9D0Z | pdb_00009d0z

X-ray crystal structure of H157Q variant Thermothelomyces thermophilus polysaccharide monooxygenase 9E


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.236 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Second-Sphere Histidine Catalytic Function in a Fungal Polysaccharide Monooxygenase.

Batka, A.E.Thomas, W.C.Tudorica, D.A.Sayler, R.I.Marletta, M.A.

(2024) Biochemistry 63: 3136-3146

  • DOI: https://doi.org/10.1021/acs.biochem.4c00527
  • Primary Citation of Related Structures:  
    9D0Z

  • PubMed Abstract: 

    Fungal polysaccharide monooxygenases (PMOs) oxidatively degrade cellulose and other carbohydrate polymers via a mononuclear copper active site using either O 2 or H 2 O 2 as a cosubstrate. Cellulose-active fungal PMOs in the auxiliary activity 9 (AA9) family have a conserved second-sphere hydrogen-bonding network consisting of histidine, glutamine, and tyrosine residues. The second-sphere histidine has been hypothesized to play a role in proton transfer in the O 2 -dependent PMO reaction. Here the role of the second-sphere histidine (H157) in an AA9 PMO, Mt PMO9E, was investigated. This PMO is active on soluble cello-oligosaccharides such as cellohexaose (Glc6), thus enabling kinetic analysis with the point variants H157A and H157Q. The variants appeared to fold similarly to the wild-type (WT) enzyme and yet exhibited weaker affinity toward Glc6 than WT (WT K D = 20 ± 3 μM). The variants had comparable oxidase (O 2 reduction to H 2 O 2 ) activity to WT at all pH values tested. Using O 2 as a cosubstrate, the variants were less active for Glc6 hydroxylation than WT, with H157A being the least active. Similarly, H157Q was competent for Glc6 hydroxylation with H 2 O 2 , but H157A was less active. Comparison of the crystal structures of H157Q and WT Mt PMO9E reveals that a terminal heteroatom of Q157 overlays with N ε of H157. Altogether, the data suggest that H157 is not important for proton transfer, but support a role for H157 as a hydrogen-bond donor to diatomic-oxygen intermediates, thus facilitating catalysis with either O 2 or H 2 O 2 .


  • Organizational Affiliation
    • Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycoside hydrolase family 61 protein
A, B
229Thermothelomyces thermophilusMutation(s): 1 
Gene Names: MYCTH_79765
EC: 1.14.99.56
UniProt
Find proteins for G2Q7A5 (Thermothelomyces thermophilus (strain ATCC 42464 / BCRC 31852 / DSM 1799))
Explore G2Q7A5 
Go to UniProtKB:  G2Q7A5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG2Q7A5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

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

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
I [auth B],
J [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
OXY
Query on OXY

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.236 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.41α = 90
b = 122.473β = 90
c = 91.478γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesF32-GM149060

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-04
    Type: Initial release
  • Version 1.1: 2024-12-18
    Changes: Database references