2YYK | pdb_00002yyk

Crystal structure of the mutant of HpaB (T198I, A276G, and R466H)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.203 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.192 (DCC) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 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: 54.64 kDa 
  • Atom Count: 4,178 
  • Modeled Residue Count: 472 
  • Deposited Residue Count: 481 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
4-hydroxyphenylacetate-3-hydroxylase481Thermus thermophilus HB8Mutation(s): 3 
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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.203 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.192 (DCC) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.819α = 90
b = 99.612β = 90
c = 131.091γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SHARPphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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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: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.3: 2024-05-29
    Changes: Data collection