4PEU

Structure of the polysaccharide lyase-like protein Cthe_2159 from C. thermocellum, native form with Calcium bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.149 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A new family of beta-helix proteins with similarities to the polysaccharide lyases.

Close, D.W.D'Angelo, S.Bradbury, A.R.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2583-2592

  • DOI: 10.1107/S1399004714015934
  • Primary Citation of Related Structures:  
    4PEU, 4PHB

  • PubMed Abstract: 
  • Microorganisms that degrade biomass produce diverse assortments of carbohydrate-active enzymes and binding modules. Despite tremendous advances in the genomic sequencing of these organisms, many genes do not have an ascribed function owing to low sequence identity to genes that have been annotated ...

    Microorganisms that degrade biomass produce diverse assortments of carbohydrate-active enzymes and binding modules. Despite tremendous advances in the genomic sequencing of these organisms, many genes do not have an ascribed function owing to low sequence identity to genes that have been annotated. Consequently, biochemical and structural characterization of genes with unknown function is required to complement the rapidly growing pool of genomic sequencing data. A protein with previously unknown function (Cthe_2159) was recently isolated in a genome-wide screen using phage display to identify cellulose-binding protein domains from the biomass-degrading bacterium Clostridium thermocellum. Here, the crystal structure of Cthe_2159 is presented and it is shown that it is a unique right-handed parallel β-helix protein. Despite very low sequence identity to known β-helix or carbohydrate-active proteins, Cthe_2159 displays structural features that are very similar to those of polysaccharide lyase (PL) families 1, 3, 6 and 9. Cthe_2159 is conserved across bacteria and some archaea and is a member of the domain of unknown function family DUF4353. This suggests that Cthe_2159 is the first representative of a previously unknown family of cellulose and/or acid-sugar binding β-helix proteins that share structural similarities with PLs. Importantly, these results demonstrate how functional annotation by biochemical and structural analysis remains a critical tool in the characterization of new gene products.


    Organizational Affiliation

    Bioscience Division, Los Alamos National Laboratory, MS888, Los Alamos, NM 87545, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinA313Hungateiclostridium thermocellum ATCC 27405Mutation(s): 2 
Gene Names: Cthe_2159
UniProt
Find proteins for A3DHD2 (Hungateiclostridium thermocellum (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372))
Explore A3DHD2 
Go to UniProtKB:  A3DHD2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.149 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.6997α = 90
b = 123.429β = 90
c = 34.5297γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data collection
MOSFLMdata reduction
SCALAdata scaling
Cootmodel building
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-01
    Type: Initial release
  • Version 1.1: 2014-10-22
    Changes: Database references
  • Version 1.2: 2015-02-04
    Changes: Derived calculations
  • Version 1.3: 2017-11-22
    Changes: Advisory, Derived calculations, Other, Refinement description, Source and taxonomy