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PDBsum entry 1ubd
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protein dna_rna metals links
Transcription/DNA PDB id
1ubd

 

 

 

 

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Contents
Protein chain
114 a.a. *
DNA/RNA
Metals
_ZN ×4
Waters ×87
* Residue conservation analysis
PDB id:
1ubd
Name: Transcription/DNA
Title: Co-crystal structure of human yy1 zinc finger domain bound to the adeno-associated virus p5 initiator element
Structure: DNA (5'- d( Ap Gp Gp Gp Tp Cp Tp Cp Cp Ap Tp Tp Tp Tp Gp Ap A p Gp Cp G)-3'). Chain: a. Engineered: yes. DNA (5'- d( Cp Gp Cp Tp Tp Cp Ap Ap Ap Ap Tp Gp Gp Ap Gp Ap C p Cp Cp T)-3'). Chain: b. Engineered: yes. Protein (yy1 zinc finger domain).
Source: Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Trimer (from PQS)
Resolution:
2.50Å     R-factor:   0.212     R-free:   0.330
Authors: H.B.Houbaviy,A.Usheva,T.Shenk,S.K.Burley
Key ref: H.B.Houbaviy et al. (1996). Cocrystal structure of YY1 bound to the adeno-associated virus P5 initiator. Proc Natl Acad Sci U S A, 93, 13577-13582. PubMed id: 8942976
Date:
04-Oct-96     Release date:   23-Dec-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P25490  (TYY1_HUMAN) -  Transcriptional repressor protein YY1 from Homo sapiens
Seq:
Struc: 		414 a.a.
114 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

DNA/RNA chains
  A-G-G-G-T-C-T-C-C-A-T-T-T-T-G-A-A-G-C-G 20 bases
  C-G-C-T-T-C-A-A-A-A-T-G-G-A-G-A-C-C-C-T 20 bases

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
Proc Natl Acad Sci U S A 93:13577-13582 (1996)
PubMed id: 8942976  
 
 
Cocrystal structure of YY1 bound to the adeno-associated virus P5 initiator.
H.B.Houbaviy, A.Usheva, T.Shenk, S.K.Burley.
 
  ABSTRACT  
 
Ying-Yang 1 protein (YY1) supports specific, unidirectional initiation of messenger RNA production by RNA polymerase II from two adjacent start sites in the adeno-associated virus P5 promoter, a process which is independent of the TATA box-binding protein (TBP). The 2.5-A resolution YY1-initiator element cocrystal structure reveals four zinc fingers recognizing a YY1-binding consensus sequence. Upstream of the transcription start sites protein-DNA contacts involve both strands and downstream they are virtually restricted to the template strand, permitting access to the active center of RNA polymerase II and ensuring specificity and directionality. The observed pattern of protein-DNA contacts also explains YY1 binding to a preformed transcription bubble, and YY1 binding to a DNA/RNA hybrid analog of the P5 promoter region containing a nascent RNA transcript. A model is proposed for YY1-directed, TBP-independent transcription initiation.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20565873 C.C.Chou, M.Rajasekaran, and C.Chen (2010).
An effective approach for generating a three-Cys2His2 zinc-finger-DNA complex model by docking.
  BMC Bioinformatics, 11, 334.  
20544958 C.C.Chou, Y.C.Lou, T.K.Tang, and C.Chen (2010).
Structure and DNA binding characteristics of the three-Cys(2)His(2) domain of mouse testis zinc finger protein.
  Proteins, 78, 2202-2212.  
20717154 F.D.Urnov, E.J.Rebar, M.C.Holmes, H.S.Zhang, and P.D.Gregory (2010).
Genome editing with engineered zinc finger nucleases.
  Nat Rev Genet, 11, 636-646.  
20167128 M.Hatayama, and J.Aruga (2010).
Characterization of the tandem CWCH2 sequence motif: a hallmark of inter-zinc finger interactions.
  BMC Evol Biol, 10, 53.  
21172036 M.R.Kantorovitz, Z.Rapti, V.Gelev, and A.Usheva (2010).
Computing DNA duplex instability profiles efficiently with a two-state model: trends of promoters and binding sites.
  BMC Bioinformatics, 11, 604.  
20070175 Y.B.Yue, Y.Y.Xue, L.Tian, J.L.Xue, J.Z.Chen, and W.Jia (2010).
Functional differentiation between Rep-mediated site-specific integration and transcriptional repression of the adeno-associated viral p5 promoter.
  Hum Gene Ther, 21, 728-738.  
  21326896 Z.Deng, P.Cao, M.Wan, and G.Sui (2010).
Yin Yang 1: A multifaceted protein beyond a transcription factor.
  Transcr, 1, 81-84.  
19297611 B.A.Knutson, J.Oh, and S.S.Broyles (2009).
Downregulation of vaccinia virus intermediate and late promoters by host transcription factor YY1.
  J Gen Virol, 90, 1592-1599.  
18950698 J.Kim, and J.Kim (2009).
YY1's longer DNA-binding motifs.
  Genomics, 93, 152-158.  
18253864 K.J.Brayer, and D.J.Segal (2008).
Keep your fingers off my DNA: protein-protein interactions mediated by C2H2 zinc finger domains.
  Cell Biochem Biophys, 50, 111-131.  
17478514 J.D.Kim, C.Faulk, and J.Kim (2007).
Retroposition and evolution of the DNA-binding motifs of YY1, YY2 and REX1.
  Nucleic Acids Res, 35, 3442-3452.  
17626045 K.Rothfels, O.Rowland, and J.Segall (2007).
Zinc fingers 1 and 7 of yeast TFIIIA are essential for assembly of a functional transcription complex on the 5 S RNA gene.
  Nucleic Acids Res, 35, 4869-4881.  
17158804 F.H.Wilkinson, K.Park, and M.L.Atchison (2006).
Polycomb recruitment to DNA in vivo by the YY1 REPO domain.
  Proc Natl Acad Sci U S A, 103, 19296-19301.  
16402211 J.Miertus, W.Borozdin, V.Frecer, G.Tonini, S.Bertok, A.Amoroso, S.Miertus, and J.Kohlhase (2006).
A SALL4 zinc finger missense mutation predicted to result in increased DNA binding affinity is associated with cranial midline defects and mild features of Okihiro syndrome.
  Hum Genet, 119, 154-161.  
16865673 N.P.Mongan, K.M.Martin, and L.J.Gudas (2006).
The putative human stem cell marker, Rex-1 (Zfp42): structural classification and expression in normal human epithelial and carcinoma cell cultures.
  Mol Carcinog, 45, 887-900.  
16314846 S.Gordon, G.Akopyan, H.Garban, and B.Bonavida (2006).
Transcription factor YY1: structure, function, and therapeutic implications in cancer biology.
  Oncogene, 25, 1125-1142.  
15843152 A.E.Smith, F.Farzaneh, and K.G.Ford (2005).
Single zinc-finger extension: enhancing transcriptional activity and specificity of three-zinc-finger proteins.
  Biol Chem, 386, 95-99.  
16103159 A.François, M.Guilbaud, R.Awedikian, G.Chadeuf, P.Moullier, and A.Salvetti (2005).
The cellular TATA binding protein is required for rep-dependent replication of a minimal adeno-associated virus type 2 p5 element.
  J Virol, 79, 11082-11094.  
16188987 J.Oh, and S.S.Broyles (2005).
Host cell nuclear proteins are recruited to cytoplasmic vaccinia virus replication complexes.
  J Virol, 79, 12852-12860.  
15833072 S.Zolotukhin (2005).
Gene therapy for obesity.
  Expert Opin Biol Ther, 5, 347-357.  
15004245 C.H.Choi, G.Kalosakas, K.O.Rasmussen, M.Hiromura, A.R.Bishop, and A.Usheva (2004).
DNA dynamically directs its own transcription initiation.
  Nucleic Acids Res, 32, 1584-1590.  
14747579 S.S.Broyles, M.Kremer, and B.A.Knutson (2004).
Antiviral activity of distamycin A against vaccinia virus is the result of inhibition of postreplicative mRNA synthesis.
  J Virol, 78, 2137-2141.  
12750739 A.C.Jamieson, J.C.Miller, and C.O.Pabo (2003).
Drug discovery with engineered zinc-finger proteins.
  Nat Rev Drug Discov, 2, 361-368.  
12616630 C.Isernia, E.Bucci, M.Leone, L.Zaccaro, P.Di Lello, G.Digilio, S.Esposito, M.Saviano, B.Di Blasio, C.Pedone, P.V.Pedone, and R.Fattorusso (2003).
NMR structure of the single QALGGH zinc finger domain from the Arabidopsis thaliana SUPERMAN protein.
  Chembiochem, 4, 171-180.
PDB code: 1njq
12101091 F.D.Urnov, E.J.Rebar, A.Reik, and P.P.Pandolfi (2002).
Designed transcription factors as structural, functional and therapeutic probes of chromatin in vivo. Fourth in review series on chromatin dynamics.
  EMBO Rep, 3, 610-615.  
11395410 C.O.Pabo, E.Peisach, and R.A.Grant (2001).
Design and selection of novel Cys2His2 zinc finger proteins.
  Annu Rev Biochem, 70, 313-340.  
11554446 D.P.Giedroc, X.Chen, and J.L.Apuy (2001).
Metal response element (MRE)-binding transcription factor-1 (MTF-1): structure, function, and regulation.
  Antioxid Redox Signal, 3, 577-596.  
11251291 H.B.Houbaviy, and S.K.Burley (2001).
Thermodynamic analysis of the interaction between YY1 and the AAV P5 promoter initiator element.
  Chem Biol, 8, 179-187.  
11533193 I.Kukimoto, and T.Kanda (2001).
Displacement of YY1 by differentiation-specific transcription factor hSkn-1a activates the P(670) promoter of human papillomavirus type 16.
  J Virol, 75, 9302-9311.  
11151005 U.Dengler, A.S.Siddiqui, and G.J.Barton (2001).
Protein structural domains: analysis of the 3Dee domains database.
  Proteins, 42, 332-344.  
11327841 Y.Uno, K.Matsushita, M.Nagaoka, and Y.Sugiura (2001).
Finger-positional change in three zinc finger protein Sp1: influence of terminal finger in DNA recognition.
  Biochemistry, 40, 1787-1795.  
11050227 J.H.Laity, H.J.Dyson, and P.E.Wright (2000).
Molecular basis for modulation of biological function by alternate splicing of the Wilms' tumor suppressor protein.
  Proc Natl Acad Sci U S A, 97, 11932-11935.  
10940247 S.A.Wolfe, L.Nekludova, and C.O.Pabo (2000).
DNA recognition by Cys2His2 zinc finger proteins.
  Annu Rev Biophys Biomol Struct, 29, 183-212.  
10077584 D.J.Segal, B.Dreier, R.R.Beerli, and C.F.Barbas (1999).
Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5'-GNN-3' DNA target sequences.
  Proc Natl Acad Sci U S A, 96, 2758-2763.  
10026283 K.Nadassy, S.J.Wodak, and J.Janin (1999).
Structural features of protein-nucleic acid recognition sites.
  Biochemistry, 38, 1999-2017.  
10452940 M.J.Thomas, and E.Seto (1999).
Unlocking the mechanisms of transcription factor YY1: are chromatin modifying enzymes the key?
  Gene, 236, 197-208.  
9651589 J.L.Brown, D.Mucci, M.Whiteley, M.L.Dirksen, and J.A.Kassis (1998).
The Drosophila Polycomb group gene pleiohomeotic encodes a DNA binding protein with homology to the transcription factor YY1.
  Mol Cell, 1, 1057-1064.  
9467467 J.L.Pomerantz, S.A.Wolfe, and C.O.Pabo (1998).
Structure-based design of a dimeric zinc finger protein.
  Biochemistry, 37, 965-970.  
10384271 L.B.Rothman-Denes, X.Dai, E.Davydova, R.Carter, and K.Kazmierczak (1998).
Transcriptional regulation by DNA structural transitions and single-stranded DNA-binding proteins.
  Cold Spring Harb Symp Quant Biol, 63, 63-73.  
9562555 M.Elrod-Erickson, T.E.Benson, and C.O.Pabo (1998).
High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition.
  Structure, 6, 451-464.
PDB codes: 1a1f 1a1g 1a1h 1a1i 1a1j 1a1k 1a1l
9578568 M.Yokono, N.Saegusa, K.Matsushita, and Y.Sugiura (1998).
Unique DNA binding mode of the N-terminal zinc finger of transcription factor Sp1.
  Biochemistry, 37, 6824-6832.  
9501194 R.T.Nolte, R.M.Conlin, S.C.Harrison, and R.S.Brown (1998).
Differing roles for zinc fingers in DNA recognition: structure of a six-finger transcription factor IIIA complex.
  Proc Natl Acad Sci U S A, 95, 2938-2943.
PDB code: 1tf6
9519295 S.Tan, and T.J.Richmond (1998).
Eukaryotic transcription factors.
  Curr Opin Struct Biol, 8, 41-48.  
9546210 Y.Choo, and J.W.Schwabe (1998).
All wrapped up.
  Nat Struct Biol, 5, 253-255.  
9144164 D.A.Leonard, N.Rajaram, and T.K.Kerppola (1997).
Structural basis of DNA bending and oriented heterodimer binding by the basic leucine zipper domains of Fos and Jun.
  Proc Natl Acad Sci U S A, 94, 4913-4918.  
9241421 G.Patikoglou, and S.K.Burley (1997).
Eukaryotic transcription factor-DNA complexes.
  Annu Rev Biophys Biomol Struct, 26, 289-325.  
  9199306 K.M.Galvin, and Y.Shi (1997).
Multiple mechanisms of transcriptional repression by YY1.
  Mol Cell Biol, 17, 3723-3732.  
9396800 N.M.Luscombe, R.A.Laskowski, and J.M.Thornton (1997).
NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions.
  Nucleic Acids Res, 25, 4940-4945.  
9782776 R.E.Dickerson, and T.K.Chiu (1997).
Helix bending as a factor in protein/DNA recognition.
  Biopolymers, 44, 361-403.  
9283077 T.K.Kerppola (1997).
Comparison of DNA bending by Fos-Jun and phased A tracts by multifactorial phasing analysis.
  Biochemistry, 36, 10872-10884.  
9032060 Y.Choo, and A.Klug (1997).
Physical basis of a protein-DNA recognition code.
  Curr Opin Struct Biol, 7, 117-125.  
9141463 Y.Shi, J.S.Lee, and K.M.Galvin (1997).
Everything you have ever wanted to know about Yin Yang 1......
  Biochim Biophys Acta, 1332, F49-F66.  
8942976 H.B.Houbaviy, A.Usheva, T.Shenk, and S.K.Burley (1996).
Cocrystal structure of YY1 bound to the adeno-associated virus P5 initiator.
  Proc Natl Acad Sci U S A, 93, 13577-13582.
PDB code: 1ubd
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.

 

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