3G4E

Crystal structure of human senescence marker protein-30(SMP30)(Calcium bound)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.136 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of human senescence marker protein 30: insights linking structural, enzymatic, and physiological functions .

Chakraborti, S.Bahnson, B.J.

(2010) Biochemistry 49: 3436-3444

  • DOI: 10.1021/bi9022297
  • Primary Citation of Related Structures:  
    3G4H, 3G4E

  • PubMed Abstract: 
  • Human senescence marker protein 30 (SMP30), which functions enzymatically as a lactonase, hydrolyzes various carbohydrate lactones. The penultimate step in vitamin-C biosynthesis is catalyzed by this enzyme in nonprimate mammals. It has also been imp ...

    Human senescence marker protein 30 (SMP30), which functions enzymatically as a lactonase, hydrolyzes various carbohydrate lactones. The penultimate step in vitamin-C biosynthesis is catalyzed by this enzyme in nonprimate mammals. It has also been implicated as an organophosphate hydrolase, with the ability to hydrolyze diisopropyl phosphofluoridate and other nerve agents. SMP30 was originally identified as an aging marker protein, whose expression decreased androgen independently in aging cells. SMP30 is also referred to as regucalcin and has been suggested to have functions in calcium homeostasis. The crystal structure of the human enzyme has been solved from X-ray diffraction data collected to a resolution of 1.4 A. The protein has a 6-bladed beta-propeller fold, and it contains a single metal ion. Crystal structures have been solved with the metal site bound with either a Ca(2+) or a Zn(2+) atom. The catalytic role of the metal ion has been confirmed by mutagenesis of the metal coordinating residues. Kinetic studies using the substrate gluconolactone showed a k(cat) preference of divalent cations in the order Zn(2+) > Mn(2+) > Ca(2+) > Mg(2+). Notably, the Ca(2+) had a significantly higher value of K(d) compared to those of the other metal ions tested (566, 82, 7, and 0.6 mum for Ca(2+), Mg(2+), Zn(2+), and Mn(2+), respectively), suggesting that the Ca(2+)-bound form may be physiologically relevant for stressed cells with an elevated free calcium level.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RegucalcinAB297Homo sapiensMutation(s): 0 
Gene Names: RGNSMP30
EC: 3.1.1.17
Find proteins for Q15493 (Homo sapiens)
Explore Q15493 
Go to UniProtKB:  Q15493
NIH Common Fund Data Resources
PHAROS  Q15493
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.136 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.474α = 90
b = 51.001β = 100.11
c = 86.124γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
SHELXrefinement
PDB_EXTRACTdata extraction
SHELXL-97refinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Advisory, Refinement description