5LB5

Crystal structure of human RECQL5 helicase in complex with ADP/Mg (tricilinc form).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 

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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

Insights into the RecQ helicase mechanism revealed by the structure of the helicase domain of human RECQL5.

Newman, J.A.Aitkenhead, H.Savitsky, P.Gileadi, O.

(2017) Nucleic Acids Res 45: 4231-4243

  • DOI: https://doi.org/10.1093/nar/gkw1362
  • Primary Citation of Related Structures:  
    5LB3, 5LB5, 5LB8

  • PubMed Abstract: 

    RecQ helicases are important maintainers of genome integrity with distinct roles in almost every cellular process requiring access to DNA. RECQL5 is one of five human RecQ proteins and is particularly versatile in this regard, forming protein complexes with a diverse set of cellular partners in order to coordinate its helicase activity to various processes including replication, recombination and DNA repair. In this study, we have determined crystal structures of the core helicase domain of RECQL5 both with and without the nucleotide ADP in two distinctly different ('Open' and 'Closed') conformations. Small angle X-ray scattering studies show that the 'Open' form of the protein predominates in solution and we discuss implications of this with regards to the RECQL5 mechanism and conformational changes. We have measured the ATPase, helicase and DNA binding properties of various RECQL5 constructs and variants and discuss the role of these regions and residues in the various RECQL5 activities. Finally, we have performed a systematic comparison of the RECQL5 structures with other RecQ family structures and based on these comparisons we have constructed a model for the mechano-chemical cycle of the common catalytic core of these helicases.


  • Organizational Affiliation

    Structural Genomics Consortium, State University of Campinas, Campinas SP 13083-886, Brazil.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent DNA helicase Q5
A, B, C, D
445Homo sapiensMutation(s): 0 
Gene Names: RECQL5RECQ5
EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for O94762 (Homo sapiens)
Explore O94762 
Go to UniProtKB:  O94762
GTEx:  ENSG00000108469 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO94762
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
H [auth A],
L [auth B],
O [auth C],
S [auth D]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
Q [auth D]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
M [auth C],
P [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
N [auth C],
R [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.59α = 108.82
b = 84.75β = 90.06
c = 106.691γ = 96.86
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 1.1: 2017-01-18
    Changes: Database references
  • Version 1.2: 2017-02-01
    Changes: Database references
  • Version 1.3: 2017-05-03
    Changes: Database references
  • Version 1.4: 2017-08-23
    Changes: Author supporting evidence
  • Version 1.5: 2018-01-24
    Changes: Structure summary
  • Version 1.6: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description