The structure of a carbohydrate active P450

Experimental Data Snapshot

  • Resolution: 2.25 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

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Specificity and mechanism of carbohydrate demethylation by cytochrome P450 monooxygenases.

Robb, C.S.Reisky, L.Bornscheuer, U.T.Hehemann, J.H.

(2018) Biochem J 475: 3875-3886

  • DOI: https://doi.org/10.1042/BCJ20180762
  • Primary Citation of Related Structures:  
    6G5O, 6G5Q

  • PubMed Abstract: 

    Degradation of carbohydrates by bacteria represents a key step in energy metabolism that can be inhibited by methylated sugars. Removal of methyl groups, which is critical for further processing, poses a biocatalytic challenge because enzymes need to overcome a high energy barrier. Our structural and computational analysis revealed how a member of the cytochrome P450 family evolved to oxidize a carbohydrate ligand. Using structural biology, we ascertained the molecular determinants of substrate specificity and revealed a highly specialized active site complementary to the substrate chemistry. Invariance of the residues involved in substrate recognition across the subfamily suggests that they are critical for enzyme function and when mutated, the enzyme lost substrate recognition. The structure of a carbohydrate-active P450 adds mechanistic insight into monooxygenase action on a methylated monosaccharide and reveals the broad conservation of the active site machinery across the subfamily.

  • Organizational Affiliation

    Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen 28359, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450
A, B
399Zobellia galactanivoransMutation(s): 0 
Gene Names: cypAzobellia_4677
EC: 1.14.15
Find proteins for G0L713 (Zobellia galactanivorans (strain DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij))
Explore G0L713 
Go to UniProtKB:  G0L713
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0L713
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C34 H32 Fe N4 O4
Experimental Data & Validation

Experimental Data

  • Resolution: 2.25 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.28α = 90
b = 68.152β = 90
c = 199.728γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research FoundationGermanyHE 7217/1-1

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2018-12-26
    Changes: Data collection, Database references, Source and taxonomy
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description