Balasundaram Padmanabhan

Summary

Publications

  1. pmc Structure of putative 4-amino-4-deoxychorismate lyase from Thermus thermophilus HB8
    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 65:1234-9. 2009
  2. pmc 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
  3. pmc 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
  4. ncbi request reprint Structural basis for the recognition between the regulatory particles Nas6 and Rpt3 of the yeast 26S proteasome
    Yoshihiro Nakamura
    RIKEN Genomic Sciences Center, Tsurumi, Yokohama 230 0045, Japan
    Biochem Biophys Res Commun 359:503-9. 2007
  5. pmc 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
  6. doi request reprint Structural implications for K5/K12-di-acetylated histone H4 recognition by the second bromodomain of BRD2
    Takashi Umehara
    RIKEN Systems and Structural Biology Center, Tsurumi, Yokohama, Japan
    FEBS Lett 584:3901-8. 2010
  7. pmc 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
  8. ncbi request reprint 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
  9. doi request reprint 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
  10. pmc 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

Collaborators

Detail Information

Publications18

  1. pmc Structure of putative 4-amino-4-deoxychorismate lyase from Thermus thermophilus HB8
    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 65:1234-9. 2009
    ..1.3.38) from Escherichia coli suggest that the TTHA0621 protein may also possess 4-amino-4-deoxychorismate lyase activity...
  2. pmc 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...
  3. pmc 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...
  4. ncbi request reprint Structural basis for the recognition between the regulatory particles Nas6 and Rpt3 of the yeast 26S proteasome
    Yoshihiro 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...
  5. pmc 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...
  6. doi request reprint Structural implications for K5/K12-di-acetylated histone H4 recognition by the second bromodomain of BRD2
    Takashi 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...
  7. pmc 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...
  8. ncbi request reprint 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...
  9. doi request reprint 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...
  10. pmc 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...
  11. pmc 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
    ....
  12. pmc 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...
  13. pmc 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...
  14. pmc 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...
  15. ncbi request reprint 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...
  16. pmc 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...
  17. ncbi request reprint 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...
  18. ncbi request reprint 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...