PDBsum entry 1buo

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Gene regulation PDB id
Jmol PyMol
Protein chain
121 a.a. *
Waters ×129
* Residue conservation analysis
PDB id:
Name: Gene regulation
Title: Btb domain from plzf
Structure: Protein (promyelocytic leukemia zinc finger prote chain: a. Fragment: btb domain. Synonym: poz domain. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell_line: b834(de3).
Biol. unit: Dimer (from PDB file)
1.90Å     R-factor:   0.212     R-free:   0.252
Authors: K.F.Ahmad,C.K.Engel,G.G.Prive
Key ref:
K.F.Ahmad et al. (1998). Crystal structure of the BTB domain from PLZF. Proc Natl Acad Sci U S A, 95, 12123-12128. PubMed id: 9770450 DOI: 10.1073/pnas.95.21.12123
04-Sep-98     Release date:   14-Oct-98    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q05516  (ZBT16_HUMAN) -  Zinc finger and BTB domain-containing protein 16
673 a.a.
121 a.a.
Key:    PfamA domain  Secondary structure  CATH domain


DOI no: 10.1073/pnas.95.21.12123 Proc Natl Acad Sci U S A 95:12123-12128 (1998)
PubMed id: 9770450  
Crystal structure of the BTB domain from PLZF.
K.F.Ahmad, C.K.Engel, G.G.Privé.
The BTB domain (also known as the POZ domain) is an evolutionarily conserved protein-protein interaction motif found at the N terminus of 5-10% of C2H2-type zinc-finger transcription factors, as well as in some actin-associated proteins bearing the kelch motif. Many BTB proteins are transcriptional regulators that mediate gene expression through the control of chromatin conformation. In the human promyelocytic leukemia zinc finger (PLZF) protein, the BTB domain has transcriptional repression activity, directs the protein to a nuclear punctate pattern, and interacts with components of the histone deacetylase complex. The association of the PLZF BTB domain with the histone deacetylase complex provides a mechanism of linking the transcription factor with enzymatic activities that regulate chromatin conformation. The crystal structure of the BTB domain of PLZF was determined at 1.9 A resolution and reveals a tightly intertwined dimer with an extensive hydrophobic interface. Approximately one-quarter of the monomer surface area is involved in the dimer intermolecular contact. These features are typical of obligate homodimers, and we expect the full-length PLZF protein to exist as a branched transcription factor with two C-terminal DNA-binding regions. A surface-exposed groove lined with conserved amino acids is formed at the dimer interface, suggestive of a peptide-binding site. This groove may represent the site of interaction of the PLZF BTB domain with nuclear corepressors or other nuclear proteins.
  Selected figure(s)  
Figure 3.
Fig. 3. View of one monomer displayed as a solvent accessible surface in GRASP (26). The orientation is roughly the same as for the blue monomer in Fig. 2A. The surface buried upon dimer formation is indicated in magenta, and residues that contribute at least 2% of the buried surface of the dimer (Fig. 1) are labeled. Residues from the closed interface are indicated with arrows. Not shown in the diagram are the residues from 5 and 6, which form a groove on the underside of the monomer that accommodates 1' from the adjoining monomer. The entrance to this groove is lined with Ala-90 and Tyr-113.
Figure 4.
Fig. 4. Sequence conservation in the exposed surface of the BTB dimer. (A) View in the same orientation as in Fig. 2A. (B) View looking directly down the twofold axis of the dimer. A multiple sequence alignment was constructed as follows: residues 6-126 of PLZF were used in a FASTA3 (38) search of the SWALL database (Nonredundant Protein sequence database including Swissprot, Trembl, and TremblNew) at the EMBL- European Bioinformatics Institute server ( Entries with E score <0.1 were used for further processing. Identical and closely matching sequences were removed from the set, so that the no two pairs in the final set of 42 sequences had >88% sequence identity. The set was then aligned, and the sequence variability was calculated as the number of different amino acids present at each residue position. The sequence variability was then displayed on the solvent accessible surface of the dimer by using GRASP (26). In this variability scoring scheme, a fully conserved residue is assigned a value of 1, and the maximum variability is 20. The only exposed, fully conserved residue in the structure is Asp-35, present in the center of the groove.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21131782 E.Södersten, T.Lilja, and O.Hermanson (2010).
The novel BTB/POZ and zinc finger factor Zbtb45 is essential for proper glial differentiation of neural and oligodendrocyte progenitor cells.
  Cell Cycle, 9, 4866-4875.  
20065070 K.Howell, S.Arur, T.Schedl, and M.V.Sundaram (2010).
EOR-2 is an obligate binding partner of the BTB-zinc finger protein EOR-1 in Caenorhabditis elegans.
  Genetics, 184, 899-913.  
20554658 S.Cirak, F.von Deimling, S.Sachdev, W.J.Errington, R.Herrmann, C.Bönnemann, K.Brockmann, S.Hinderlich, T.H.Lindner, A.Steinbrecher, K.Hoffmann, G.G.Privé, M.Hannink, P.Nürnberg, and T.Voit (2010).
Kelch-like homologue 9 mutation is associated with an early onset autosomal dominant distal myopathy.
  Brain, 133, 2123-2135.  
20703935 S.N.Shchelkunov (2010).
Interaction of orthopoxviruses with the cellular ubiquitin-ligase system.
  Virus Genes, 41, 309-318.  
20338044 Y.H.Ching, L.A.Wilson, and J.C.Schimenti (2010).
An allele separating skeletal patterning and spermatogonial renewal functions of PLZF.
  BMC Dev Biol, 10, 33.  
18723112 C.Fleuriel, M.Touka, G.Boulay, C.Guérardel, B.R.Rood, and D.Leprince (2009).
HIC1 (Hypermethylated in Cancer 1) epigenetic silencing in tumors.
  Int J Biochem Cell Biol, 41, 26-33.  
19523849 D.Xu, M.Holko, A.J.Sadler, B.Scott, S.Higashiyama, W.Berkofsky-Fessler, M.J.McConnell, P.P.Pandolfi, J.D.Licht, and B.R.Williams (2009).
Promyelocytic leukemia zinc finger protein regulates interferon-mediated innate immunity.
  Immunity, 30, 802-816.  
19256485 K.S.Plafker, J.D.Singer, and S.M.Plafker (2009).
The ubiquitin conjugating enzyme, UbcM2, engages in novel interactions with components of cullin-3 based E3 ligases.
  Biochemistry, 48, 3527-3537.  
19170764 N.Ito, M.Watanabe-Matsui, K.Igarashi, and K.Murayama (2009).
Crystal structure of the Bach1 BTB domain and its regulation of homodimerization.
  Genes Cells, 14, 167-178.  
19955409 Q.Zhang, Q.Shi, Y.Chen, T.Yue, S.Li, B.Wang, and J.Jiang (2009).
Multiple Ser/Thr-rich degrons mediate the degradation of Ci/Gli by the Cul3-HIB/SPOP E3 ubiquitin ligase.
  Proc Natl Acad Sci U S A, 106, 21191-21196.  
19129218 Y.C.Chen, S.I.Lin, Y.K.Chen, C.S.Chiang, and G.J.Liaw (2009).
The Torso signaling pathway modulates a dual transcriptional switch to regulate tailless expression.
  Nucleic Acids Res, 37, 1061-1072.  
18221766 B.A.Wilton, S.Campbell, N.Van Buuren, R.Garneau, M.Furukawa, Y.Xiong, and M.Barry (2008).
Ectromelia virus BTB/kelch proteins, EVM150 and EVM167, interact with cullin-3-based ubiquitin ligases.
  Virology, 374, 82-99.  
  19052359 M.A.Stead, G.O.Rosbrook, J.M.Hadden, C.H.Trinh, S.B.Carr, and S.C.Wright (2008).
Structure of the wild-type human BCL6 POZ domain.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 1101-1104.
PDB code: 3e4u
18452090 S.Parekh, G.Privé, and A.Melnick (2008).
Therapeutic targeting of the BCL6 oncogene for diffuse large B-cell lymphomas.
  Leuk Lymphoma, 49, 874-882.  
17101769 A.Golovnin, A.Mazur, M.Kopantseva, M.Kurshakova, P.V.Gulak, B.Gilmore, W.G.Whitfield, P.Geyer, V.Pirrotta, and P.Georgiev (2007).
Integrity of the Mod(mdg4)-67.2 BTB domain is critical to insulator function in Drosophila melanogaster.
  Mol Cell Biol, 27, 963-974.  
17605815 A.M.Burroughs, S.Balaji, L.M.Iyer, and L.Aravind (2007).
Small but versatile: the extraordinary functional and structural diversity of the beta-grasp fold.
  Biol Direct, 2, 18.  
17189472 P.J.Stogios, L.Chen, and G.G.Privé (2007).
Crystal structure of the BTB domain from the LRF/ZBTB7 transcriptional regulator.
  Protein Sci, 16, 336-342.
PDB code: 2nn2
16331266 A.Chattopadhyay, S.A.Tate, R.W.Beswick, S.D.Wagner, and P.Ko Ferrigno (2006).
A peptide aptamer to antagonize BCL-6 function.
  Oncogene, 25, 2223-2233.  
16641104 D.F.Erezyilmaz, L.M.Riddiford, and J.W.Truman (2006).
The pupal specifier broad directs progressive morphogenesis in a direct-developing insect.
  Proc Natl Acad Sci U S A, 103, 6925-6930.  
16542149 F.Schoenen, and B.Wirth (2006).
The zinc finger protein ZNF297B interacts with BDP1, a subunit of TFIIIB.
  Biol Chem, 387, 277-284.  
16354688 G.J.Filion, S.Zhenilo, S.Salozhin, D.Yamada, E.Prokhortchouk, and P.A.Defossez (2006).
A family of human zinc finger proteins that bind methylated DNA and repress transcription.
  Mol Cell Biol, 26, 169-181.  
16394099 H.Schaefer, and C.Rongo (2006).
KEL-8 is a substrate receptor for CUL3-dependent ubiquitin ligase that regulates synaptic glutamate receptor turnover.
  Mol Biol Cell, 17, 1250-1260.  
16718364 J.Qi, X.Zhang, H.K.Zhang, H.M.Yang, Y.B.Zhou, and Z.G.Han (2006).
ZBTB34, a novel human BTB/POZ zinc finger protein, is a potential transcriptional repressor.
  Mol Cell Biochem, 290, 159-167.  
17120193 R.Perez-Torrado, D.Yamada, and P.A.Defossez (2006).
Born to bind: the BTB protein-protein interaction domain.
  Bioessays, 28, 1194-1202.  
15684717 A.Inoue, M.Kang, L.Fujimura, Y.Takamori, K.Sasagawa, H.Itoh, T.Tokuhisa, and M.Hatano (2005).
Overexpression of Nd1-s, a variant form of new kelch family protein, perturbs the cell cycle progression of fibroblasts.
  DNA Cell Biol, 24, 30-34.  
15526281 A.J.Edgar, S.L.Dover, M.N.Lodrick, I.J.McKay, F.J.Hughes, and W.Turner (2005).
Bone morphogenetic protein-2 induces expression of murine zinc finger transcription factor ZNF450.
  J Cell Biochem, 94, 202-215.  
16006525 A.L.Eggler, G.Liu, J.M.Pezzuto, R.B.van Breemen, and A.D.Mesecar (2005).
Modifying specific cysteines of the electrophile-sensing human Keap1 protein is insufficient to disrupt binding to the Nrf2 domain Neh2.
  Proc Natl Acad Sci U S A, 102, 10070-10075.  
16247600 C.Greco, E.Sacco, M.Vanoni, and L.De Gioia (2005).
Identification and in silico analysis of a new group of double-histone fold-containing proteins.
  J Mol Model, 12, 76-84.  
15897867 E.Nitta, K.Izutsu, Y.Yamaguchi, Y.Imai, S.Ogawa, S.Chiba, M.Kurokawa, and H.Hirai (2005).
Oligomerization of Evi-1 regulated by the PR domain contributes to recruitment of corepressor CtBP.
  Oncogene, 24, 6165-6173.  
15964811 F.Guidez, L.Howell, M.Isalan, M.Cebrat, R.M.Alani, S.Ivins, I.Hormaeche, M.J.McConnell, S.Pierce, P.A.Cole, J.Licht, and A.Zelent (2005).
Histone acetyltransferase activity of p300 is required for transcriptional repression by the promyelocytic leukemia zinc finger protein.
  Mol Cell Biol, 25, 5552-5566.  
15824883 G.Kochneva, I.Kolosova, T.Maksyutova, E.Ryabchikova, and S.Shchelkunov (2005).
Effects of deletions of kelch-like genes on cowpox virus biological properties.
  Arch Virol, 150, 1857-1870.  
15750595 G.Sun, X.Liu, P.Mercado, S.R.Jenkinson, M.Kypriotou, L.Feigenbaum, P.Galéra, and R.Bosselut (2005).
The zinc finger protein cKrox directs CD4 lineage differentiation during intrathymic T cell positive selection.
  Nat Immunol, 6, 373-381.  
15726626 J.Zhou, X.Hu, X.Xiong, X.Liu, Y.Liu, K.Ren, T.Jiang, X.Hu, and J.Zhang (2005).
Cloning of two rat PDIP1 related genes and their interactions with proliferating cell nuclear antigen.
  J Exp Zoolog A Comp Exp Biol, 303, 227-240.  
15601839 M.Furukawa, and Y.Xiong (2005).
BTB protein Keap1 targets antioxidant transcription factor Nrf2 for ubiquitination by the Cullin 3-Roc1 ligase.
  Mol Cell Biol, 25, 162-171.  
16207353 P.J.Stogios, G.S.Downs, J.J.Jauhal, S.K.Nandra, and G.G.Privé (2005).
Sequence and structural analysis of BTB domain proteins.
  Genome Biol, 6, R82.  
16169482 S.Luke-Glaser, L.Pintard, C.Lu, P.E.Mains, and M.Peter (2005).
The BTB protein MEL-26 promotes cytokinesis in C. elegans by a CUL-3-independent mechanism.
  Curr Biol, 15, 1605-1615.  
14694499 C.Cifuentes-Diaz, M.Bitoun, D.Goudou, N.Seddiqi, N.Romero, F.Rieger, J.P.Perin, and P.M.Alliel (2004).
Neuromuscular expression of the BTB/POZ and zinc finger protein myoneurin.
  Muscle Nerve, 29, 59-65.  
15094115 J.Engel (2004).
Role of oligomerization domains in thrombospondins and other extracellular matrix proteins.
  Int J Biochem Cell Biol, 36, 997.  
15071497 L.Pintard, A.Willems, and M.Peter (2004).
Cullin-based ubiquitin ligases: Cul3-BTB complexes join the family.
  EMBO J, 23, 1681-1687.  
15583386 X.Li, D.Zhang, M.Hannink, and L.J.Beamer (2004).
Crystallization and initial crystallographic analysis of the Kelch domain from human Keap1.
  Acta Crystallogr D Biol Crystallogr, 60, 2346-2348.  
12954775 C.Lours, O.Bardot, D.Godt, F.A.Laski, and J.L.Couderc (2003).
The Drosophila melanogaster BTB proteins bric à brac bind DNA through a composite DNA binding domain containing a pipsqueak and an AT-Hook motif.
  Nucleic Acids Res, 31, 5389-5398.  
14690607 K.F.Ahmad, A.Melnick, S.Lax, D.Bouchard, J.Liu, C.L.Kiang, S.Mayer, S.Takahashi, J.D.Licht, and G.G.Privé (2003).
Mechanism of SMRT corepressor recruitment by the BCL6 BTB domain.
  Mol Cell, 12, 1551-1564.
PDB codes: 1r28 1r29 1r2b
12556479 M.Faucheux, J.Y.Roignant, S.Netter, J.Charollais, C.Antoniewski, and L.Théodore (2003).
batman Interacts with polycomb and trithorax group genes and encodes a BTB/POZ protein that is included in a complex containing GAGA factor.
  Mol Cell Biol, 23, 1181-1195.  
12517336 P.Sliz, S.C.Harrison, and G.Rosenbaum (2003).
How does radiation damage in protein crystals depend on X-ray dose?
  Structure, 11, 13-19.  
14527422 R.Geyer, S.Wee, S.Anderson, J.Yates, and D.A.Wolf (2003).
BTB/POZ domain proteins are putative substrate adaptors for cullin 3 ubiquitin ligases.
  Mol Cell, 12, 783-790.  
11865059 A.Melnick, G.Carlile, K.F.Ahmad, C.L.Kiang, C.Corcoran, V.Bardwell, G.G.Prive, and J.D.Licht (2002).
Critical residues within the BTB domain of PLZF and Bcl-6 modulate interaction with corepressors.
  Mol Cell Biol, 22, 1804-1818.  
12271134 A.Schwendemann, and M.Lehmann (2002).
Pipsqueak and GAGA factor act in concert as partners at homeotic and many other loci.
  Proc Natl Acad Sci U S A, 99, 12883-12888.  
12501160 A.V.Veselovsky, Y.D.Ivanov, A.S.Ivanov, A.I.Archakov, P.Lewi, and P.Janssen (2002).
Protein-protein interactions: mechanisms and modification by drugs.
  J Mol Recognit, 15, 405-422.  
  11818025 L.Xu, L.Yang, K.Hashimoto, M.Anderson, G.Kohlhagen, Y.Pommier, and P.D'Arpa (2002).
Characterization of BTBD1 and BTBD2, two similar BTB-domain-containing Kelch-like proteins that interact with Topoisomerase I.
  BMC Genomics, 3, 1.  
11854310 R.J.Kelso, A.M.Hudson, and L.Cooley (2002).
Drosophila Kelch regulates actin organization via Src64-dependent tyrosine phosphorylation.
  J Cell Biol, 156, 703-713.  
12052894 S.Deltour, S.Pinte, C.Guerardel, B.Wasylyk, and D.Leprince (2002).
The human candidate tumor suppressor gene HIC1 recruits CtBP through a degenerate GLDLSKK motif.
  Mol Cell Biol, 22, 4890-4901.  
12215542 S.Li, C.Xu, and R.W.Carthew (2002).
Phyllopod acts as an adaptor protein to link the sina ubiquitin ligase to the substrate protein tramtrack.
  Mol Cell Biol, 22, 6854-6865.  
12384587 S.Pagans, M.Ortiz-Lombardía, M.L.Espinás, J.Bernués, and F.Azorín (2002).
The Drosophila transcription factor tramtrack (TTK) interacts with Trithorax-like (GAGA) and represses GAGA-mediated activation.
  Nucleic Acids Res, 30, 4406-4413.  
12021428 Y.Liu, and D.Eisenberg (2002).
3D domain swapping: as domains continue to swap.
  Protein Sci, 11, 1285-1299.  
11452024 A.A.Schäffer, L.Aravind, T.L.Madden, S.Shavirin, J.L.Spouge, Y.I.Wolf, E.V.Koonin, and S.F.Altschul (2001).
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements.
  Nucleic Acids Res, 29, 2994-3005.  
11483520 C.A.Kim, M.L.Phillips, W.Kim, M.Gingery, H.H.Tran, M.A.Robinson, S.Faham, and J.U.Bowie (2001).
Polymerization of the SAM domain of TEL in leukemogenesis and transcriptional repression.
  EMBO J, 20, 4173-4182.
PDB code: 1ji7
11350941 D.Ghosh, T.I.Gerasimova, and V.G.Corces (2001).
Interactions between the Su(Hw) and Mod(mdg4) proteins required for gypsy insulator function.
  EMBO J, 20, 2518-2527.  
11222756 F.Rivero, H.Dislich, G.Glöckner, and A.A.Noegel (2001).
The Dictyostelium discoideum family of Rho-related proteins.
  Nucleic Acids Res, 29, 1068-1079.  
11493677 R.Dorn, G.Reuter, and A.Loewendorf (2001).
Transgene analysis proves mRNA trans-splicing at the complex mod(mdg4) locus in Drosophila.
  Proc Natl Acad Sci U S A, 98, 9724-9729.  
11340155 T.Collins, J.R.Stone, and A.J.Williams (2001).
All in the family: the BTB/POZ, KRAB, and SCAN domains.
  Mol Cell Biol, 21, 3609-3615.  
11357190 T.Goto, K.Hasegawa, T.Kinoshita, and H.Y.Kubota (2001).
A novel POZ/zinc finger protein, champignon, interferes with gastrulation movements in Xenopus.
  Dev Dyn, 221, 14-25.  
10669750 A.Kobayashi, H.Yamagiwa, H.Hoshino, A.Muto, K.Sato, M.Morita, N.Hayashi, M.Yamamoto, and K.Igarashi (2000).
A combinatorial code for gene expression generated by transcription factor Bach2 and MAZR (MAZ-related factor) through the BTB/POZ domain.
  Mol Cell Biol, 20, 1733-1746.  
10938130 A.Melnick, K.F.Ahmad, S.Arai, A.Polinger, H.Ball, K.L.Borden, G.W.Carlile, G.G.Prive, and J.D.Licht (2000).
In-depth mutational analysis of the promyelocytic leukemia zinc finger BTB/POZ domain reveals motifs and residues required for biological and transcriptional functions.
  Mol Cell Biol, 20, 6550-6567.  
11024164 D.Read, M.J.Butte, A.F.Dernburg, M.Frasch, and T.B.Kornberg (2000).
Functional studies of the BTB domain in the Drosophila GAGA and Mod(mdg4) proteins.
  Nucleic Acids Res, 28, 3864-3870.  
10603472 J.Adams, R.Kelso, and L.Cooley (2000).
The kelch repeat superfamily of proteins: propellers of cell function.
  Trends Cell Biol, 10, 17-24.  
  10790390 K.Büchner, P.Roth, G.Schotta, V.Krauss, H.Saumweber, G.Reuter, and R.Dorn (2000).
Genetic and molecular complexity of the position effect variegation modifier mod(mdg4) in Drosophila.
  Genetics, 155, 141-157.  
  10898795 K.D.Huynh, W.Fischle, E.Verdin, and V.J.Bardwell (2000).
BCoR, a novel corepressor involved in BCL-6 repression.
  Genes Dev, 14, 1810-1823.  
10981635 P.C.Biggin, T.Roosild, and S.Choe (2000).
Potassium channel structure: domain by domain.
  Curr Opin Struct Biol, 10, 456-461.  
10882117 S.Minucci, M.Maccarana, M.Cioce, P.De Luca, V.Gelmetti, S.Segalla, L.Di Croce, S.Giavara, C.Matteucci, A.Gobbi, A.Bianchini, E.Colombo, I.Schiavoni, G.Badaracco, X.Hu, M.A.Lazar, N.Landsberger, C.Nervi, and P.G.Pelicci (2000).
Oligomerization of RAR and AML1 transcription factors as a novel mechanism of oncogenic activation.
  Mol Cell, 5, 811-820.  
  10567577 A.J.Williams, S.C.Blacklow, and T.Collins (1999).
The zinc finger-associated SCAN box is a conserved oligomerization domain.
  Mol Cell Biol, 19, 8526-8535.  
10620011 C.Yoshida, F.Tokumasu, K.I.Hohmura, J.Bungert, N.Hayashi, T.Nagasawa, J.D.Engel, M.Yamamoto, K.Takeyasu, and K.Igarashi (1999).
Long range interaction of cis-DNA elements mediated by architectural transcription factor Bach1.
  Genes Cells, 4, 643-655.  
10470033 S.Choe, A.Kreusch, and P.J.Pfaffinger (1999).
Towards the three-dimensional structure of voltage-gated potassium channels.
  Trends Biochem Sci, 24, 345-349.  
10611298 S.Deltour, C.Guerardel, and D.Leprince (1999).
Recruitment of SMRT/N-CoR-mSin3A-HDAC-repressing complexes is not a general mechanism for BTB/POZ transcriptional repressors: the case of HIC-1 and gammaFBP-B.
  Proc Natl Acad Sci U S A, 96, 14831-14836.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.