3KTA

Structural Basis for Adenylate Kinase Activity in ABC ATPases


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural Basis for Adenylate Kinase Activity in ABC ATPases.

Lammens, A.Hopfner, K.P.

(2010) J Mol Biol 401: 265-273

  • DOI: 10.1016/j.jmb.2010.06.029
  • Primary Citation of Related Structures:  
    3KTA

  • PubMed Abstract: 
  • ATP-binding cassette (ABC) enzymes are involved in diverse biological processes ranging from transmembrane transport to chromosome cohesion and DNA repair. They typically use ATP hydrolysis to conduct energy-dependent biological reactions. However, the cystic fibrosis transmembrane conductance regulator and the DNA repair protein Rad50 can also catalyze the adenylate kinase reaction (ATP+AMP<-->2ADP) ...

    ATP-binding cassette (ABC) enzymes are involved in diverse biological processes ranging from transmembrane transport to chromosome cohesion and DNA repair. They typically use ATP hydrolysis to conduct energy-dependent biological reactions. However, the cystic fibrosis transmembrane conductance regulator and the DNA repair protein Rad50 can also catalyze the adenylate kinase reaction (ATP+AMP<-->2ADP). To clarify and provide a mechanistic basis for the adenylate kinase activity of ABC enzymes, we report the crystal structure of the nucleotide-binding domain of the Pyrococcus furiosus structural maintenance of chromosome protein (pfSMC(nbd)) in complex with the adenylate kinase inhibitor P(1),P(5)-di(adenosine-5')pentaphosphate. We show that pfSMC(nbd) possesses reverse adenylate kinase activity. Our results suggest that in adenylate kinase reactions, ATP binds to its canonical binding site while AMP binds to the Q-loop glutamine and a hydration water of the Mg(2+) ion. Furthermore, mutational analysis indicates that adenylate kinase reaction occurs in the engaged pfSMC(nbd) dimer and requires the Signature motif for phosphate transfer. Our results explain how ATP hydrolysis and adenylate kinase reactions can be catalyzed by the same functional motifs within the structural framework of ABC enzymes. Thus, adenylate kinase activity is likely to be a latent activity in many ABC enzymes.


    Organizational Affiliation

    Center for Integrated Protein Science and Gene Center, Department of Biochemistry, Ludwig-Maximilians University of Munich, Feodor-Lynen-Str. 25, 81377 Munich, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Chromosome segregation protein smcA, C182Pyrococcus furiosusMutation(s): 0 
Gene Names: PF1843
UniProt
Find proteins for Q8TZY2 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8TZY2 
Go to UniProtKB:  Q8TZY2
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Chromosome segregation protein smcB, D173Pyrococcus furiosusMutation(s): 0 
Gene Names: PF1843
UniProt
Find proteins for Q8TZY2 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8TZY2 
Go to UniProtKB:  Q8TZY2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AP5 (Subject of Investigation/LOI)
Query on AP5

Download Ideal Coordinates CCD File 
E [auth A], G [auth C]BIS(ADENOSINE)-5'-PENTAPHOSPHATE
C20 H29 N10 O22 P5
OIMACDRJUANHTJ-XPWFQUROSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A], H [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, CL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65α = 90
b = 86.1β = 116.6
c = 70.1γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CNSrefinement
XDSdata reduction
XDSdata scaling
CNSphasing
ADSCdata collection

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-07-17
    Changes: Advisory, Data collection, Derived calculations, Refinement description