6DRT

Crystal structure of the processivity clamp GP45 complexed with recognition peptide of ligase from bacteriophage T4

  • Classification: GENE REGULATION
  • Organism(s): Escherichia virus T4
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2018-06-13 Released: 2018-09-26 
  • Deposition Author(s): Shi, K., Aihara, H.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

T4 DNA ligase structure reveals a prototypical ATP-dependent ligase with a unique mode of sliding clamp interaction.

Shi, K.Bohl, T.E.Park, J.Zasada, A.Malik, S.Banerjee, S.Tran, V.Li, N.Yin, Z.Kurniawan, F.Orellana, K.Aihara, H.

(2018) Nucleic Acids Res 46: 10474-10488

  • DOI: 10.1093/nar/gky776
  • Primary Citation of Related Structures:  
    6DRT, 6DT1, 5WFY

  • PubMed Abstract: 
  • DNA ligases play essential roles in DNA replication and repair. Bacteriophage T4 DNA ligase is the first ATP-dependent ligase enzyme to be discovered and is widely used in molecular biology, but its structure remained unknown. Our crystal structure of T4 DNA ligase bound to DNA shows a compact α-helical DNA-binding domain (DBD), nucleotidyl-transferase (NTase) domain, and OB-fold domain, which together fully encircle DNA ...

    DNA ligases play essential roles in DNA replication and repair. Bacteriophage T4 DNA ligase is the first ATP-dependent ligase enzyme to be discovered and is widely used in molecular biology, but its structure remained unknown. Our crystal structure of T4 DNA ligase bound to DNA shows a compact α-helical DNA-binding domain (DBD), nucleotidyl-transferase (NTase) domain, and OB-fold domain, which together fully encircle DNA. The DBD of T4 DNA ligase exhibits remarkable structural homology to the core DNA-binding helices of the larger DBDs from eukaryotic and archaeal DNA ligases, but it lacks additional structural components required for protein interactions. T4 DNA ligase instead has a flexible loop insertion within the NTase domain, which binds tightly to the T4 sliding clamp gp45 in a novel α-helical PIP-box conformation. Thus, T4 DNA ligase represents a prototype of the larger eukaryotic and archaeal DNA ligases, with a uniquely evolved mode of protein interaction that may be important for efficient DNA replication.


    Organizational Affiliation

    Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church Street S.E. Minneapolis, MN 55455, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase clampA, B, C236Escherichia virus T4Mutation(s): 0 
Gene Names: 45
UniProt
Find proteins for P04525 (Enterobacteria phage T4)
Explore P04525 
Go to UniProtKB:  P04525
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GP45 recognition loopD, E, F13Escherichia virus T4Mutation(s): 0 
Gene Names: 30
EC: 6.5.1.1
UniProt
Find proteins for P00970 (Enterobacteria phage T4)
Explore P00970 
Go to UniProtKB:  P00970
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.757α = 90
b = 90.95β = 90
c = 151.403γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-06-13 
  • Released Date: 2018-09-26 
  • Deposition Author(s): Shi, K., Aihara, H.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM095558
National Science Foundation (NSF, United States)United StatesMCB-0213124

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-26
    Type: Initial release
  • Version 1.1: 2018-11-14
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence