9FDL | pdb_00009fdl

Crystal structure of the catalytic domain of an AA9 lytic polysaccharide monooxygenase from Thermothelomyces thermophilus (TtLPMO9F)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 
    0.204 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.162 (Depositor), 0.169 (DCC) 

Starting Model: experimental
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Literature

Mutational study of a lytic polysaccharide monooxygenase from Myceliophthora thermophila (MtLPMO9F): Structural insights into substrate specificity and regioselectivity.

Kosinas, C.Chorozian, K.Sandgren, M.Topakas, E.Dimarogona, M.

(2024) Int J Biol Macromol 288: 138574-138574

  • DOI: https://doi.org/10.1016/j.ijbiomac.2024.138574
  • Primary Citation of Related Structures:  
    9FDL

  • PubMed Abstract: 

    Lytic polysaccharide monooxygenases (LPMOs) are key enzymes for the biotechnological exploitation of lignocellulosic biomass, yet their efficient application depends on the in-depth understanding of their mechanism of action. Here, we describe the structural and mutational characterization of a C4-active LPMO from Myceliophthora thermophila, MtLPMO9F, that belongs to auxiliary activity family 9 (AA9). MtLPMO9F is active on cellulose, cello-oligosaccharides and xyloglucan. The crystal structure of MtLPMO9F catalytic domain, determined at 2.3 Å resolution, revealed a double conformation for loop L3 with a potential implication in the formation of aglycon subsites. Product analysis of reactions with cello-oligosaccharides showed a prevalent -4 to +2 binding mode. Subsequent biochemical characterization of 4 MtLPMO9F point mutants further provided insights in LPMO structure-function relationships regarding both substrate binding and the role of second-coordination sphere residues.


  • Organizational Affiliation
    • Laboratory of Structural Biology and Biotechnology, Department of Chemical Engineering University of Patras, Patras, Greece.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycoside hydrolase family 61 protein
A, B, C
230Thermothelomyces thermophilus ATCC 42464Mutation(s): 0 
Gene Names: MYCTH_111088
EC: 1.14.99.56
UniProt
Find proteins for G2Q9F7 (Thermothelomyces thermophilus (strain ATCC 42464 / BCRC 31852 / DSM 1799))
Explore G2Q9F7 
Go to UniProtKB:  G2Q9F7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG2Q9F7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
E [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG
Query on PEG

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D [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
CU (Subject of Investigation/LOI)
Query on CU

Download Ideal Coordinates CCD File 
H [auth A],
I [auth B],
J [auth C]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT
Query on FMT

Download Ideal Coordinates CCD File 
G [auth A]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free:  0.204 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.162 (Depositor), 0.169 (DCC) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.891α = 90
b = 112.293β = 90
c = 262.381γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
University of PatrasGreece81074

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-25
    Type: Initial release