2EXX

Crystal structure of HSCARG from Homo sapiens in complex with NADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Restructuring of the dinucleotide-binding fold in an NADP(H) sensor protein.

Zheng, X.Dai, X.Zhao, Y.Chen, Q.Lu, F.Yao, D.Yu, Q.Liu, X.Zhang, C.Gu, X.Luo, M.

(2007) Proc Natl Acad Sci U S A 104: 8809-8814

  • DOI: https://doi.org/10.1073/pnas.0700480104
  • Primary Citation of Related Structures:  
    2EXX

  • PubMed Abstract: 

    NAD(P) has long been known as an essential energy-carrying molecule in cells. Recent data, however, indicate that NAD(P) also plays critical signaling roles in regulating cellular functions. The crystal structure of a human protein, HSCARG, with functions previously unknown, has been determined to 2.4-A resolution. The structure reveals that HSCARG can form an asymmetrical dimer with one subunit occupied by one NADP molecule and the other empty. Restructuring of its NAD(P)-binding Rossmann fold upon NADP binding changes an extended loop to an alpha-helix to restore the integrity of the Rossmann fold. The previously unobserved restructuring suggests that HSCARG may assume a resting state when the level of NADP(H) is normal within the cell. When the NADP(H) level passes a threshold, an extensive restructuring of HSCARG would result in the activation of its regulatory functions. Immunofluorescent imaging shows that HSCARG redistributes from being associated with intermediate filaments in the resting state to being dispersed in the nucleus and the cytoplasm. The structural change of HSCARG upon NADP(H) binding could be a new regulatory mechanism that responds only to a significant change of NADP(H) levels. One of the functions regulated by HSCARG may be argininosuccinate synthetase that is involved in NO synthesis.


  • Organizational Affiliation

    National Laboratory of Protein Engineering and Plant Genetic Engineering, Department of Biochemistry and Molecular Biology, College of Life Sciences, Peking University, Beijing 100871, China. xiaofengz@pku.edu.cn


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HSCARG protein
A, B
306Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HBL8 (Homo sapiens)
Explore Q9HBL8 
Go to UniProtKB:  Q9HBL8
PHAROS:  Q9HBL8
GTEx:  ENSG00000153406 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HBL8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
C [auth A]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
NAP Binding MOAD:  2EXX Kd: 1.35e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 
  • Space Group: F 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 223.3α = 90
b = 223.3β = 90
c = 223.3γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SHARPphasing
CNSrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-11-21
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description