spacer
spacer

PDBsum entry 2rny
Go to PDB code: 
protein Protein-protein interface(s) links
Transferase/nuclear protein PDB id
2rny

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chains
121 a.a. *
15 a.a. *
* Residue conservation analysis
PDB id:
2rny
Name: Transferase/nuclear protein
Title: Complex structures of cbp bromodomain with h4 ack20 peptide
Structure: Creb-binding protein. Chain: a. Fragment: unp residues 1081-1197. Engineered: yes. Histone h4. Chain: b. Fragment: unp residues 14-28. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Expression_system_variant: bl21.
NMR struc: 20 models
Authors: L.Zeng,Q.Zhang,G.Gerona-Navarro,M.M.Zhou
Key ref:
L.Zeng et al. (2008). Structural basis of site-specific histone recognition by the bromodomains of human coactivators PCAF and CBP/p300. Structure, 16, 643-652. PubMed id: 18400184 DOI: 10.1016/j.str.2008.01.010
Date:
03-Feb-08     Release date:   06-May-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q92793  (CBP_HUMAN) -  CREB-binding protein from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		2442 a.a.
121 a.a.*
Protein chain
Pfam   ArchSchema ?
P62805  (H4_HUMAN) -  Histone H4 from Homo sapiens
Seq:
Struc: 		103 a.a.
15 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 2: Chain A: E.C.2.3.1.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
   Enzyme class 3: Chain A: E.C.2.3.1.48  - histone acetyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-lysyl-[protein] + acetyl-CoA = N6-acetyl-L-lysyl-[protein] + CoA + H+
L-lysyl-[protein]
 + acetyl-CoA
 = N(6)-acetyl-L-lysyl-[protein]
 + CoA
 + H(+)
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
DOI no: 10.1016/j.str.2008.01.010 Structure 16:643-652 (2008)
PubMed id: 18400184  
 
 
Structural basis of site-specific histone recognition by the bromodomains of human coactivators PCAF and CBP/p300.
L.Zeng, Q.Zhang, G.Gerona-Navarro, N.Moshkina, M.M.Zhou.
 
  ABSTRACT  
 
Histone lysine acetylation is central to epigenetic control of gene transcription. Bromodomains of chromosomal proteins function as acetyl-lysine (Kac) binding domains. However, how bromodomains recognize site-specific histones remains unanswered. Here, we report three three-dimensional solution structures of the bromodomains of the human transcriptional coactivators CREB-binding protein (CBP) and p300/CBP-associated factor (PCAF) bound to peptides derived from histone acetylation sites at lysines 36 and 9 in H3, and lysine 20 in H4. From structural and biochemical binding analyses, we determine consensus histone recognition by the bromodomains of PCAF and CBP, which represent two different subgroups of the bromodomain family. Through bromodomain residues in the ZA and BC loops, PCAF prefers acetylation sites with a hydrophobic residue at (Kac+2) position and a positively charged or aromatic residue at (Kac+3), whereas CBP favors bulky hydrophobic residues at (Kac+1) and (Kac+2), a positively charged residue at (Kac-1), and an aromatic residue at (Kac-2).
 
  Selected figure(s)  
 
Figure 1.
Figure 1. 3D Structures of Bromodomains Bound to Acetylated Histone Peptides
The structures of the bromodomain/acetylated histone peptide complexes are shown in three different illustrations: stereoview of the backbone atoms (N, Cα, and C′) of 25 superimposed NMR structures of the complexes (left); ribbons representation of the average minimized NMR structure of the complexes in a similar orientation, prepared using Pymol (middle); and surface electrostatic potential representation of the protein with the peptide in a ball-and-stick depiction (right).
(A–C) The PCAF bromodomain/H3-K36ac complex.
(D–F) The PCAF bromodomain/H3-K9ac complex.
(G–I) The CBP bromodomain/H4-K20ac complex. 		Figure 3.
Figure 3. The Structural Basis of Histone Recognition by the CBP Bromodomain
(A and B) Recognition of the acetyl-lysine and its flanking residues in the H4-K20ac peptide by the human CBP bromodomain, respectively.
(C and D) Recognition of the acetyl-lysine and its flanking residues of the p53-K382ac peptide by the human CBP bromodomain (PDB code: 1JSP), respectively.
Side chains of protein or peptide residues are color-coded by atom types in the same scheme as that in Figure 2.
 
  The above figures are reprinted by permission from Cell Press: Structure (2008, 16, 643-652) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21513889 J.C.Borah, S.Mujtaba, I.Karakikes, L.Zeng, M.Muller, J.Patel, N.Moshkina, K.Morohashi, W.Zhang, G.Gerona-Navarro, R.J.Hajjar, and M.M.Zhou (2011).
A small molecule binding to the coactivator CREB-binding protein blocks apoptosis in cardiomyocytes.
  Chem Biol, 18, 531-541.
PDB codes: 2l84 2l85
21243712 P.Voigt, and D.Reinberg (2011).
Histone tails: ideal motifs for probing epigenetics through chemical biology approaches.
  Chembiochem, 12, 236-252.  
21167713 S.M.Fuchs, K.Krajewski, R.W.Baker, V.L.Miller, and B.D.Strahl (2011).
Influence of combinatorial histone modifications on antibody and effector protein recognition.
  Curr Biol, 21, 53-58.  
19731376 K.D.Eichenbaum, Y.Rodríguez, M.Mezei, and R.Osman (2010).
The energetics of the acetylation switch in p53-mediated transcriptional activation.
  Proteins, 78, 447-456.  
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.  
20613843 L.Zeng, Q.Zhang, S.Li, A.N.Plotnikov, M.J.Walsh, and M.M.Zhou (2010).
Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b.
  Nature, 466, 258-262.
PDB codes: 2kwj 2kwk 2kwn 2kwo
19682614 X.Lu, and S.J.Triezenberg (2010).
Chromatin assembly on herpes simplex virus genomes during lytic infection.
  Biochim Biophys Acta, 1799, 217-222.  
20368734 Z.Charlop-Powers, L.Zeng, Q.Zhang, and M.M.Zhou (2010).
Structural insights into selective histone H3 recognition by the human Polybromo bromodomain 2.
  Cell Res, 20, 529-538.
PDB codes: 2ktb 3ljw
19581291 A.Gradolatto, S.K.Smart, S.Byrum, L.P.Blair, R.S.Rogers, E.A.Kolar, H.Lavender, S.K.Larson, J.D.Aitchison, S.D.Taverna, and A.J.Tackett (2009).
A noncanonical bromodomain in the AAA ATPase protein Yta7 directs chromosomal positioning and barrier chromatin activity.
  Mol Cell Biol, 29, 4604-4611.  
19122196 A.Saramäki, S.Diermeier, R.Kellner, H.Laitinen, S.Vaïsänen, and C.Carlberg (2009).
Cyclical Chromatin Looping and Transcription Factor Association on the Regulatory Regions of the p21 (CDKN1A) Gene in Response to 1{alpha},25-Dihydroxyvitamin D3.
  J Biol Chem, 284, 8073-8082.  
19828451 F.Vollmuth, W.Blankenfeldt, and M.Geyer (2009).
Structures of the dual bromodomains of the P-TEFb-activating protein Brd4 at atomic resolution.
  J Biol Chem, 284, 36547-36556.
PDB codes: 3jvj 3jvk 3jvl 3jvm
19234530 J.K.Choi, and L.J.Howe (2009).
Histone acetylation: truth of consequences?
  Biochem Cell Biol, 87, 139-150.  
19276081 M.A.Glozak, and E.Seto (2009).
Acetylation/Deacetylation modulates the stability of DNA replication licensing factor cdt1.
  J Biol Chem, 284, 11446-11453.  
19084573 M.Thompson (2009).
Polybromo-1: the chromatin targeting subunit of the PBAF complex.
  Biochimie, 91, 309-319.  
  19736624 R.Sanchez, and M.M.Zhou (2009).
The role of human bromodomains in chromatin biology and gene transcription.
  Curr Opin Drug Discov Devel, 12, 659-665.  
19218239 S.Li, and M.A.Shogren-Knaak (2009).
The Gcn5 bromodomain of the SAGA complex facilitates cooperative and cross-tail acetylation of nucleosomes.
  J Biol Chem, 284, 9411-9417.  
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 codes are shown on the right.

 

spacer
spacer