5YFD | pdb_00005yfd

Crystal structure of a new DPP III family member


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 
    0.217 (Depositor), 0.226 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.182 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5YFD

This is version 1.1 of the entry. See complete history

Literature

Crystal structures of Aflatoxin-oxidase from Armillariella tabescens reveal a dual activity enzyme.

Xu, T.Xie, C.Yao, D.Zhou, C.Z.Liu, J.

(2017) Biochem Biophys Res Commun 494: 621-625

  • DOI: https://doi.org/10.1016/j.bbrc.2017.10.077
  • Primary Citation Related Structures: 
    5YFB, 5YFC, 5YFD

  • PubMed Abstract: 

    Aflatoxin-oxidase (AFO), a newly discovered oxidase isolated from Armillariella tabescens, was reported to perform aflatoxin B1 (AFB1) detoxification through breaking the bisfuran ring of AFB1. However, based on sequence alignment, we found that AFO shares high sequence identities with dipeptidyl peptidase III (DPP III) family members. To understand the functions of AFO, we determined its crystal structures in the absence and presence of zinc, copper ion, and employed HPLC to test if AFO could cleave the substrates of DPP III. Our structures reveal that AFO contains the classic DPP III activity center and the HPLC results further confirm that AFO possesses the dipeptidyl peptidase activity. Therefore, AFO should belong to DPP III family. Interestingly, unlike reported classic DPP III structure that has a large domain movement upon substrate binding, the AFO structures all adopt the closed conformation, independent of substrate binding. This conformation characteristic of AFO may be related to its enzyme activities. Taken together, our results demonstrate that AFO is a dual activity enzyme with both aflatoxin-oxidase and dipeptidyl peptidase activities and its unique conformation feature expands our understanding on the mode of reaction for this enzyme family.


  • Organizational Affiliation
    • School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China; State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.

Macromolecule Content 

  • Total Structure Weight: 157.48 kDa 
  • Atom Count: 11,736 
  • Modeled Residue Count: 1,378 
  • Deposited Residue Count: 1,406 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dipeptidyl peptidase 3
A, B
703Desarmillaria tabescensMutation(s): 0 
EC: 3.4.14.4
UniProt
Find proteins for B0S4Q0 (Armillaria tabescens)
Explore B0S4Q0 
Go to UniProtKB:  B0S4Q0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0S4Q0
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS

Query on TRS



Download:Ideal Coordinates CCD File
M [auth B]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CU

Query on CU



Download:Ideal Coordinates CCD File
H [auth A],
N [auth B]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free:  0.217 (Depositor), 0.226 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.46α = 90
b = 207.14β = 90.02
c = 58.99γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2018-01-03 
  • Deposition Author(s): Xu, T., Liu, J.

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-03
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references, Derived calculations, Refinement description