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PDBsum entry 1h0x
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DNA binding PDB id
1h0x

 

 

 

 

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Contents
Protein chains
89 a.a. *
Waters ×86
* Residue conservation analysis
PDB id:
1h0x
Name: DNA binding
Title: Structure of alba: an archaeal chromatin protein modulated by acetylation
Structure: DNA binding protein sso10b. Chain: a, b. Synonym: alba. Engineered: yes
Source: Sulfolobus solfataricus. Organism_taxid: 2287. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Biol. unit: Dimer (from PDB file)
Resolution:
2.60Å     R-factor:   0.235     R-free:   0.285
Authors: B.N.Wardleworth,R.J.M.Russell,S.D.Bell,G.L.Taylor,M.F.White
Key ref:
B.N.Wardleworth et al. (2002). Structure of Alba: an archaeal chromatin protein modulated by acetylation. EMBO J, 21, 4654-4662. PubMed id: 12198167 DOI: 10.1093/emboj/cdf465
Date:
01-Jul-02     Release date:   05-Sep-02    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P60849  (ALBA1_SULSO) -  DNA/RNA-binding protein Alba 1 from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
Seq:
Struc: 		97 a.a.
89 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

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

 

 
DOI no: 10.1093/emboj/cdf465 EMBO J 21:4654-4662 (2002)
PubMed id: 12198167  
 
 
Structure of Alba: an archaeal chromatin protein modulated by acetylation.
B.N.Wardleworth, R.J.Russell, S.D.Bell, G.L.Taylor, M.F.White.
 
  ABSTRACT  
 
Eukaryotic DNA is packaged into nucleosomes that regulate the accessibility of the genome to replication, transcription and repair factors. Chromatin accessibility is controlled by histone modifications including acetylation and methylation. Archaea possess eukary otic-like machineries for DNA replication, transcription and information processing. The conserved archaeal DNA binding protein Alba (formerly Sso10b) interacts with the silencing protein Sir2, which regulates Alba's DNA binding affinity by deacetylation of a lysine residue. We present the crystal structure of Alba from Sulfolobus solfataricus at 2.6 A resolution (PDB code 1h0x). The fold is reminiscent of the N-terminal DNA binding domain of DNase I and the C-terminal domain of initiation factor IF3. The Alba dimer has two extended beta-hairpins flanking a central body containing the acetylated lysine, Lys16, suggesting three main points of contact with the DNA. Fluorescence, calorimetry and electrophoresis data suggest a final binding stoichiometry of approximately 5 bp DNA per Alba dimer. We present a model for the Alba-DNA interaction consistent with the available structural, biophysical and electron microscopy data.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 The Alba dimer. (A) Stereo views of the dimer coloured by B-factor (dark blue to deep red representing a span of B-factor from 30 to 100 Å^2). The lower view is related to the upper view by a 90° rotation around a vertical axis. The strands and helices of one monomer are labelled as in Figure 1. The N- and C-termini are highlighted by blue and red spheres, respectively. Lysines 16 and 17 are also shown. (B) Orthogonal views of the dimer showing the location of exposed residues conserved across the Archaea: A (Gly15, Lys17, Pro18, Asn21, Tyr22), B (Lys40, Arg42, Glu91) and C (Phe60). (C) Stereo view of the Alba dimer coloured by electrostatic potential. The groove formed between the two loops containing Lys16 and Lys17 is apparent. Figures 2, 3 and 5 were drawn with BOBSCRIPT (Esnouf, 1997) and GL_RENDER (L.Esser and J.Deisenhofer, unpublished). 		Figure 3.
Figure 3 Comparison of DNase I with Alba. The N-terminal domain, residues 1−86, of DNase I is coloured magenta, in complex with a nicked DNA octamer (PDB code 2DNJ), and showing the -hairpin that interacts with the DNA minor groove. An Alba monomer is superimposed in yellow, revealing the more extensive -hairpin of Alba, and suggesting that the orientation of the DNA will be different in the Alba−DNA complex. The phosphorus atoms of the DNA are coloured green, and the side-chains of lysines 16 and 17 of Alba are shown.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2002, 21, 4654-4662) copyright 2002.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21148291 H.Maruyama, M.Shin, T.Oda, R.Matsumi, R.L.Ohniwa, T.Itoh, K.Shirahige, T.Imanaka, H.Atomi, S.H.Yoshimura, and K.Takeyasu (2011).
Histone and TK0471/TrmBL2 form a novel heterogeneous genome architecture in the hyperthermophilic archaeon Thermococcus kodakarensis.
  Mol Biol Cell, 22, 386-398.  
21265758 R.P.Driessen, and R.T.Dame (2011).
Nucleoid-associated proteins in Crenarchaea.
  Biochem Soc Trans, 39, 116-121.  
20075859 A.Perederina, O.Esakova, C.Quan, E.Khanova, and A.S.Krasilnikov (2010).
Eukaryotic ribonucleases P/MRP: the crystal structure of the P3 domain.
  EMBO J, 29, 761-769.
PDB code: 3iab
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.  
21078128 F.Paquet, K.Loth, H.Meudal, F.Culard, D.Genest, and G.Lancelot (2010).
Refined solution structure and backbone dynamics of the archaeal MC1 protein.
  FEBS J, 277, 5133-5145.
PDB code: 2khl
  20885971 J.Soppa (2010).
Protein acetylation in archaea, bacteria, and eukaryotes.
  Archaea, 2010, 0.  
20215441 K.L.Hands-Taylor, L.Martino, R.Tata, J.J.Babon, T.T.Bui, A.F.Drake, R.L.Beavil, G.J.Pruijn, P.R.Brown, and M.R.Conte (2010).
Heterodimerization of the human RNase P/MRP subunits Rpp20 and Rpp25 is a prerequisite for interaction with the P3 arm of RNase MRP RNA.
  Nucleic Acids Res, 38, 4052-4066.  
20627997 O.Esakova, and A.S.Krasilnikov (2010).
Of proteins and RNA: the RNase P/MRP family.
  RNA, 16, 1725-1747.  
20693323 W.H.Ramos-Vera, V.Labonté, M.Weiss, J.Pauly, and G.Fuchs (2010).
Regulation of autotrophic CO2 fixation in the archaeon Thermoproteus neutrophilus.
  J Bacteriol, 192, 5329-5340.  
19262980 M.Ge, and X.M.Pan (2009).
The contribution of proline residues to protein stability is associated with isomerization equilibrium in both unfolded and folded states.
  Extremophiles, 13, 481-489.  
19002648 M.Ge, Y.J.Mao, and X.M.Pan (2009).
Refolding of the hyperthermophilic protein Ssh10b involves a kinetic dimeric intermediate.
  Extremophiles, 13, 131-137.  
19473964 M.M.Brent, A.Iwata, J.Carten, K.Zhao, and R.Marmorstein (2009).
Structure and Biochemical Characterization of Protein Acetyltransferase from Sulfolobus solfataricus.
  J Biol Chem, 284, 19412-19419.
PDB code: 3f8k
19168623 Y.Liu, L.Guo, R.Guo, R.L.Wong, H.Hernandez, J.Hu, Y.Chu, I.J.Amster, W.B.Whitman, and L.Huang (2009).
The Sac10b homolog in Methanococcus maripaludis binds DNA at specific sites.
  J Bacteriol, 191, 2315-2329.  
18562273 D.J.Rigden, and M.Y.Galperin (2008).
Sequence analysis of GerM and SpoVS, uncharacterized bacterial 'sporulation' proteins with widespread phylogenetic distribution.
  Bioinformatics, 24, 1793-1797.  
18487328 J.G.Gardner, and J.C.Escalante-Semerena (2008).
Biochemical and mutational analyses of AcuA, the acetyltransferase enzyme that controls the activity of the acetyl coenzyme a synthetase (AcsA) in Bacillus subtilis.
  J Bacteriol, 190, 5132-5136.  
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
18779322 M.Ge, X.Y.Xia, and X.M.Pan (2008).
Salt bridges in the hyperthermophilic protein ssh10b are resilient to temperature increases.
  J Biol Chem, 283, 31690-31696.  
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.  
17033733 A.Morana, O.Paris, L.Maurelli, M.Rossi, and R.Cannio (2007).
Gene cloning and expression in Escherichia coli of a bi-functional beta-D-xylosidase/alpha-L-arabinosidase from Sulfolobus solfataricus involved in xylan degradation.
  Extremophiles, 11, 123-132.  
17511810 D.T.Mackay, C.H.Botting, G.L.Taylor, and M.F.White (2007).
An acetylase with relaxed specificity catalyses protein N-terminal acetylation in Sulfolobus solfataricus.
  Mol Microbiol, 64, 1540-1548.  
17881380 T.V.Aspinall, J.M.Gordon, H.J.Bennett, P.Karahalios, J.P.Bukowski, S.C.Walker, D.R.Engelke, and J.M.Avis (2007).
Interactions between subunits of Saccharomyces cerevisiae RNase MRP support a conserved eukaryotic RNase P/MRP architecture.
  Nucleic Acids Res, 35, 6439-6450.  
18096085 Y.J.Mao, X.R.Sheng, and X.M.Pan (2007).
The effects of NaCl concentration and pH on the stability of hyperthermophilic protein Ssh10b.
  BMC Biochem, 8, 28.  
16148304 J.Eichler, and M.W.Adams (2005).
Posttranslational protein modification in Archaea.
  Microbiol Mol Biol Rev, 69, 393-425.  
16030242 L.Cubonová, K.Sandman, S.J.Hallam, E.F.Delong, and J.N.Reeve (2005).
Histones in crenarchaea.
  J Bacteriol, 187, 5482-5485.  
15824122 V.L.Marsh, S.Y.Peak-Chew, and S.D.Bell (2005).
Sir2 and the acetyltransferase, Pat, regulate the archaeal chromatin protein, Alba.
  J Biol Chem, 280, 21122-21128.  
15570068 C.P.Guy, A.I.Majerník, J.P.Chong, and E.L.Bolt (2004).
A novel nuclease-ATPase (Nar71) from archaea is part of a proposed thermophilic DNA repair system.
  Nucleic Acids Res, 32, 6176-6186.  
14872062 D.J.Richard, S.D.Bell, and M.F.White (2004).
Physical and functional interaction of the archaeal single-stranded DNA-binding protein SSB with RNA polymerase.
  Nucleic Acids Res, 32, 1065-1074.  
15281131 V.Anantharaman, and L.Aravind (2004).
The SHS2 module is a common structural theme in functionally diverse protein groups, like Rpb7p, FtsA, GyrI, and MTH1598/TM1083 superfamilies.
  Proteins, 56, 795-807.  
12837780 C.C.Chou, T.W.Lin, C.Y.Chen, and A.H.Wang (2003).
Crystal structure of the hyperthermophilic archaeal DNA-binding protein Sso10b2 at a resolution of 1.85 Angstroms.
  J Bacteriol, 185, 4066-4073.
PDB code: 1udv
12754245 D.J.Soares, F.Marc, and J.N.Reeve (2003).
Conserved eukaryotic histone-fold residues substituted into an archaeal histone increase DNA affinity but reduce complex flexibility.
  J Bacteriol, 185, 3453-3457.  
12813087 G.Fiorentino, R.Cannio, M.Rossi, and S.Bartolucci (2003).
Transcriptional regulation of the gene encoding an alcohol dehydrogenase in the archaeon Sulfolobus solfataricus involves multiple factors and control elements.
  J Bacteriol, 185, 3926-3934.  
14573942 G.Taylor (2003).
The phase problem.
  Acta Crystallogr D Biol Crystallogr, 59, 1881-1890.  
14627741 G.Wang, R.Guo, M.Bartlam, H.Yang, H.Xue, Y.Liu, L.Huang, and Z.Rao (2003).
Crystal structure of a DNA binding protein from the hyperthermophilic euryarchaeon Methanococcus jannaschii.
  Protein Sci, 12, 2815-2822.
PDB code: 1nh9
12694606 J.N.Reeve (2003).
Archaeal chromatin and transcription.
  Mol Microbiol, 48, 587-598.  
12914651 K.S.Makarova, and E.V.Koonin (2003).
Comparative genomics of Archaea: how much have we learned in six years, and what's next?
  Genome Biol, 4, 115.  
12730210 K.Zhao, X.Chai, and R.Marmorstein (2003).
Structure of a Sir2 substrate, Alba, reveals a mechanism for deacetylation-induced enhancement of DNA binding.
  J Biol Chem, 278, 26071-26077.
PDB codes: 1nfh 1nfj
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.  
12832799 M.J.Teale, M.Kahsai, S.K.Singh, S.P.Edmondson, R.Gupta, J.W.Shriver, and E.Meehan (2003).
Cloning, expression, crystallization and preliminary X-ray analysis of the DNA-binding protein Sso10a from Sulfolobus solfataricus.
  Acta Crystallogr D Biol Crystallogr, 59, 1320-1322.  
14523014 Q.Cui, Y.Tong, H.Xue, L.Huang, Y.Feng, and J.Wang (2003).
Two conformations of archaeal Ssh10b. The origin of its temperature-dependent interaction with DNA.
  J Biol Chem, 278, 51015-51022.  
14651642 R.Guo, H.Xue, and L.Huang (2003).
Ssh10b, a conserved thermophilic archaeal protein, binds RNA in vivo.
  Mol Microbiol, 50, 1605-1615.  
12446147 M.F.White, and S.D.Bell (2002).
Holding it together: chromatin in the Archaea.
  Trends Genet, 18, 621-626.  
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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