1ytd
From Proteopedia
(New page: 200px<br /><applet load="1ytd" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ytd, resolution 2.80Å" /> '''Crystal structure of...) |
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| - | [[Image:1ytd.gif|left|200px]]<br /><applet load="1ytd" size=" | + | [[Image:1ytd.gif|left|200px]]<br /><applet load="1ytd" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1ytd, resolution 2.80Å" /> | caption="1ytd, resolution 2.80Å" /> | ||
'''Crystal structure of a nicotinate phosphoribosyltransferase from Thermoplasma acidophilum, Native Structure'''<br /> | '''Crystal structure of a nicotinate phosphoribosyltransferase from Thermoplasma acidophilum, Native Structure'''<br /> | ||
==Overview== | ==Overview== | ||
| - | We have determined the crystal structure of nicotinate | + | 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. |
==About this Structure== | ==About this Structure== | ||
| - | 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:// | + | 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1YTD OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Thermoplasma acidophilum dsm 1728]] | [[Category: Thermoplasma acidophilum dsm 1728]] | ||
| - | [[Category: BSGC, Berkeley | + | [[Category: BSGC, Berkeley Structural Genomics Center.]] |
| - | [[Category: Shin, D | + | [[Category: Shin, D H.]] |
[[Category: berkeley structural genomics center]] | [[Category: berkeley structural genomics center]] | ||
[[Category: bsgc]] | [[Category: bsgc]] | ||
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[[Category: zinc-knuckle motif]] | [[Category: zinc-knuckle motif]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:08:51 2008'' |
Revision as of 14:08, 21 February 2008
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Crystal structure of a nicotinate phosphoribosyltransferase from Thermoplasma acidophilum, Native Structure
Overview
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.
About this Structure
1YTD is a Single protein structure of sequence from Thermoplasma acidophilum dsm 1728. Active as Nicotinate phosphoribosyltransferase, with EC number 2.4.2.11 Full crystallographic information is available from OCA.
Reference
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
Page seeded by OCA on Thu Feb 21 16:08:51 2008
Categories: Nicotinate phosphoribosyltransferase | Single protein | Thermoplasma acidophilum dsm 1728 | BSGC, Berkeley Structural Genomics Center. | Shin, D H. | Berkeley structural genomics center | Bsgc | Crystal structure | Protein structure initiative | Psi | Structural genomics | Type ii phosphoribosyltransferase | Zinc-knuckle motif
