3a02 › Citations

Cooperative DNA-binding and sequence-recognition mechanism of aristaless and clawless.

Miyazono K, Zhi Y, Takamura Y, Nagata K, Saigo K, Kojima T, Tanokura M
EMBO J 29 1613-23 (2010)
Related entries: 3a01, 3a03, 3lnq

Cited: 28 times
EuropePMC logo PMID: 20389279

Abstract

To achieve accurate gene regulation, some homeodomain proteins bind cooperatively to DNA to increase those site specificities. We report a ternary complex structure containing two homeodomain proteins, aristaless (Al) and clawless (Cll), bound to DNA. Our results show that the extended conserved sequences of the Cll homeodomain are indispensable to cooperative DNA binding. In the Al-Cll-DNA complex structure, the residues in the extended regions are used not only for the intermolecular contacts between the two homeodomain proteins but also for the sequence-recognition mechanism of DNA by direct interactions. The residues in the extended N-terminal arm lie within the minor groove of DNA to form direct interactions with bases, whereas the extended conserved region of the C-terminus of the homeodomain interacts with Al to stabilize and localize the third alpha helix of the Cll homeodomain. This structure suggests a novel mode for the cooperativity of homeodomain proteins.

Articles - 3a02 mentioned but not cited (5)

  1. Cooperative DNA-binding and sequence-recognition mechanism of aristaless and clawless. Miyazono K, Zhi Y, Takamura Y, Nagata K, Saigo K, Kojima T, Tanokura M. EMBO J 29 1613-1623 (2010)
  2. First exposure to the pandemic H1N1 virus induced broadly neutralizing antibodies targeting hemagglutinin head epitopes. Guthmiller JJ, Han J, Li L, Freyn AW, Liu STH, Stovicek O, Stamper CT, Dugan HL, Tepora ME, Utset HA, Bitar DJ, Hamel NJ, Changrob S, Zheng NY, Huang M, Krammer F, Nachbagauer R, Palese P, Ward AB, Wilson PC. Sci Transl Med 13 eabg4535 (2021)
  3. Specificity landscapes unmask submaximal binding site preferences of transcription factors. Bhimsaria D, Rodríguez-Martínez JA, Pan J, Roston D, Korkmaz EN, Cui Q, Ramanathan P, Ansari AZ. Proc Natl Acad Sci U S A 115 E10586-E10595 (2018)
  4. Structural changes in DNA-binding proteins on complexation. Poddar S, Chakravarty D, Chakrabarti P. Nucleic Acids Res 46 3298-3308 (2018)
  5. The oxygen-oxygen distance of water in crystallographic data sets. Palese LL. Data Brief 28 105076 (2020)


Reviews citing this publication (1)

  1. Investigating Developmental and Epileptic Encephalopathy Using Drosophila melanogaster. Takai A, Yamaguchi M, Yoshida H, Chiyonobu T. Int J Mol Sci 21 E6442 (2020)

Articles citing this publication (22)

  1. Single-molecule imaging and kinetic analysis of cooperative cofilin-actin filament interactions. Hayakawa K, Sakakibara S, Sokabe M, Tatsumi H. Proc Natl Acad Sci U S A 111 9810-9815 (2014)
  2. Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy. Dorboz I, Aiello C, Simons C, Stone RT, Niceta M, Elmaleh M, Abuawad M, Doummar D, Bruselles A, Wolf NI, Travaglini L, Boespflug-Tanguy O, Tartaglia M, Vanderver A, Rodriguez D, Bertini E. Brain 140 2550-2556 (2017)
  3. Biallelic sequence and structural variants in RAX2 are a novel cause for autosomal recessive inherited retinal disease. Van de Sompele S, Smith C, Karali M, Corton M, Van Schil K, Peelman F, Cherry T, Rosseel T, Verdin H, Derolez J, Van Laethem T, Khan KN, McKibbin M, Toomes C, Ali M, Torella A, Testa F, Jimenez B, Simonelli F, De Zaeytijd J, Van den Ende J, Leroy BP, Coppieters F, Ayuso C, Inglehearn CF, Banfi S, De Baere E. Genet Med 21 1319-1329 (2019)
  4. Cephalopod eye evolution was modulated by the acquisition of Pax-6 splicing variants. Yoshida MA, Yura K, Ogura A. Sci Rep 4 4256 (2014)
  5. Phylogenetic and mutational analyses of human LEUTX, a homeobox gene implicated in embryogenesis. Katayama S, Ranga V, Jouhilahti EM, Airenne TT, Johnson MS, Mukherjee K, Bürglin TR, Kere J. Sci Rep 8 17421 (2018)
  6. Beamline AR-NW12A: high-throughput beamline for macromolecular crystallography at the Photon Factory. Chavas LM, Matsugaki N, Yamada Y, Hiraki M, Igarashi N, Suzuki M, Wakatsuki S. J Synchrotron Radiat 19 450-454 (2012)
  7. Correlation between Gene Variants, Signaling Pathways, and Efficacy of Chemotherapy Drugs against Colon Cancers. Tripathi S, Belkacemi L, Cheung MS, Bose RN. Cancer Inform 15 1-13 (2016)
  8. Investigating dynamic and energetic determinants of protein nucleic acid recognition: analysis of the zinc finger zif268-DNA complexes. Torella R, Moroni E, Caselle M, Morra G, Colombo G. BMC Struct Biol 10 42 (2010)
  9. Tissue-specific enhancer repression through molecular integration of cell signaling inputs. Mojica-Vázquez LH, Benetah MH, Baanannou A, Bernat-Fabre S, Deplancke B, Cribbs DL, Bourbon HM, Boube M. PLoS Genet 13 e1006718 (2017)
  10. Unheeded SARS-CoV-2 proteins? A deep look into negative-sense RNA. Bartas M, Volná A, Beaudoin CA, Poulsen ET, Červeň J, Brázda V, Špunda V, Blundell TL, Pečinka P. Brief Bioinform 23 bbac045 (2022)
  11. Distortion of double-stranded DNA structure by the binding of the restriction DNA glycosylase R.PabI. Miyazono KI, Wang D, Ito T, Tanokura M. Nucleic Acids Res 48 5106-5118 (2020)
  12. Dynamic Molecular Evolution of Mammalian Homeobox Genes: Duplication, Loss, Divergence and Gene Conversion Sculpt PRD Class Repertoires. Lewin TD, Royall AH, Holland PWH. J Mol Evol 89 396-414 (2021)
  13. A Novel Approach to Predict Core Residues on Cancer-Related DNA-Binding Domains. Wong KC. Cancer Inform 15 1-7 (2016)
  14. Structural and functional analysis of the human cone-rod homeobox transcription factor. Clanor PB, Buchholz CN, Hayes JE, Friedman MA, White AM, Enke RA, Berndsen CE. Proteins 90 1584-1593 (2022)
  15. Role of DNA conformation & energetic insights in Msx-1-DNA recognition as revealed by molecular dynamics studies on specific and nonspecific complexes. Kachhap S, Singh B. J Biomol Struct Dyn 33 2069-2082 (2015)
  16. Solution NMR structures of homeodomains from human proteins ALX4, ZHX1, and CASP8AP2 contribute to the structural coverage of the Human Cancer Protein Interaction Network. Xu X, Pulavarti SV, Eletsky A, Huang YJ, Acton TB, Xiao R, Everett JK, Montelione GT, Szyperski T. J Struct Funct Genomics 15 201-207 (2014)
  17. Arginine side chain stacking with peptide plane stabilizes the protein helix conformation in a cooperative way. Wang J, Chen J, Li J, An L, Wang Y, Huang Q, Yao L. Proteins 86 684-692 (2018)
  18. Coevolution of the Tlx homeobox gene with medusa development (Cnidaria: Medusozoa). Travert M, Boohar R, Sanders SM, Boosten M, Leclère L, Steele RE, Cartwright P. Commun Biol 6 709 (2023)
  19. Molecular dynamics simulations show altered secondary structure of clawless in binary complex with DNA providing insights into aristaless-clawless-DNA ternary complex formation. Kachhap S, Priyadarshini P, Singh B. J Biomol Struct Dyn 35 1153-1167 (2017)
  20. Rapid Evolution of the Embryonically Expressed Homeobox Gene LEUTX within Primates. Lewin TD, Blagrove JR, Holland PWH. Genome Biol Evol 15 evad097 (2023)
  21. Solution structure of CEH-37 homeodomain of the nematode Caenorhabditis elegans. Moon S, Lee YW, Kim WT, Lee W. Biochem Biophys Res Commun 443 370-375 (2014)
  22. Structure of the unique tetrameric STENOFOLIA homeodomain bound with target promoter DNA. Pathak PK, Zhang F, Peng S, Niu L, Chaturvedi J, Elliott J, Xiang Y, Tadege M, Deng J. Acta Crystallogr D Struct Biol 77 1050-1063 (2021)


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