8UK9

Structure of T4 Bacteriophage clamp loader mutant D110C bound to the T4 clamp, primer-template DNA, and ATP analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.253 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Autoinhibition of a clamp-loader ATPase revealed by deep mutagenesis and cryo-EM.

Marcus, K.Huang, Y.Subramanian, S.Gee, C.L.Gorday, K.Ghaffari-Kashani, S.Luo, X.R.Zheng, L.O'Donnell, M.Subramaniam, S.Kuriyan, J.

(2024) Nat Struct Mol Biol 31: 424-435

  • DOI: https://doi.org/10.1038/s41594-023-01177-3
  • Primary Citation of Related Structures:  
    8UH7, 8UK9, 8UNF, 8UNH

  • PubMed Abstract: 

    Clamp loaders are AAA+ ATPases that facilitate high-speed DNA replication. In eukaryotic and bacteriophage clamp loaders, ATP hydrolysis requires interactions between aspartate residues in one protomer, present in conserved 'DEAD-box' motifs, and arginine residues in adjacent protomers. We show that functional defects resulting from a DEAD-box mutation in the T4 bacteriophage clamp loader can be compensated by widely distributed single mutations in the ATPase domain. Using cryo-EM, we discovered an unsuspected inactive conformation of the clamp loader, in which DNA binding is blocked and the catalytic sites are disassembled. Mutations that restore function map to regions of conformational change upon activation, suggesting that these mutations may increase DNA affinity by altering the energetic balance between inactive and active states. Our results show that there are extensive opportunities for evolution to improve catalytic efficiency when an inactive intermediate is involved.


  • Organizational Affiliation

    Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sliding-clamp-loader small subunit
A, Q
187Tequatrovirus T4Mutation(s): 0 
Gene Names: 62
UniProt
Find proteins for P04527 (Enterobacteria phage T4)
Explore P04527 
Go to UniProtKB:  P04527
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04527
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Sliding-clamp-loader large subunit
B, C, D, E, K
B, C, D, E, K, L, M, N
320Tequatrovirus T4Mutation(s): 1 
Gene Names: 44
EC: 3.6.4
UniProt
Find proteins for P04526 (Enterobacteria phage T4)
Explore P04526 
Go to UniProtKB:  P04526
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04526
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Sliding clamp
F, G, H, R, S
F, G, H, R, S, T
228Tequatrovirus T4Mutation(s): 0 
Gene Names: 45
UniProt
Find proteins for P04525 (Enterobacteria phage T4)
Explore P04525 
Go to UniProtKB:  P04525
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04525
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 4
MoleculeChains LengthOrganismImage
DNA template
I, O
24Tequatrovirus T4
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 5
MoleculeChains LengthOrganismImage
DNA primer
J, P
20Tequatrovirus T4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
CA [auth D]
DA [auth E]
HA [auth K]
KA [auth L]
NA [auth M]
CA [auth D],
DA [auth E],
HA [auth K],
KA [auth L],
NA [auth M],
OA [auth N],
V [auth B],
Z [auth C]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
AF3
Query on AF3

Download Ideal Coordinates CCD File 
BA [auth D]
GA [auth K]
JA [auth L]
MA [auth M]
U [auth B]
BA [auth D],
GA [auth K],
JA [auth L],
MA [auth M],
U [auth B],
Y [auth C]
ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth D]
EA [auth E]
FA [auth K]
IA [auth L]
LA [auth M]
AA [auth D],
EA [auth E],
FA [auth K],
IA [auth L],
LA [auth M],
PA [auth N],
W [auth B],
X [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.253 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.243α = 90
b = 231.991β = 90
c = 264.511γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-13
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Database references
  • Version 1.2: 2024-04-03
    Changes: Database references