2YYJ | pdb_00002yyj

Crystal structure of the oxygenase component (HpaB) of 4-hydroxyphenylacetate 3-monooxygenase complexed with FAD and 4-hydroxyphenylacetate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 
    0.167 (Depositor), 0.157 (DCC) 
  • R-Value Work: 
    0.159 (Depositor), 0.159 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 2YYJ

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of the Oxygenase Component (HpaB) of the 4-Hydroxyphenylacetate 3-Monooxygenase from Thermus thermophilus HB8

Kim, S.-H.Hisano, T.Takeda, K.Iwasaki, W.Ebihara, A.Miki, K.

(2007) J Biological Chem 282: 33107-33117

  • DOI: https://doi.org/10.1074/jbc.M703440200
  • Primary Citation Related Structures: 
    2YYG, 2YYI, 2YYJ, 2YYK, 2YYL, 2YYM

  • PubMed Abstract: 

    The 4-hydroxyphenylacetate (4HPA) 3-monooxygenase is involved in the initial step of the 4HPA degradation pathway and catalyzes 4HPA hydroxylation to 3,4-dihydroxyphenylacetate. This enzyme consists of two components, an oxygenase (HpaB) and a reductase (HpaC). To understand the structural basis of the catalytic mechanism of HpaB, crystal structures of HpaB from Thermus thermophilus HB8 were determined in three states: a ligand-free form, a binary complex with FAD, and a ternary complex with FAD and 4HPA. Structural analysis revealed that the binding and dissociation of flavin are accompanied by conformational changes of the loop between beta5 and beta6 and of the loop between beta8 and beta9, leading to preformation of part of the substrate-binding site (Ser-197 and Thr-198). The latter loop further changes its conformation upon binding of 4HPA and obstructs the active site from the bulk solvent. Arg-100 is located adjacent to the putative oxygen-binding site and may be involved in the formation and stabilization of the C4a-hydroperoxyflavin intermediate.


  • Organizational Affiliation
    • SPring-8 Center, RIKEN Harima Institute, Koto 1-1-1, Sayo-cho, Sayo-gun, Hyogo, Japan.

Macromolecule Content 

  • Total Structure Weight: 56.04 kDa 
  • Atom Count: 4,460 
  • Modeled Residue Count: 476 
  • Deposited Residue Count: 481 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
4-hydroxyphenylacetate-3-hydroxylase481Thermus thermophilus HB8Mutation(s): 0 
EC: 1.14.13.3 (PDB Primary Data), 1.14.14.9 (UniProt)
UniProt
Find proteins for Q5SJP8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SJP8 
Go to UniProtKB:  Q5SJP8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SJP8
Sequence Annotations
Expand
Reference Sequence

Small Molecules

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

Query on FAD



Download:Ideal Coordinates CCD File
H [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
4HP

Query on 4HP



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A]
4-HYDROXYPHENYLACETATE
C8 H8 O3
XQXPVVBIMDBYFF-UHFFFAOYSA-N
SO4

Query on SO4



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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free:  0.167 (Depositor), 0.157 (DCC) 
  • R-Value Work:  0.159 (Depositor), 0.159 (DCC) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.894α = 90
b = 98.466β = 90
c = 130.586γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
ARP/wARPmodel building
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-09-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.2: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description