nicotinate_phosphoribosyltransferase Nicotinate phosphoribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.4.21 6.3.4.21] </span></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=1ytk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ytk OCA], [https://pdbe.org/1ytk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ytk RCSB], [https://www.ebi.ac.uk/pdbsum/1ytk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ytk ProSAT], [https://www.topsan.org/Proteins/BSGC/1ytk TOPSAN]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ytk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ytk OCA], [http://pdbe.org/1ytk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ytk RCSB], [http://www.ebi.ac.uk/pdbsum/1ytk PDBsum], [http://www.topsan.org/Proteins/BSGC/1ytk TOPSAN]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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. | + | [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. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yt/1ytk_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yt/1ytk_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
| Line 31: |
Line 31: |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Phosphoribosyltransferase|Phosphoribosyltransferase]] | + | *[[Phosphoribosyltransferase 3D structures|Phosphoribosyltransferase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Nicotinate phosphoribosyltransferase]] | + | [[Category: Large Structures]] |
| - | [[Category: Theac]] | + | [[Category: Thermoplasma acidophilum DSM 1728]] |
| - | [[Category: Structural genomic]]
| + | [[Category: Shin DH]] |
| - | [[Category: Shin, D H]] | + | |
| - | [[Category: Bsgc]]
| + | |
| - | [[Category: PSI, Protein structure initiative]]
| + | |
| - | [[Category: Transferase]]
| + | |
| - | [[Category: Type ii phosphoribosyltransferase]]
| + | |
| - | [[Category: Zinc-knuckle motif]]
| + | |
| Structural highlights
Function
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.
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 PubMed
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Shin DH, Oganesyan N, Jancarik J, Yokota H, Kim R, Kim SH. Crystal structure of a nicotinate phosphoribosyltransferase from Thermoplasma acidophilum. J Biol Chem. 2005 May 6;280(18):18326-35. Epub 2005 Mar 6. PMID:15753098 doi:10.1074/jbc.M501622200
|
