Abstract
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.
Highlights
THE JOURNAL OF BIOLOGICAL CHEMISTRYVol 280, No 18, Issue of May 6, pp. 18326 –18335, 2005 Printed in U.S.A. Crystal Structure of a Nicotinate Phosphoribosyltransferase from Thermoplasma acidophilum*
From the ‡Berkeley Structural Genomics Center, Lawrence Berkeley National Laboratory, Berkeley, California 94720 and the §Department of Chemistry, University of California, Berkeley, California 94720-5230
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
Summary
Vol 280, No 18, Issue of May 6, pp. 18326 –18335, 2005 Printed in U.S.A. Crystal Structure of a Nicotinate Phosphoribosyltransferase from Thermoplasma acidophilum*. 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, their substrates are quite similar to each other. The structures of TaNAPRTase provide valuable insight for other sequence subfamilies such as pre-B cell colony-enhancing factor, known to have nicotinamide phosphoribosyltransferase activity. Overexpression of enzymes of the NAD biosynthetic pathway such as nicotinate phosphoribosyltransferase (NAPRTase), nicotinate mononucleotide adenylyltransferase, or nicotinamidase in yeast results in higher activity of the NAD-dependent histone deacetylase Sir2p and concomitant life span extension [7,8,9]. To elucidate the molecular function of NAPRTase, we have determined the crystal structures of native and substratebound forms of an NAPRTase homologue from Thermoplasma acidophilum (TaNAPRTase, gi: 16082162). Subfamilies is discussed based on the crystal structures together with sequence comparisons
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