4CVU

Structure of Fungal beta-mannosidase from Glycoside Hydrolase Family 2 of Trichoderma harzianum

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 

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Literature

Insights into the structure and function of fungal beta-mannosidases from glycoside hydrolase family 2 based on multiple crystal structures of the Trichoderma harzianum enzyme.

Nascimento, A.S., Muniz, J.R., Aparicio, R., Golubev, A.M., Polikarpov, I.

(2014) FEBS J 281: 4165-4178

  • DOI: https://doi.org/10.1111/febs.12894
  • Primary Citation of Related Structures:  
    4CVU, 4UOJ

  • PubMed Abstract: 

    • Hemicellulose is an important part of the plant cell wall biomass, and is relevant to cellulosic ethanol technologies. β-Mannosidases are enzymes capable of cleaving nonreducing residues of β-d-mannose from β-d-mannosides and hemicellulose mannose-containing polysaccharides, such as mannans and galactomannans ...

    Hemicellulose is an important part of the plant cell wall biomass, and is relevant to cellulosic ethanol technologies. β-Mannosidases are enzymes capable of cleaving nonreducing residues of β-d-mannose from β-d-mannosides and hemicellulose mannose-containing polysaccharides, such as mannans and galactomannans. β-Mannosidases are distributed between glycoside hydrolase (GH) families 1, 2, and 5, and only a handful of the enzymes have been structurally characterized to date. The only published X-ray structure of a GH family 2 mannosidase is that of the bacterial Bacteroides thetaiotaomicron enzyme. No structures of eukaryotic mannosidases of this family are currently available. To fill this gap, we set out to solve the structure of Trichoderma harzianum GH family 2 β-mannosidase and to refine it to 1.9-Å resolution. Structural comparisons of the T. harzianum GH2 β-mannosidase highlight similarities in its structural architecture with other members of GH family 2, reveal the molecular mechanism of β-mannoside binding and recognition, and shed light on its putative galactomannan-binding site.

    Organizational Affiliation: 

    Instituto de Física de São Carlos, Universidade de São Paulo, Brazil.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BETA-MANNOSIDASE942Trichoderma harzianumMutation(s): 0 
EC: 3.2.1.25
UniProt
Find proteins for A0A075B5H6 (Trichoderma harzianum)
Explore A0A075B5H6 
Go to UniProtKB:  A0A075B5H6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A075B5H6
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
8N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G03321AC
GlyCosmos:  G03321AC
GlyGen:  G03321AC
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(2-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
6N/AN-Glycosylation Oligosaccharides Interaction
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
11N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G60230HH
GlyCosmos:  G60230HH
GlyGen:  G60230HH
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
PG4
Query on PG4
Download Ideal Coordinates CCD File 
IA [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N		 Ligand Interaction
CD
Query on CD
Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
CA [auth A]
M [auth A]
N [auth A]
AA [auth A],
BA [auth A],
CA [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N		 Ligand Interaction
PEG
Query on PEG
Download Ideal Coordinates CCD File 
JA [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
KA [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
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LA [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
DA [auth A]
EA [auth A]
FA [auth A]
GA [auth A]
HA [auth A]
DA [auth A],
EA [auth A],
FA [auth A],
GA [auth A],
HA [auth A],
MA [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.456α = 90
b = 166.456β = 90
c = 121.452γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
HKL2Mapphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-07-30
    Changes: Database references, Other, Source and taxonomy, Structure summary
  • Version 1.2: 2014-10-01
    Changes: Database references
  • Version 2.0: 2019-01-30
    Changes: Advisory, Atomic model, Data collection, Database references, Refinement description
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
  • Version 4.0: 2022-12-07
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 4.1: 2023-07-05
    Changes: Advisory, Derived calculations