6EB0 | pdb_00006eb0

STRUCTURE OF 4-HYDROXYPHENYLACETATE 3-MONOOXYGENASE (HPAB), OXYGENASE COMPONENT FROM ESCHERICHIA COLI

• PDB DOI: https://doi.org/10.2210/pdb6EB0/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli BL21(DE3)
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-08-03 Released: 2019-05-22 
• Deposition Author(s): Zhou, D., Kandavelu, P., Zhang, H., Wang, B.C., Yan, Y., Rose, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 
  0.195 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.160 (Depositor) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Structural Insights into Catalytic Versatility of the Flavin-dependent Hydroxylase (HpaB) from Escherichia coli.

Shen, X., Zhou, D., Lin, Y., Wang, J., Gao, S., Kandavelu, P., Zhang, H., Zhang, R., Wang, B.C., Rose, J., Yuan, Q., Yan, Y.

(2019) Sci Rep 9: 7087-7087

• PubMed: 31068633 
• DOI: https://doi.org/10.1038/s41598-019-43577-w
• Primary Citation Related Structures: 
  6B1B, 6EB0


• PubMed Abstract: 
  

  4-Hydroxyphenylacetate 3-hydroxylase (EcHpaB) from Escherichia coli is capable of efficient ortho-hydroxylation of a wide range of phenolic compounds and demonstrates great potential for broad chemoenzymatic applications. To understand the structural and mechanistic basis of its catalytic versatility, we elucidated the crystal structure of EcHpaB by X-ray crystallography, which revealed a unique loop structure covering the active site. We further performed mutagenesis studies of this loop to probe its role in substrate specificity and catalytic activity. Our results not only showed the loop has great plasticity and strong tolerance towards extensive mutagenesis, but also suggested a flexible loop that enables the entrance and stable binding of substrates into the active site is the key factor to the enzyme catalytic versatility. These findings lay the groundwork for editing the loop sequence and structure for generation of EcHpaB mutants with improved performance for broader laboratory and industrial use.

---

Organizational Affiliation: 
• Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China.
State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, China.
Department of Biochemistry & Molecular Biology, The University of Georgia, Athens, Georgia, 30602, USA.
School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA, 30602, USA.
Department of Biochemistry & Molecular Biology, The University of Georgia, Athens, Georgia, 30602, USA. [e-mail].
Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China. [e-mail].
State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, China. [e-mail].
School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA, 30602, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 239.88 kDa 
• Atom Count: 17,241 
• Modeled Residue Count: 2,072 
• Deposited Residue Count: 2,108 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxyphenylacetate 3-monooxygenase, oxygenase subunit	A, B, C, D	527	Escherichia coli BL21(DE3)	Mutation(s): 0  Gene Names: ECBD_3674

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	E [auth A], F [auth C], G [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free:  0.195 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.160 (Depositor) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.409	α = 90
b = 93.734	β = 108.23
c = 142.335	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
SCALEPACK	data scaling
BALBES	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-05-22 
Deposition Author(s): Zhou, D., Kandavelu, P., Zhang, H., Wang, B.C., Yan, Y., Rose, J.

Revision History  

• Version 1.0: 2019-05-22
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description