4B9P

Biomass sensoring module from putative Rsgi2 protein of Clostridium thermocellum resemble family 3 carbohydrate-binding module of cellulosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.182 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.124 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Fine-Structural Variance of Family 3 Carbohydrate-Binding Modules as Extracellular Biomass-Sensing Components of Clostridium Thermocellum Anti-Sigma(I) Factors.

Yaniv, O.Fichman, G.Borovok, I.Shoham, Y.Bayer, E.A.Lamed, R.Shimon, L.J.W.Frolow, F.

(2014) Acta Crystallogr.,Sect.D 70: 522

  • DOI: 10.1107/S139900471302926X
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The anaerobic, thermophilic, cellulosome-producing bacterium Clostridium thermocellum relies on a variety of carbohydrate-active enzymes in order to efficiently break down complex carbohydrates into utilizable simple sugars. The regulation mechanism ...

    The anaerobic, thermophilic, cellulosome-producing bacterium Clostridium thermocellum relies on a variety of carbohydrate-active enzymes in order to efficiently break down complex carbohydrates into utilizable simple sugars. The regulation mechanism of the cellulosomal genes was unknown until recently, when genomic analysis revealed a set of putative operons in C. thermocellum that encode σI factors (i.e. alternative σ factors that control specialized regulon activation) and their cognate anti-σI factor (RsgI). These putative anti-σI-factor proteins have modules that are believed to be carbohydrate sensors. Three of these modules were crystallized and their three-dimensional structures were solved. The structures show a high overall degree of sequence and structural similarity to the cellulosomal family 3 carbohydrate-binding modules (CBM3s). The structures of the three carbohydrate sensors (RsgI-CBM3s) and a reference CBM3 are compared in the context of the structural determinants for the specificity of cellulose and complex carbohydrate binding. Fine structural variations among the RsgI-CBM3s appear to result in alternative substrate preferences for each of the sensors.


    Organizational Affiliation

    Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978 Tel Aviv, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TYPE 3A CELLULOSE-BINDING DOMAIN PROTEIN
A
166Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)Mutation(s): 0 
Gene Names: rsgI2
Find proteins for A3DC27 (Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372))
Go to UniProtKB:  A3DC27
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.182 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.124 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 31.736α = 90.00
b = 62.289β = 90.00
c = 79.274γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALEPACKdata scaling
DENZOdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-11
    Type: Initial release
  • Version 1.1: 2014-02-12
    Type: Database references, Source and taxonomy
  • Version 1.2: 2014-02-26
    Type: Database references