3IIL

The structure of hCINAP-MgADP-Pi complex at 2.0 angstroms resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

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This is version 1.4 of the entry. See complete history


Literature

hCINAP is an atypical mammalian nuclear adenylate kinase with an ATPase motif: Structural and functional studies.

Drakou, C.E.Malekkou, A.Hayes, J.M.Lederer, C.W.Leonidas, D.D.Oikonomakos, N.G.Lamond, A.I.Santama, N.Zographos, S.E.

(2012) Proteins 80: 206-220

  • DOI: 10.1002/prot.23186
  • Primary Citation of Related Structures:  
    3IIK, 3IIL, 3IIM, 3IIJ

  • PubMed Abstract: 
  • Human coilin interacting nuclear ATPase protein (hCINAP) directly interacts with coilin, a marker protein of Cajal Bodies (CBs), nuclear organelles involved in the maturation of small nuclear ribonucleoproteins UsnRNPs and snoRNPs. hCINAP has previously been designated as an adenylate kinase (AK6), but is very atypical as it exhibits unusually broad substrate specificity, structural features characteristic of ATPase/GTPase proteins (Walker motifs A and B) and also intrinsic ATPase activity ...

    Human coilin interacting nuclear ATPase protein (hCINAP) directly interacts with coilin, a marker protein of Cajal Bodies (CBs), nuclear organelles involved in the maturation of small nuclear ribonucleoproteins UsnRNPs and snoRNPs. hCINAP has previously been designated as an adenylate kinase (AK6), but is very atypical as it exhibits unusually broad substrate specificity, structural features characteristic of ATPase/GTPase proteins (Walker motifs A and B) and also intrinsic ATPase activity. Despite its intriguing structure, unique properties and cellular localization, the enzymatic mechanism and biological function of hCINAP have remained poorly characterized. Here, we offer the first high-resolution structure of hCINAP in complex with the substrate ADP (and dADP), the structure of hCINAP with a sulfate ion bound at the AMP binding site, and the structure of the ternary complex hCINAP-Mg(2+) ADP-Pi. Induced fit docking calculations are used to predict the structure of the hCINAP-Mg(2+) ATP-AMP ternary complex. Structural analysis suggested a functional role for His79 in the Walker B motif. Kinetic analysis of mutant hCINAP-H79G indicates that His79 affects both AK and ATPase catalytic efficiency and induces homodimer formation. Finally, we show that in vivo expression of hCINAP-H79G in human cells is toxic and drastically deregulates the number and appearance of CBs in the cell nucleus. Our findings suggest that hCINAP may not simply regulate nucleotide homeostasis, but may have broader functionality, including control of CB assembly and disassembly in the nucleus of human cells.


    Organizational Affiliation

    Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, Athens 11635, Greece.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coilin-interacting nuclear ATPase proteinA180Homo sapiensMutation(s): 0 
Gene Names: CINAPTAF9hCG_37060AK6AD-004CGI-137
EC: 2.7.4.3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3D8 (Homo sapiens)
Explore Q9Y3D8 
Go to UniProtKB:  Q9Y3D8
PHAROS:  Q9Y3D8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
C [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A], I [auth A], J [auth A], K [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
G [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], F [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
LI
Query on LI

Download Ideal Coordinates CCD File 
B [auth A]LITHIUM ION
Li
HBBGRARXTFLTSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.173α = 90
b = 99.173β = 90
c = 58.048γ = 120
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-10-05
    Changes: Advisory, Database references
  • Version 1.3: 2011-11-23
    Changes: Database references
  • Version 1.4: 2012-01-18
    Changes: Database references