Structure of putative 4-amino-4-deoxychorismate lyase from Thermus thermophilus HB8Balasundaram Padmanabhan
Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1 7 22 Suehiro, Tsurumi, Yokohama 230 0045, Japan
Acta Crystallogr Sect F Struct Biol Cryst Commun 65:1234-9. 2009
..1.3.38) from Escherichia coli suggest that the TTHA0621 protein may also possess 4-amino-4-deoxychorismate lyase activity...
- Structure of dihydrodipicolinate synthase from Methanocaldococcus jannaschii
Balasundaram Padmanabhan
Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1 7 22 Suehiro, Tsurumi, Yokohama 230 0045, Japan
Acta Crystallogr Sect F Struct Biol Cryst Commun 65:1222-6. 2009
..The binding-site region of MjDHDPS is essentially similar to those found in other known DHDPS structures...
- Structure of glyceraldehyde-3-phosphate dehydrogenase from the archaeal hyperthermophile Methanocaldococcus jannaschii
Ali D Malay
Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1 7 22 Suehiro, Tsurumi, Yokohama 230 0045, Japan
Acta Crystallogr Sect F Struct Biol Cryst Commun 65:1227-33. 2009
..The key phosphate-binding residues in the active site of Mj-GAPDH are conserved in other archaeal GAPDH proteins. These residues undergo a conformational shift in response to occupancy of the inorganic phosphate site...
Structural basis for the recognition between the regulatory particles Nas6 and Rpt3 of the yeast 26S proteasomeYoshihiro Nakamura
RIKEN Genomic Sciences Center, Tsurumi, Yokohama 230 0045, Japan
Biochem Biophys Res Commun 359:503-9. 2007
..These results provide a structural basis for the association between Nas6 and the heterohexameric ATPase ring of the proteasome through Rpt3...
- Structural basis for acetylated histone H4 recognition by the human BRD2 bromodomain
Takashi Umehara
RIKEN Systems and Structural Biology Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
J Biol Chem 285:7610-8. 2010
..Our findings provide a structural basis for deciphering the histone code by the BET bromodomain through the binding with a long segment of the histone H4 tail, which presumably prevents erasure of the histone code during the cell cycle...
Structural implications for K5/K12-di-acetylated histone H4 recognition by the second bromodomain of BRD2Takashi Umehara
RIKEN Systems and Structural Biology Center, Tsurumi, Yokohama, Japan
FEBS Lett 584:3901-8. 2010
..These results provide a structural basis for the recognition of two different patterns of the histone acetylation status by a single bromodomain...
- Purification, crystallization and preliminary X-ray diffraction analysis of the Kelch-like motif region of mouse Keap1
Balasundaram Padmanabhan
RIKEN Genomic Sciences Center, Tsurumi, Yokohama 230 0045, Japan
Acta Crystallogr Sect F Struct Biol Cryst Commun 61:153-5. 2005
..95, c = 55.21 A, and contains one molecule in the asymmetric unit. A complete diffraction data was collected to 2.25 A resolution using an R-AXIS IV++ imaging plate mounted on an RA-Micro7 Cu Kalpha rotating-anode X-ray generator...
- Crystal structure analysis of the PHD domain of the transcription co-activator Pygopus
Yoshihiro Nakamura
RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
J Mol Biol 370:80-92. 2007
..These results suggest that the Pygo1 PHD dimerization is functionally important for Lgs/Bcl9 recognition as well as for the regulation of the Wnt/beta-catenin signaling pathway...
- Crystal structures of fission yeast histone chaperone Asf1 complexed with the Hip1 B-domain or the Cac2 C terminus
Ali D Malay
Yokohama Institute, RIKEN, Tsurumi, Yokohama 230 0045, Japan
J Biol Chem 283:14022-31. 2008
..1/H4 in vertebrates) in a replication-dependent pathway, whereas Asf1 and HIRA/Hip1 assemble histones H3/H4 (H3.3/H4 in vertebrates) in a replication-independent pathway...
- Purification, crystallization and preliminary X-ray diffraction analysis of the non-ATPase subunit Nas6 in complex with the ATPase subunit Rpt3 of the 26S proteasome from Saccharomyces cerevisiae
Yoshihiro Nakamura
RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
Acta Crystallogr Sect F Struct Biol Cryst Commun 63:190-2. 2007
..38, b = 100.22, c = 72.20 A, beta = 94.70 degrees and with three Nas6-Rpt3C molecules per asymmetric unit. The crystal diffracted to beyond 2.2 A resolution using synchrotron radiation...
- Structural analysis of the complex of Keap1 with a prothymosin alpha peptide
Balasundaram Padmanabhan
Genomic Sciences Center, Yokohama Institute, RIKEN, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
Acta Crystallogr Sect F Struct Biol Cryst Commun 64:233-8. 2008
....
- Solution structure of the extraterminal domain of the bromodomain-containing protein BRD4
Yi Jan Lin
1Tatsuo Miyazawa Memorial Program, RIKEN Genomic Sciences Center, Yokohama 230 0045, Japan
Protein Sci 17:2174-9. 2008
..A DALI search revealed no close structural homologs in the current Protein Data Bank. The BRD4-ET structure has an acidic patch that forms a continuous ridge with a hydrophobic cleft, which may interact with other proteins and/or DNA...
- Purification, crystallization and preliminary X-ray diffraction of the C-terminal bromodomain from human BRD2
Takashi Umehara
Genomic Sciences Center, Yokohama Institute, RIKEN, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
Acta Crystallogr Sect F Struct Biol Cryst Commun 63:613-5. 2007
..78, b = 52.60, c = 32.06 A and one molecule per asymmetric unit. The crystal diffracted beyond 1.80 A resolution using synchrotron radiation...
- Structural insights into the similar modes of Nrf2 transcription factor recognition by the cytoplasmic repressor Keap1
Balasundaram Padmanabhan
Genomic Sciences Center, Yokohama Institute, RIKEN, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
J Synchrotron Radiat 15:273-6. 2008
..Comparison of the present structure with the recently reported Keap1-DC complex structure suggests that the DLG and ETGE motifs of Neh2 in Nrf2 bind to Keap1 in a similar manner but with different binding potencies...
- Structure of the oncoprotein gankyrin in complex with S6 ATPase of the 26S proteasome
Yoshihiro Nakamura
RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
Structure 15:179-89. 2007
..These results provide a structural basis for the involvement of gankyrin in the pRb degradation pathway, through its association with S6 ATPase of the 26S proteasome...
- Purification, crystallization and preliminary X-ray diffraction analysis of the histone chaperone cia1 from fission yeast
Takashi Umehara
RIKEN Genomic Sciences Center, 1 7 22 Suehiro, Tsurumi, Yokohama 230 0045, Japan
Acta Crystallogr Sect F Struct Biol Cryst Commun 61:971-3. 2005
..16, b = 40.53, c = 69.79 A, beta = 115.93 degrees and one molecule per asymmetric unit. The crystal diffracted to beyond 2.10 A resolution using synchrotron radiation...
- Crystal structure of the human BRD2 bromodomain: insights into dimerization and recognition of acetylated histone H4
Yoshihiro Nakamura
RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
J Biol Chem 282:4193-201. 2007
..The two acetyllysine-binding pockets and a negatively charged secondary binding pocket, produced at the dimer interface in BRD2 BD1, may be the unique features that allow BRD2 BD1 to selectively bind to the acetylated H4 tail...
- Structural basis for defects of Keap1 activity provoked by its point mutations in lung cancer
Balasundaram Padmanabhan
RIKEN Genomic Sciences Center, Tsurumi, Yokohama 230 0045, Japan
Mol Cell 21:689-700. 2006
..These results provide a structural basis for the loss of Keap1 function and gain of Nrf2 function...
