4K35

The structure of a glycoside hydrolase family 81 endo-[beta]-1,3-glucanase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.144 

wwPDB Validation   3D Report Full Report


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Literature

The structure of a glycoside hydrolase family 81 endo-[beta]-1,3-glucanase

Zhou, P.Chen, Z.Z.Yan, Q.J.Yang, S.Q.Hilgenfeld, R.Jiang, Z.Q.

(2013) Acta Crystallogr D Biol Crystallogr 69: 2027-2038

  • DOI: 10.1007/s00253-008-1617-9
  • Primary Citation of Related Structures:  
    4K35, 4K3A

  • PubMed Abstract: 
  • A beta-1,3-glucanase gene, encoding a protein of 1,793 amino acids, was cloned from a strain of Paenibacillus sp. in this study. This large protein, designated as LamA, consists of many putative functional units, which include, from N to C terminus, a leader peptide, three repeats of the S-layer homologous module, a catalytic module of glycoside hydrolase family 16, four repeats of the carbohydrate-binding module of family CBM_4_9, and an analogue of coagulation factor Fa5/8C ...

    A beta-1,3-glucanase gene, encoding a protein of 1,793 amino acids, was cloned from a strain of Paenibacillus sp. in this study. This large protein, designated as LamA, consists of many putative functional units, which include, from N to C terminus, a leader peptide, three repeats of the S-layer homologous module, a catalytic module of glycoside hydrolase family 16, four repeats of the carbohydrate-binding module of family CBM_4_9, and an analogue of coagulation factor Fa5/8C. Several truncated proteins, composed of the catalytic module with various organizations of the appended modules, were successfully expressed and characterized in this study. Data indicated that the catalytic module specifically hydrolyze beta-1,3- and beta-1,3-1,4-glucans. Also, laminaritriose was the major product upon endolytic hydrolysis of laminarin. The CBM repeats and Fa5/8C analogue substantially enhanced the hydrolyzing activity of the catalytic module, particularly toward insoluble complex substrates, suggesting their modulating functions in the enzymatic activity of LamA. Carbohydrate-binding assay confirmed the binding capabilities of the CBM repeats and Fa5/8C analogue to beta-1,3-, beta-1,3-1,4-, and even beta-1,4-glucans. These appended modules also enhanced the inhibition effect of the catalytic module on the growth of Candida albicans and Rhizoctonia solani.


    Organizational Affiliation

    Graduate Institute of Biotechnology, National Chung Hsing University, 250 Kuo-Kuang Rd, Taichung, Taiwan 40227, Republic of China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
glycoside hydrolase family 81 endo-beta-1,3-glucanaseA, B771Rhizomucor mieheiMutation(s): 0 
Gene Names: Rhizomucor mieheiRmLam81A
EC: 3.2.1.39 (PDB Primary Data), 3.2.1.6 (UniProt)
UniProt
Find proteins for U5HK45 (Rhizomucor miehei)
Explore U5HK45 
Go to UniProtKB:  U5HK45
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth B], F [auth B]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
G [auth B](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.144 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.042α = 90
b = 118.802β = 90
c = 139.422γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-02
    Type: Initial release