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PDBsum entry 2gcl
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protein metals Protein-protein interface(s) links
Replication PDB id
2gcl

 

 

 

 

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Contents
Protein chains
230 a.a. *
Metals
_CL ×4
Waters ×243
* Residue conservation analysis
PDB id:
2gcl
Name: Replication
Title: Structure of the pob3 middle domain
Structure: Hypothetical 63.0 kda protein in dak1-orc1 intergenic region. Chain: a, b. Fragment: middle domain. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.21Å     R-factor:   0.210     R-free:   0.264
Authors: A.P.Vandemark
Key ref:
A.P.VanDemark et al. (2006). The structure of the yFACT Pob3-M domain, its interaction with the DNA replication factor RPA, and a potential role in nucleosome deposition. Mol Cell, 22, 363-374. PubMed id: 16678108 DOI: 10.1016/j.molcel.2006.03.025
Date:
14-Mar-06     Release date:   23-May-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q04636  (POB3_YEAST) -  FACT complex subunit POB3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		552 a.a.
230 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 

 
DOI no: 10.1016/j.molcel.2006.03.025 Mol Cell 22:363-374 (2006)
PubMed id: 16678108  
 
 
The structure of the yFACT Pob3-M domain, its interaction with the DNA replication factor RPA, and a potential role in nucleosome deposition.
A.P.VanDemark, M.Blanksma, E.Ferris, A.Heroux, C.P.Hill, T.Formosa.
 
  ABSTRACT  
 
We report the crystal structure of the middle domain of the Pob3 subunit (Pob3-M) of S. cerevisiae FACT (yFACT, facilitates chromatin transcription), which unexpectedly adopts an unusual double pleckstrin homology (PH) architecture. A mutation within a conserved surface cluster in this domain causes a defect in DNA replication that is suppressed by mutation of replication protein A (RPA). The nucleosome reorganizer yFACT therefore interacts in a physiologically important way with the central single-strand DNA (ssDNA) binding factor RPA to promote a step in DNA replication. Purified yFACT and RPA display a weak direct physical interaction, although the genetic suppression is not explained by simple changes in affinity between the purified proteins. Further genetic analysis suggests that coordinated function by yFACT and RPA is important during nucleosome deposition. These results support the model that the FACT family has an essential role in constructing nucleosomes during DNA replication, and suggest that RPA contributes to this process.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Physical Interaction between yFACT and RPA 		Figure 6.
Figure 6. Effects of Histone Overexpression or Mutation
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2006, 22, 363-374) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23288364 R.J.Burgess, and Z.Zhang (2013).
Histone chaperones in nucleosome assembly and human disease.
  Nat Struct Mol Biol, 20, 14-22.  
22358331 C.Alabert, and A.Groth (2012).
Chromatin replication and epigenome maintenance.
  Nat Rev Mol Cell Biol, 13, 153-167.  
22307274 D.Su, Q.Hu, Q.Li, J.R.Thompson, G.Cui, A.Fazly, B.A.Davies, M.V.Botuyan, Z.Zhang, and G.Mer (2012).
Structural basis for recognition of H3K56-acetylated histone H3-H4 by the chaperone Rtt106.
  Nature, 483, 104-107.
PDB codes: 2lh0 3fss 3tvv 3tw1
22290458 L.Daxinger, and E.Whitelaw (2012).
Understanding transgenerational epigenetic inheritance via the gametes in mammals.
  Nat Rev Genet, 13, 153-162.  
21232560 L.R.Kundu, M.Seki, N.Watanabe, H.Murofushi, A.Furukohri, S.Waga, A.J.Score, J.J.Blow, M.Horikoshi, T.Enomoto, and S.Tada (2011).
Biphasic chromatin binding of histone chaperone FACT during eukaryotic chromatin DNA replication.
  Biochim Biophys Acta, 1813, 1129-1136.  
21139053 A.Stanlie, M.Aida, M.Muramatsu, T.Honjo, and N.A.Begum (2010).
Histone3 lysine4 trimethylation regulated by the facilitates chromatin transcription complex is critical for DNA cleavage in class switch recombination.
  Proc Natl Acad Sci U S A, 107, 22190-22195.  
20007282 B.L.Strang, S.Boulant, and D.M.Coen (2010).
Nucleolin associates with the human cytomegalovirus DNA polymerase accessory subunit UL44 and is necessary for efficient viral replication.
  J Virol, 84, 1771-1784.  
20444609 C.Das, J.K.Tyler, and M.E.Churchill (2010).
The histone shuffle: histone chaperones in an energetic dance.
  Trends Biochem Sci, 35, 476-489.  
20432449 J.C.Hansen, J.K.Nyborg, K.Luger, and L.A.Stargell (2010).
Histone chaperones, histone acetylation, and the fluidity of the chromogenome.
  J Cell Physiol, 224, 289-299.  
20634314 J.Han, Q.Li, L.McCullough, C.Kettelkamp, T.Formosa, and Z.Zhang (2010).
Ubiquitylation of FACT by the cullin-E3 ligase Rtt101 connects FACT to DNA replication.
  Genes Dev, 24, 1485-1490.  
20126453 M.C.Espinosa, M.A.Rehman, P.Chisamore-Robert, D.Jeffery, and K.Yankulov (2010).
GCN5 is a positive regulator of origins of DNA replication in Saccharomyces cerevisiae.
  PLoS One, 5, e8964.  
20502685 M.Morillo-Huesca, D.Maya, M.C.Muñoz-Centeno, R.K.Singh, V.Oreal, G.U.Reddy, D.Liang, V.Géli, A.Gunjan, and S.Chávez (2010).
FACT prevents the accumulation of free histones evicted from transcribed chromatin and a subsequent cell cycle delay in G1.
  PLoS Genet, 6, e1000964.  
20141833 M.Ransom, B.K.Dennehey, and J.K.Tyler (2010).
Chaperoning histones during DNA replication and repair.
  Cell, 140, 183-195.  
21203924 M.Xu, and B.Zhu (2010).
Nucleosome assembly and epigenetic inheritance.
  Protein Cell, 1, 820-829.  
21070971 P.Ranjitkar, M.O.Press, X.Yi, R.Baker, M.J.MacCoss, and S.Biggins (2010).
An E3 ubiquitin ligase prevents ectopic localization of the centromeric histone H3 variant via the centromere targeting domain.
  Mol Cell, 40, 455-464.  
20879999 V.Denninger, A.Fullbrook, M.Bessat, K.Ersfeld, and G.Rudenko (2010).
The FACT subunit TbSpt16 is involved in cell cycle specific control of VSG expression sites in Trypanosoma brucei.
  Mol Microbiol, 78, 459-474.  
20007951 Y.Liu, H.Huang, B.O.Zhou, S.S.Wang, Y.Hu, X.Li, J.Liu, J.Zang, L.Niu, J.Wu, J.Q.Zhou, M.Teng, and Y.Shi (2010).
Structural analysis of Rtt106p reveals a DNA binding role required for heterochromatin silencing.
  J Biol Chem, 285, 4251-4262.
PDB codes: 3gyo 3gyp
19639603 A.Kumari, O.M.Mazina, U.Shinde, A.V.Mazin, and H.Lu (2009).
A role for SSRP1 in recombination-mediated DNA damage response.
  J Cell Biochem, 108, 508-518.  
19666464 F.Campa, H.Y.Yoon, V.L.Ha, Z.Szentpetery, T.Balla, and P.A.Randazzo (2009).
A PH domain in the Arf GTPase-activating protein (GAP) ARAP1 binds phosphatidylinositol 3,4,5-trisphosphate and regulates Arf GAP activity independently of recruitment to the plasma membranes.
  J Biol Chem, 284, 28069-28083.  
19481521 S.Takahata, Y.Yu, and D.J.Stillman (2009).
FACT and Asf1 regulate nucleosome dynamics and coactivator binding at the HO promoter.
  Mol Cell, 34, 405-415.  
19605348 Y.Tsunaka, J.Toga, H.Yamaguchi, S.Tate, S.Hirose, and K.Morikawa (2009).
Phosphorylated intrinsically disordered region of FACT masks its nucleosomal DNA binding elements.
  J Biol Chem, 284, 24610-24621.  
18089575 A.P.VanDemark, H.Xin, L.McCullough, R.Rawlins, S.Bentley, A.Heroux, D.J.Stillman, C.P.Hill, and T.Formosa (2008).
Structural and functional analysis of the Spt16p N-terminal domain reveals overlapping roles of yFACT subunits.
  J Biol Chem, 283, 5058-5068.
PDB codes: 3bip 3biq 3bit
18490440 D.Biswas, S.Takahata, and D.J.Stillman (2008).
Different genetic functions for the Rpd3(L) and Rpd3(S) complexes suggest competition between NuA4 and Rpd3(S).
  Mol Cell Biol, 28, 4445-4458.  
18245327 D.Biswas, S.Takahata, H.Xin, R.Dutta-Biswas, Y.Yu, T.Formosa, and D.J.Stillman (2008).
A role for Chd1 and Set2 in negatively regulating DNA replication in Saccharomyces cerevisiae.
  Genetics, 178, 649-659.  
18662540 Q.Li, H.Zhou, H.Wurtele, B.Davies, B.Horazdovsky, A.Verreault, and Z.Zhang (2008).
Acetylation of histone H3 lysine 56 regulates replication-coupled nucleosome assembly.
  Cell, 134, 244-255.  
18931784 T.Formosa (2008).
FACT and the reorganized nucleosome.
  Mol Biosyst, 4, 1085-1093.  
18579787 T.Stuwe, M.Hothorn, E.Lejeune, V.Rybin, M.Bortfeld, K.Scheffzek, and A.G.Ladurner (2008).
The FACT Spt16 "peptidase" domain is a histone H3-H4 binding module.
  Proc Natl Acad Sci U S A, 105, 8884-8889.
PDB codes: 3cb5 3cb6
17603125 A.A.Duina, A.Rufiange, J.Bracey, J.Hall, A.Nourani, and F.Winston (2007).
Evidence that the localization of the elongation factor Spt16 across transcribed genes is dependent upon histone H3 integrity in Saccharomyces cerevisiae.
  Genetics, 177, 101-112.  
17157503 F.Mongelard, and P.Bouvet (2007).
Nucleolin: a multiFACeTed protein.
  Trends Cell Biol, 17, 80-86.  
16977311 D.Biswas, R.Dutta-Biswas, D.Mitra, Y.Shibata, B.D.Strahl, T.Formosa, and D.J.Stillman (2006).
Opposing roles for Set2 and yFACT in regulating TBP binding at promoters.
  EMBO J, 25, 4479-4489.  
16766522 D.Reinberg, and R.J.Sims (2006).
de FACTo nucleosome dynamics.
  J Biol Chem, 281, 23297-23301.  
16935876 E.Fanning, V.Klimovich, and A.R.Nager (2006).
A dynamic model for replication protein A (RPA) function in DNA processing pathways.
  Nucleic Acids Res, 34, 4126-4137.  
17000768 S.Jimeno-González, F.Gómez-Herreros, P.M.Alepuz, and S.Chávez (2006).
A gene-specific requirement for FACT during transcription is related to the chromatin organization of the transcribed region.
  Mol Cell Biol, 26, 8710-8721.  
22334206 , (0).
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22334207 , (0).
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22334208 , (0).
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22334209 , (0).
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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.

 

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