Crystal structure of beta-mannanase from Streptomyces thermolilacinus

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 

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This is version 1.5 of the entry. See complete history


The loop structure of Actinomycete glycoside hydrolase family 5 mannanases governs substrate recognition

Kumagai, Y.Yamashita, K.Tagami, T.Uraji, M.Wan, K.Okuyama, M.Yao, M.Kimura, A.Hatanaka, T.

(2015) FEBS J 282: 4001-4014

  • DOI: https://doi.org/10.1111/febs.13401
  • Primary Citation of Related Structures:  
    3WSU, 4Y7E

  • PubMed Abstract: 

    Endo-β-1,4-mannanases from Streptomyces thermolilacinus (StMan) and Thermobifida fusca (TfMan) demonstrated different substrate specificities. StMan hydrolyzed galactosylmannooligosaccharide (GGM5; 6(III) ,6(IV) -α-d-galactosyl mannopentaose) to GGM3 and M2, whereas TfMan hydrolyzed GGM5 to GGM4 and M1. To determine the region involved in the substrate specificity, we constructed chimeric enzymes of StMan and TfMan and evaluated their substrate specificities. Moreover, the crystal structure of the catalytic domain of StMan (StMandC) and the complex structure of the inactive mutant StE273AdC with M6 were solved at resolutions of 1.60 and 1.50 Å, respectively. Structural comparisons of StMandC and the catalytic domain of TfMan lead to the identification of a subsite around -1 in StMandC that could accommodate a galactose branch. These findings demonstrate that the two loops (loop7 and loop8) are responsible for substrate recognition in GH5 actinomycete mannanases. In particular, Trp281 in loop7 of StMan, which is located in a narrow and deep cleft, plays an important role in its affinity toward linear substrates. Asp310 in loop8 of StMan specifically bound to the galactosyl unit in the -1 subsite.

  • Organizational Affiliation

    Graduate School of Life Science, Hokkaido University, Sapporo, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
346Streptomyces thermolilacinusMutation(s): 0 
Gene Names: beta-mannanase
Find proteins for F5HR99 (Streptomyces thermolilacinus)
Explore F5HR99 
Go to UniProtKB:  F5HR99
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF5HR99
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
I [auth B]
J [auth B]
K [auth B]
E [auth A],
F [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B]
C3 H8 O3
Query on NA

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
G [auth B],
H [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.864α = 90
b = 100.846β = 90
c = 105.244γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
BSSdata collection
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-20
    Type: Initial release
  • Version 1.1: 2015-09-23
    Changes: Database references
  • Version 1.2: 2015-10-14
    Changes: Other
  • Version 1.3: 2015-10-28
    Changes: Database references
  • Version 1.4: 2017-11-22
    Changes: Refinement description
  • Version 1.5: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description