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Crystal Structure of a Nicotinate Phosphoribosyltransferase from Thermoplasma acidophilum
Shin, Dong-Hae,Oganesyan, Natalia,Jancarik, Jaru,Yokota, Hisao,Kim, Rosalind,Kim, Sung-Hou 이화여자대학교 약학연구소 2005 藥學硏究論文集 Vol.- No.16
We have determined the crystal structure of nicotinate phosphoribosyltransferase from Themopaasma 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 phosphatemoiety of PRPP and NAMN is anchored to the phosphate-binding loops formed by backbone amides, as found in many α/β barrel enzymes. The pyrophosphatemoiety 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.
Shin, Dong Hae,Michael Proudfoot,Lim, Hyo Jin,Choi, In-Kyu,Hisao Yokota,Alexander F. Yaunin,Kim, Rosalind,Kim, Sung-Hou 이화여자대학교 세포신호전달연구센터 2007 고사리 세포신호전달 심포지움 Vol. No.9
We have determined the crystal structure of DR1281 from Deinococcus radiodurans. DR1281 is a protein of unknown function with over 170 homologs found in prokaryotes and eukaryotes. In order to elucidate the molecular function of DR1281, its crystal structure at 2.3Å resolution was determined and a series of biochemical screens for catalytic activity was performed. The crystal structure shows that DR1281 has two domains, a small α domain, and a putative catalytic domain formed by a four-layered structure of two β-sheets flanked by five α-helices on both sides. The small α domain interacts with other molecules in the asymmetric unit and contributes to the formation of oligomers. The structural comparison of the putative catalytic domain with known structures suggested its biochemical function to be a phosphatase, phosphodiesterase, nuclease, or nucleotidase. Structural analyses with its homologues also indicated that there is a dinuclear center at the interface of two domains formed by Asp8, Glu37, Asn38, Asn65, His148, His173, and His175. An absolute requirement of metal ions for activity has been proved by enzymatic assay with various divalent metal ions. A panel of general enzymatic assays of DR1281 revealed metal-dependent catalytic activity toward model substrates for phosphatases(p-nitrophenyl phosphate) and phosphodiesterases(bis-p-nitrophenyl phosphate). Subsequent secondary enzymatic screens with natural substrates demonstrated significant phosphatase activity toward phosphoenolpyruvate and phosphodiesterase activity toward 2',3'-cAMP. Thus, our structural and enzymatic studies have identified the biochemical function of DR1281 as a novel phosphatase/phosphodiesterase and disclosed key conserved residues involved in metal binding and catalytic activity.
Crystal Structure of ScpB from Chlorobium tepidum, a Protein Involved in Chromosome Partitioning
Kim, Jeong-Sun,Shin, Dong Hae,Pufan, Ramona,Huang, Candice,Yokota, Hisao,Kim, Rosalind,Kim, Sung-Hou 이화여자대학교 약학연구소 2008 藥學硏究論文集 Vol.- No.17
Structural maintenance of chromo- some (SMC) Proteins are essential in chromosome condensation and interact with non-SMC proteins in eukaryotes and with segregation and condensation proteins (ScpA and ScpB) in prokaryotes. The highly conserved gene in Chlorobium tepidum gi 21646405 encodes ScpB (ScpB_ChTe). The high resolution crystal structure of ScpB_ChTe shows that the monomeric structure consists of two similarly shaped globular domains composed of three helices sided by β-strands [a winged helix-turn-helix (HTH)], a motif observed in the C-terminal domain of Scc1, a functionally related eukaryotic ScpA homolog, as well as in many DNA binding proteins, Proteins 2006;62:322-328. ⓒ 2005 Wiley-Liss, Inc.
On the mechanism of chaperone activity of the small heat-shock protein of Methanococcus jannaschii
Kim, Rosalind,Luhua Lai,Lee, Hi-Hong,Cheong, Gang-Won,Kim, Kyeong-Kyu,Zheng Wu,Hisao Yokota,Susan Marqusee,Kim, Sung-Hou Plant molecular biology and biotechnology research 2003 Plant molecular biology and biotechnology research Vol.2003 No.-
The small heat-shock protein (sHSP) from Methanococcus jannaschii (Mj HSP16.5) forms a homomeric complex of 24 subunits and has an overall structure of a multiwindowed hollow sphere with an external diameter of ≈120 Å and an internal diameter of ≈65 Å with six square "windows" of ≈17 Å across and eight triangular windows of ≈30 Å across. This sHSP has been known to protect other proteins from thermal denaturation. Using purified single-chain monellin as a substrate and a series of methods such as protease digestion, antibody binding, and electron microscopy, we show that the substrates bind to Mj HSP16.5 at a high temperature (80℃) on the outside surface of the sphere and are prevented from forming insoluble substrate aggregates in vitro. Circular dichroism studies suggest that a very small, if any, conformational change occurs in sHSP even at 80℃, but substantial conformational changes of the substrate are required for complex formation at 80℃. Furthermore, deletion mutation studies of Mj HSP16.5 suggest that the N-terminal region of the protein has no structural role but may play an important kinetic role in the assembly of the sphere by "preassembly condensation" of multiple monomers before final assembly of the sphere.