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PDBsum entry 1nfh
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protein Protein-protein interface(s) links
Gene regulation PDB id
1nfh

 

 

 

 

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Contents
Protein chains
86 a.a. *
Waters ×85
* Residue conservation analysis
PDB id:
1nfh
Name: Gene regulation
Title: Structure of a sir2 substrate, alba, reveals a mechanism for deactylation-induced enhancement of DNA-binding
Structure: Conserved hypothetical protein af1956. Chain: a, b. Synonym: alba. Engineered: yes
Source: Archaeoglobus fulgidus. Organism_taxid: 2234. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PDB file)
Resolution:
2.65Å     R-factor:   0.237     R-free:   0.285
Authors: K.Zhao,X.Chai,R.Marmorstein
Key ref:
K.Zhao et al. (2003). Structure of a Sir2 substrate, Alba, reveals a mechanism for deacetylation-induced enhancement of DNA binding. J Biol Chem, 278, 26071-26077. PubMed id: 12730210 DOI: 10.1074/jbc.M303666200
Date:
15-Dec-02     Release date:   05-Aug-03    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
O28323  (ALBA2_ARCFU) -  DNA/RNA-binding protein Alba 2 from Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)
Seq:
Struc: 		89 a.a.
86 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

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

 

 
DOI no: 10.1074/jbc.M303666200 J Biol Chem 278:26071-26077 (2003)
PubMed id: 12730210  
 
 
Structure of a Sir2 substrate, Alba, reveals a mechanism for deacetylation-induced enhancement of DNA binding.
K.Zhao, X.Chai, R.Marmorstein.
 
  ABSTRACT  
 
The targeted acetylation status of histones and several other transcriptional regulatory proteins plays an important role in gene expression, although the mechanism for this is not well understood. As a model to understand how targeted acetylation may effect transcription, we determined the x-ray crystal structure of the chromatin protein Alba from Archaeoglobus fulgidus, a substrate for the Sir2 protein that deacetylates it at lysine 11 to promote DNA binding by Alba. The structure reveals a dimer of dimers in which the dimer-dimer interface is stabilized by several conserved hydrophobic residues as well as the lysine 11 target of Sir2. We show that, in solution, the mutation of these hydrophobic residues or lysine 11 disrupts dimer-dimer formation and decreases DNA-binding affinity. We propose that the in vivo deacetylation of lysine 11 of archaeal Alba by Sir2 promotes protein oligomerization for optimal DNA binding. Implications for the mechanism by which histone acetylation modulates gene expression are discussed.
 
  Selected figure(s)  
 
Figure 1.
FIG. 1. Structure of Af-Alba. Structure of the Alba monomer (a), dimer (b), and tetramer (c) in the crystals. 		Figure 5.
FIG. 5. Model for DNA binding by Alba. a, model for how the Af-Alba tetramer binds DNA. b, electrostatic surface of the Af-Alba tetramer modeled on DNA. Blue, red, and white represent the degree of electropositive, electronegative, and neutral surface potential, respectively.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 26071-26077) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20842312 B.M.Hirsch, and W.Zheng (2011).
Sirtuin mechanism and inhibition: explored with N(ε)-acetyl-lysine analogs.
  Mol Biosyst, 7, 16-28.  
21239213 S.Thao, and J.C.Escalante-Semerena (2011).
Control of protein function by reversible N(ɛ)-lysine acetylation in bacteria.
  Curr Opin Microbiol, 14, 200-204.  
20082605 C.Jelinska, B.Petrovic-Stojanovska, W.J.Ingledew, and M.F.White (2010).
Dimer-dimer stacking interactions are important for nucleic acid binding by the archaeal chromatin protein Alba.
  Biochem J, 427, 49-55.  
  20885971 J.Soppa (2010).
Protein acetylation in archaea, bacteria, and eukaryotes.
  Archaea, 2010, 0.  
21217812 S.Thao, C.S.Chen, H.Zhu, and J.C.Escalante-Semerena (2010).
Nε-lysine acetylation of a bacterial transcription factor inhibits Its DNA-binding activity.
  PLoS One, 5, e15123.  
18723842 J.Zhang, R.Sprung, J.Pei, X.Tan, S.Kim, H.Zhu, C.F.Liu, N.V.Grishin, and Y.Zhao (2009).
Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli.
  Mol Cell Proteomics, 8, 215-225.  
19114494 N.Altman-Price, and M.Mevarech (2009).
Genetic evidence for the importance of protein acetylation and protein deacetylation in the halophilic archaeon Haloferax volcanii.
  J Bacteriol, 191, 1610-1617.  
18323660 K.Hada, T.Nakashima, T.Osawa, H.Shimada, Y.Kakuta, and M.Kimura (2008).
Crystal structure and functional analysis of an archaeal chromatin protein Alba from the hyperthermophilic archaeon Pyrococcus horikoshii OT3.
  Biosci Biotechnol Biochem, 72, 749-758.
PDB code: 2z7c
18004791 T.Kumarevel, K.Sakamoto, S.C.Gopinath, A.Shinkai, P.K.Kumar, and S.Yokoyama (2008).
Crystal structure of an archaeal specific DNA-binding protein (Ape10b2) from Aeropyrum pernix K1.
  Proteins, 71, 1156-1162.  
16256418 K.Sandman, and J.N.Reeve (2005).
Archaeal chromatin proteins: different structures but common function?
  Curr Opin Microbiol, 8, 656-661.  
16356270 K.Usui, S.Katayama, M.Kanamori-Katayama, C.Ogawa, C.Kai, M.Okada, J.Kawai, T.Arakawa, P.Carninci, M.Itoh, K.Takio, M.Miyano, S.Kidoaki, T.Matsuda, Y.Hayashizaki, and H.Suzuki (2005).
Protein-protein interactions of the hyperthermophilic archaeon Pyrococcus horikoshii OT3.
  Genome Biol, 6, R98.  
15831786 M.Pellegrini-Calace, and J.M.Thornton (2005).
Detecting DNA-binding helix-turn-helix structural motifs using sequence and structure information.
  Nucleic Acids Res, 33, 2129-2140.  
14960713 X.J.Yang (2004).
The diverse superfamily of lysine acetyltransferases and their roles in leukemia and other diseases.
  Nucleic Acids Res, 32, 959-976.  
14519199 L.Aravind, L.M.Iyer, and V.Anantharaman (2003).
The two faces of Alba: the evolutionary connection between proteins participating in chromatin structure and RNA metabolism.
  Genome Biol, 4, R64.  
14651642 R.Guo, H.Xue, and L.Huang (2003).
Ssh10b, a conserved thermophilic archaeal protein, binds RNA in vivo.
  Mol Microbiol, 50, 1605-1615.  
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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