5JDK

Crystal structure of the DNA binding domain of Sap1 in fission yeast S.pombe


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Sap1 is a replication-initiation factor essential for the assembly of pre-replicative complex in the fission yeast Schizosaccharomyces pombe.

Guan, L.He, P.Yang, F.Zhang, Y.Hu, Y.Ding, J.Hua, Y.Zhang, Y.Ye, Q.Hu, J.Wang, T.Jin, C.Kong, D.

(2017) J Biol Chem 292: 6056-6075

  • DOI: 10.1074/jbc.M116.767806
  • Primary Citation of Related Structures:  
    5B7J, 5JDK

  • PubMed Abstract: 
  • A central step in the initiation of chromosomal DNA replication in eukaryotes is the assembly of pre-replicative complex (pre-RC) at late M and early G 1 phase of the cell cycles. Since 1973, four proteins or protein complexes, including cell division control protein 6 (Cdc6)/Cdc18, minichromosome maintenance protein complex, origin recognition complex (ORC), and Cdt1, are known components of the pre-RC ...

    A central step in the initiation of chromosomal DNA replication in eukaryotes is the assembly of pre-replicative complex (pre-RC) at late M and early G 1 phase of the cell cycles. Since 1973, four proteins or protein complexes, including cell division control protein 6 (Cdc6)/Cdc18, minichromosome maintenance protein complex, origin recognition complex (ORC), and Cdt1, are known components of the pre-RC. Previously, we reported that a non-ORC protein binds to the essential element Δ9 of the Schizosaccharomyces pombe DNA-replication origin ARS3001. In this study, we identified that the non-ORC protein is Sap1. Like ORC, Sap1 binds to DNA origins during cell growth cycles. But unlike ORC, which binds to asymmetric AT-rich sequences through its nine AT-hook motifs, Sap1 preferentially binds to a DNA sequence of 5'-(A/T) n (C/G)(A/T) 9-10 (G/C)(A/T) n -3' ( n ≥ 1). We also found that Sap1 and ORC physically interact. We further demonstrated that Sap1 is required for the assembly of the pre-RC because of its essential role in recruiting Cdc18 to DNA origins. Thus, we conclude that Sap1 is a replication-initiation factor that directly participates in the assembly of the pre-RC. DNA-replication origins in fission yeast are defined by possessing two essential elements with one bound by ORC and the other by Sap1.


    Organizational Affiliation

    From the Peking-Tsinghua Center for Life Sciences, National Laboratory of Protein and Plant Gene Research, College of Life Sciences, kongdc@pku.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Switch-activating protein 1A137Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: sap1SPCC1672.02c
UniProt
Find proteins for P40847 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore P40847 
Go to UniProtKB:  P40847
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40847
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.84α = 90
b = 40.88β = 90
c = 70.14γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
CrystalCleardata scaling
PHENIXphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-04-17 
  • Released Date: 2017-02-22 
  • Deposition Author(s): He, P., Wang, T.

Funding OrganizationLocationGrant Number
MOSTChina2013CB911500
National Natural Science Foundation of ChinaChina31300600

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-10-18
    Changes: Author supporting evidence
  • Version 1.2: 2018-01-24
    Changes: Database references