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Transcription PDB id
1f62
Jmol
Contents
Protein chain
51 a.a. *
Metals
_ZN ×2
* Residue conservation analysis
PDB id:
1f62
Name: Transcription
Title: Wstf-phd
Structure: Transcription factor wstf. Chain: a. Fragment: phd zinc finger. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
NMR struc: 20 models
Authors: J.Pascual,M.Martinez-Yamout,H.J.Dyson,P.E.Wright
Key ref: J.Pascual et al. (2000). Structure of the PHD zinc finger from human Williams-Beuren syndrome transcription factor. J Mol Biol, 304, 723-729. PubMed id: 11124022 DOI: 10.1006/jmbi.2000.4113
Date:
19-Jun-00     Release date:   27-Dec-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9UIG0  (BAZ1B_HUMAN) -  Tyrosine-protein kinase BAZ1B
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1483 a.a.
51 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.10.2  - Non-specific protein-tyrosine kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
ATP
 + [protein]-L-tyrosine
 = ADP
 + [protein]-L-tyrosine phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     protein binding     2 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.2000.4113 J Mol Biol 304:723-729 (2000)
PubMed id: 11124022  
 
 
Structure of the PHD zinc finger from human Williams-Beuren syndrome transcription factor.
J.Pascual, M.Martinez-Yamout, H.J.Dyson, P.E.Wright.
 
  ABSTRACT  
 
The PHD (plant homeo domain) is a approximately 50-residue motif found mainly in proteins involved in eukaryotic transcription regulation. The characteristic sequence feature is a conserved Cys(4)-HisCys(3) zinc binding motif. We have determined the solution structure of the PHD motif from the human Williams-Beuren syndrome transcription factor (WSTF) protein. The domain folds into an interleaved zinc finger which binds two Zn(2+) in a similar manner to that of the RING and FYVE domains. The structure reveals a conserved zinc-binding core, together with two variable loops that are likely candidates for interactions between the various PHD domains and their specific ligands.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20803232 A.H.Aguissa-Touré, R.P.Wong, and G.Li (2011).
The ING family tumor suppressors: from structure to function.
  Cell Mol Life Sci, 68, 45-54.  
21326359 C.Barnett, and J.E.Krebs (2011).
WSTF does it all: a multifunctional protein in transcription, repair, and replication.
  Biochem Cell Biol, 89, 12-23.  
20923397 K.L.Yap, and M.M.Zhou (2010).
Keeping it in the family: diverse histone recognition by conserved structural folds.
  Crit Rev Biochem Mol Biol, 45, 488-505.  
20637214 T.C.Miller, T.J.Rutherford, C.M.Johnson, M.Fiedler, and M.Bienz (2010).
Allosteric remodelling of the histone H3 binding pocket in the Pygo2 PHD finger triggered by its binding to the B9L/BCL9 co-factor.
  J Mol Biol, 401, 969-984.
PDB code: 2xb1
20567261 Y.Yang, L.Hu, P.Wang, H.Hou, Y.Lin, Y.Liu, Z.Li, R.Gong, X.Feng, L.Zhou, W.Zhang, Y.Dong, H.Yang, H.Lin, Y.Wang, C.D.Chen, and Y.Xu (2010).
Structural insights into a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans.
  Cell Res, 20, 886-898.
PDB codes: 3n9l 3n9m 3n9n 3n9o 3n9p 3n9q
18780289 A.H.Coles, and S.N.Jones (2009).
The ING gene family in the regulation of cell growth and tumorigenesis.
  J Cell Physiol, 218, 45-57.  
19362589 M.J.Hitchler, and F.E.Domann (2009).
Metabolic defects provide a spark for the epigenetic switch in cancer.
  Free Radic Biol Med, 47, 115-127.  
18381289 A.Palacios, I.G.Muñoz, D.Pantoja-Uceda, M.J.Marcaida, D.Torres, J.M.Martín-García, I.Luque, G.Montoya, and F.J.Blanco (2008).
Molecular basis of histone H3K4me3 recognition by ING4.
  J Biol Chem, 283, 15956-15964.
PDB code: 2vnf
18682226 H.van Ingen, F.M.van Schaik, H.Wienk, J.Ballering, H.Rehmann, A.C.Dechesne, J.A.Kruijzer, R.M.Liskamp, H.T.Timmers, and R.Boelens (2008).
Structural insight into the recognition of the H3K4me3 mark by the TFIID subunit TAF3.
  Structure, 16, 1245-1256.  
18623064 K.S.Champagne, N.Saksouk, P.V.Peña, K.Johnson, M.Ullah, X.J.Yang, J.Côté, and T.G.Kutateladze (2008).
The crystal structure of the ING5 PHD finger in complex with an H3K4me3 histone peptide.
  Proteins, 72, 1371-1376.
PDB code: 3c6w
18533182 P.V.Peña, R.A.Hom, T.Hung, H.Lin, A.J.Kuo, R.P.Wong, O.M.Subach, K.S.Champagne, R.Zhao, V.V.Verkhusha, G.Li, O.Gozani, and T.G.Kutateladze (2008).
Histone H3K4me3 binding is required for the DNA repair and apoptotic activities of ING1 tumor suppressor.
  J Mol Biol, 380, 303-312.
PDB code: 2qic
17609377 A.Argentaro, J.C.Yang, L.Chapman, M.S.Kowalczyk, R.J.Gibbons, D.R.Higgs, D.Neuhaus, and D.Rhodes (2007).
Structural consequences of disease-causing mutations in the ATRX-DNMT3-DNMT3L (ADD) domain of the chromatin-associated protein ATRX.
  Proc Natl Acad Sci U S A, 104, 11939-11944.
PDB codes: 2jm1 2ld1
17947424 S.Ahmed, B.Dul, X.Qiu, and N.C.Walworth (2007).
Msc1 acts through histone H2A.Z to promote chromosome stability in Schizosaccharomyces pombe.
  Genetics, 177, 1487-1497.  
17560331 Y.Liu, W.Chen, J.Gaudet, M.D.Cheney, L.Roudaia, T.Cierpicki, R.C.Klet, K.Hartman, T.M.Laue, N.A.Speck, and J.H.Bushweller (2007).
Structural basis for recognition of SMRT/N-CoR by the MYND domain and its contribution to AML1/ETO's activity.
  Cancer Cell, 11, 483-497.
PDB codes: 2od1 2odd
16672239 D.M.Kristensen, B.Y.Chen, V.Y.Fofanov, R.M.Ward, A.M.Lisewski, M.Kimmel, L.E.Kavraki, and O.Lichtarge (2006).
Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity.
  Protein Sci, 15, 1530-1536.  
16728978 H.Li, S.Ilin, W.Wang, E.M.Duncan, J.Wysocka, C.D.Allis, and D.J.Patel (2006).
Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF.
  Nature, 442, 91-95.
PDB codes: 2f6j 2f6n 2fsa 2fui 2fuu
16297627 M.Bienz (2006).
The PHD finger, a nuclear protein-interaction domain.
  Trends Biochem Sci, 31, 35-40.  
16267839 M.L.Gonzales, and R.A.Anderson (2006).
Nuclear phosphoinositide kinases and inositol phospholipids.
  J Cell Biochem, 97, 252-260.  
16728977 P.V.Peña, F.Davrazou, X.Shi, K.L.Walter, V.V.Verkhusha, O.Gozani, R.Zhao, and T.G.Kutateladze (2006).
Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2.
  Nature, 442, 100-103.
PDB code: 2g6q
15790357 J.Villaseñor, C.Benoist, and D.Mathis (2005).
AIRE and APECED: molecular insights into an autoimmune disease.
  Immunol Rev, 204, 156-164.  
15649886 M.J.Bottomley, G.Stier, D.Pennacchini, G.Legube, B.Simon, A.Akhtar, M.Sattler, and G.Musco (2005).
NMR structure of the first PHD finger of autoimmune regulator protein (AIRE1). Insights into autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) disease.
  J Biol Chem, 280, 11505-11512.
PDB code: 1xwh
15964836 S.K.Elkin, D.Ivanov, M.Ewalt, C.G.Ferguson, S.G.Hyberts, Z.Y.Sun, G.D.Prestwich, J.Yuan, G.Wagner, M.A.Oettinger, and O.P.Gozani (2005).
A PHD finger motif in the C terminus of RAG2 modulates recombination activity.
  J Biol Chem, 280, 28701-28710.
PDB codes: 2a23 2jwo
15869386 W.Cho, and R.V.Stahelin (2005).
Membrane-protein interactions in cell signaling and membrane trafficking.
  Annu Rev Biophys Biomol Struct, 34, 119-151.  
15743678 W.Gong, K.Suzuki, M.Russell, and K.Riabowol (2005).
Function of the ING family of PHD proteins in cancer.
  Int J Biochem Cell Biol, 37, 1054-1065.  
16167330 X.Shi, and O.Gozani (2005).
The fellowships of the INGs.
  J Cell Biochem, 96, 1127-1136.  
15457208 A.Eberharter, I.Vetter, R.Ferreira, and P.B.Becker (2004).
ACF1 improves the effectiveness of nucleosome mobilization by ISWI through PHD-histone contacts.
  EMBO J, 23, 4029-4039.  
15169884 A.L.Nielsen, P.Jørgensen, T.Lerouge, M.Cerviño, P.Chambon, and R.Losson (2004).
Nizp1, a novel multitype zinc finger protein that interacts with the NSD1 histone lysine methyltransferase through a unique C2HR motif.
  Mol Cell Biol, 24, 5184-5196.  
15196467 D.R.Jones, and N.Divecha (2004).
Linking lipids to chromatin.
  Curr Opin Genet Dev, 14, 196-202.  
14734522 D.Uchida, S.Hatakeyama, A.Matsushima, H.Han, S.Ishido, H.Hotta, J.Kudoh, N.Shimizu, V.Doucas, K.I.Nakayama, N.Kuroda, and M.Matsumoto (2004).
AIRE functions as an E3 ubiquitin ligase.
  J Exp Med, 199, 167-172.  
14612447 F.M.Townsley, B.Thompson, and M.Bienz (2004).
Pygopus residues required for its binding to Legless are critical for transcription and development.
  J Biol Chem, 279, 5177-5183.  
15150263 H.Akiyoshi, S.Hatakeyama, J.Pitkänen, Y.Mouri, V.Doucas, J.Kudoh, K.Tsurugaya, D.Uchida, A.Matsushima, K.Oshikawa, K.I.Nakayama, N.Shimizu, P.Peterson, and M.Matsumoto (2004).
Subcellular expression of autoimmune regulator is organized in a spatiotemporal manner.
  J Biol Chem, 279, 33984-33991.  
15565467 W.Bi, G.M.Saifi, C.J.Shaw, K.Walz, P.Fonseca, M.Wilson, L.Potocki, and J.R.Lupski (2004).
Mutations of RAI1, a PHD-containing protein, in nondeletion patients with Smith-Magenis syndrome.
  Hum Genet, 115, 515-524.  
  12842043 A.H.Kwan, D.A.Gell, A.Verger, M.Crossley, J.M.Matthews, and J.P.Mackay (2003).
Engineering a protein scaffold from a PHD finger.
  Structure, 11, 803-813.
PDB codes: 1mm2 1mm3
12697833 F.Tie, J.Prasad-Sinha, A.Birve, A.Rasmuson-Lestander, and P.J.Harte (2003).
A 1-megadalton ESC/E(Z) complex from Drosophila that contains polycomblike and RPD3.
  Mol Cell Biol, 23, 3352-3362.  
12456688 J.A.Witowsky, and G.L.Johnson (2003).
Ubiquitylation of MEKK1 inhibits its phosphorylation of MKK1 and MKK4 and activation of the ERK1/2 and JNK pathways.
  J Biol Chem, 278, 1403-1406.  
  14704181 M.G.Voas, and I.Rebay (2003).
The novel plant homeodomain protein rhinoceros antagonizes Ras signaling in the Drosophila eye.
  Genetics, 165, 1993-2006.  
12859901 O.Gozani, P.Karuman, D.R.Jones, D.Ivanov, J.Cha, A.A.Lugovskoy, C.L.Baird, H.Zhu, S.J.Field, S.L.Lessnick, J.Villasenor, B.Mehrotra, J.Chen, V.R.Rao, J.S.Brugge, C.G.Ferguson, B.Payrastre, D.G.Myszka, L.C.Cantley, G.Wagner, N.Divecha, G.D.Prestwich, and J.Yuan (2003).
The PHD finger of the chromatin-associated protein ING2 functions as a nuclear phosphoinositide receptor.
  Cell, 114, 99.  
11839497 A.J.Warren (2002).
Eukaryotic transcription factors.
  Curr Opin Struct Biol, 12, 107-114.  
11988739 B.Thompson, F.Townsley, R.Rosin-Arbesfeld, H.Musisi, and M.Bienz (2002).
A new nuclear component of the Wnt signalling pathway.
  Nat Cell Biol, 4, 367-373.  
11751860 D.J.Sanchez, L.Coscoy, and D.Ganem (2002).
Functional organization of MIR2, a novel viral regulator of selective endocytosis.
  J Biol Chem, 277, 6124-6130.  
11884585 E.Kalkhoven, H.Teunissen, A.Houweling, C.P.Verrijzer, and A.Zantema (2002).
The PHD type zinc finger is an integral part of the CBP acetyltransferase domain.
  Mol Cell Biol, 22, 1961-1970.  
11875024 H.Kawaji, C.Schönbach, Y.Matsuo, J.Kawai, Y.Okazaki, Y.Hayashizaki, and H.Matsuda (2002).
Exploration of novel motifs derived from mouse cDNA sequences.
  Genome Res, 12, 367-378.  
12112470 J.J.Henry, M.E.Carinato, J.J.Schaefer, A.D.Wolfe, B.E.Walter, K.J.Perry, and T.N.Elbl (2002).
Characterizing gene expression during lens formation in Xenopus laevis: evaluating the model for embryonic lens induction.
  Dev Dyn, 224, 168-185.  
11839485 O.Lichtarge, and M.E.Sowa (2002).
Evolutionary predictions of binding surfaces and interactions.
  Curr Opin Struct Biol, 12, 21-27.  
12049732 Z.Lu, S.Xu, C.Joazeiro, M.H.Cobb, and T.Hunter (2002).
The PHD domain of MEKK1 acts as an E3 ubiquitin ligase and mediates ubiquitination and degradation of ERK1/2.
  Mol Cell, 9, 945-956.  
11447119 A.Eberharter, S.Ferrari, G.Längst, T.Straub, A.Imhof, P.Varga-Weisz, M.Wilm, and P.B.Becker (2001).
Acf1, the largest subunit of CHRAC, regulates ISWI-induced nucleosome remodelling.
  EMBO J, 20, 3781-3788.  
11390640 G.S.Yochum, and D.E.Ayer (2001).
Pf1, a novel PHD zinc finger protein that links the TLE corepressor to the mSin3A-histone deacetylase complex.
  Mol Cell Biol, 21, 4110-4118.  
11179890 J.H.Laity, B.M.Lee, and P.E.Wright (2001).
Zinc finger proteins: new insights into structural and functional diversity.
  Curr Opin Struct Biol, 11, 39-46.  
11756476 L.Coscoy, D.J.Sanchez, and D.Ganem (2001).
A novel class of herpesvirus-encoded membrane-bound E3 ubiquitin ligases regulates endocytosis of proteins involved in immune recognition.
  J Cell Biol, 155, 1265-1273.  
11711434 W.W.Pijnappel, D.Schaft, A.Roguev, A.Shevchenko, H.Tekotte, M.Wilm, G.Rigaut, B.Séraphin, R.Aasland, and A.F.Stewart (2001).
The S. cerevisiae SET3 complex includes two histone deacetylases, Hos2 and Hst1, and is a meiotic-specific repressor of the sporulation gene program.
  Genes Dev, 15, 2991-3004.  
11438666 Y.G.Gangloff, J.C.Pointud, S.Thuault, L.Carré, C.Romier, S.Muratoglu, M.Brand, L.Tora, J.L.Couderc, and I.Davidson (2001).
The TFIID components human TAF(II)140 and Drosophila BIP2 (TAF(II)155) are novel metazoan homologues of yeast TAF(II)47 containing a histone fold and a PHD finger.
  Mol Cell Biol, 21, 5109-5121.  
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.