1P4E

Flpe W330F mutant-DNA Holliday Junction Complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.236 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

The role of the conserved Trp330 in Flp-mediated recombination. Functional and structural analysis

Rice, P.A., Chen, Y.

(2003) J Biol Chem 278: 24800-24807

  • DOI: https://doi.org/10.1074/jbc.M300853200
  • Primary Citation of Related Structures:  
    1P4E

  • PubMed Abstract: 

    • The active site of Flp contains, in addition to a transdonated nucleophilic tyrosine, five other residues that are highly conserved within the lambda-integrase family of site-specific recombinases and the type IB topoisomerases. We have used site-directed mutagenesis and x-ray crystallography to investigate the roles of two such residues, Lys223 and Trp330 ...

    The active site of Flp contains, in addition to a transdonated nucleophilic tyrosine, five other residues that are highly conserved within the lambda-integrase family of site-specific recombinases and the type IB topoisomerases. We have used site-directed mutagenesis and x-ray crystallography to investigate the roles of two such residues, Lys223 and Trp330. Our findings agree with studies on related enzymes showing the importance of Lys223 in catalysis but demonstrate that in Flp-mediated recombination the primary role of Trp330 is architectural rather than catalytic. Eliminating the hydrogen bonding potential of Trp330 by phenylalanine substitution results in surprisingly small changes in reaction rates, compared with dramatic decreases in the activities of W330A, W330H, and W330Q. The structure of a W330F mutant-DNA complex reveals an active site nearly identical to that of the wild type. The phenylalanine side chain preserves most of the van der Waals interactions Trp330 forms with the Tyr343-containing trans helix, which may be particularly important for the docking of this helix. Our studies of Trp330 provide the first detailed examination of this conserved residue in the lambda-integrase family, suggesting that the relative importance of active site residues may differ among Flp and related enzymes.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Biology, the University of Chicago, Illinois 60637, USA.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Recombinase FLP proteinG [auth A],
H [auth B]		429Saccharomyces cerevisiaeMutation(s): 2 
Gene Names: FLP1
UniProt
Find proteins for P03870 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P03870 
Go to UniProtKB:  P03870
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03870
Protein Feature View
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Recombinase FLP proteinI [auth C],
J [auth D]		429Saccharomyces cerevisiaeMutation(s): 2 
Gene Names: FLP1
UniProt
Find proteins for P03870 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P03870 
Go to UniProtKB:  P03870
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03870
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*TP*AP*AP*GP*TP*TP*CP*CP*TP*AP*TP*TP*C)-3'A [auth E],
C [auth F]		13N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*TP*TP*TP*AP*AP*AP*AP*GP*AP*AP*TP*AP*GP*GP*AP*AP*CP*TP*TP*C)-3'B [auth I],
D [auth J]		20N/A
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsLengthOrganismImage
33-MERE [auth G],
F [auth H]		33N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2PO
Query on 2PO
Download Ideal Coordinates CCD File 
K [auth H]PHOSPHONATE
H O3 P
ABLZXFCXXLZCGV-UHFFFAOYSA-L		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR		I [auth C],
J [auth D]		L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.236 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.76α = 90
b = 116.715β = 97.64
c = 142.053γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-05-20
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-16
    Changes: Data collection, Refinement description