5Z6E | pdb_00005z6e

Crystal structure of a beta gamma-crystallin domain of Abundant Perithecial Protein (APP) from Neurospora crassa in the Ca2+-bound form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 
    0.201 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.159 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.161 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5Z6E

This is version 1.2 of the entry. See complete history

Literature

Interface interactions between beta gamma-crystallin domain and Ig-like domain render Ca2+-binding site inoperative in abundant perithecial protein of Neurospora crassa.

Swaroop Srivastava, S.Raman, R.Kiran, U.Garg, R.Chadalawada, S.Pawar, A.D.Sankaranarayanan, R.Sharma, Y.

(2018) Mol Microbiol 110: 955-972

  • DOI: https://doi.org/10.1111/mmi.14130
  • Primary Citation Related Structures: 
    5Z6D, 5Z6E

  • PubMed Abstract: 

    We describe a set of proteins in which a βγ-crystallin domain pairs with an Ig-like domain, and which are confined to microbes, like bacteria, slime molds and fungi. DdCAD-1 (Ca 2+ -dependent cell adhesion molecule-1) and abundant perithecial protein (APP) represent this class of molecules. Using the crystal structure of APP-NTD (N-terminal domain of APP), we describe its mode of Ca 2+ binding and provide a generalized theme for correct identification of the Ca 2+ -binding site within this class of molecules. As a common feature, one of the two Ca 2+ -binding sites is non-functional in the βγ-crystallin domains of these proteins. While APP-NTD binds Ca 2+ with a micromolar affinity which is comparable to DdCAD-1, APP surprisingly does not bind Ca 2+ . Crystal structures of APP and Ca 2+ -bound APP-NTD reveal that the interface interactions in APP render its Ca 2+ -binding site inoperative. Thus, heterodomain association provides a novel mode of Ca 2+ -binding regulation in APP. Breaking the interface interactions (mutating Asp30Ala, Leu132Ala and Ile135Ala) or separation from the Ig-like domain removes the constraints upon the required conformational transition and enables the βγ-crystallin domain to bind Ca 2+ . In mechanistic detail, our work demonstrates an interdomain interface adapted to distinct functional niches in APP and its homolog DdCAD-1.


  • Organizational Affiliation
    • CSIR - Centre for Cellular and Molecular Biology (CCMB), Hyderabad, 500 007, India.

Macromolecule Content 

  • Total Structure Weight: 11.24 kDa 
  • Atom Count: 815 
  • Modeled Residue Count: 90 
  • Deposited Residue Count: 101 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DUF1881 domain-containing protein101Neurospora crassa OR74AMutation(s): 0 
Gene Names: appNCU04533
UniProt
Find proteins for Q7RY31 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
Explore Q7RY31 
Go to UniProtKB:  Q7RY31
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7RY31
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free:  0.201 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.159 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.161 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.951α = 90
b = 48.951β = 90
c = 81.844γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Council of Scientific and Industrial ResearchIndia--

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-08-07
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description