8RAF | pdb_00008raf

Crystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis point mutant R90I (holo form)

• PDB DOI: https://doi.org/10.2210/pdb8RAF/pdb

• Classification: TRANSFERASE
• Organism(s): Haliscomenobacter hydrossis DSM 1100
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-12-01 Released: 2023-12-27 
• Deposition Author(s): Matyuta, I.O., Bakunova, A.K., Minyaev, M.E., Popov, V.O., Bezsudnova, E.Y., Boyko, K.M.
• Funding Organization(s): Russian Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Multifunctionality of arginine residues in the active sites of non-canonical d-amino acid transaminases.

Bakunova, A.K., Matyuta, I.O., Minyaev, M.E., Isaikina, T.Y., Boyko, K.M., Popov, V.O., Bezsudnova, E.Y.

(2024) Arch Biochem Biophys 756: 110011-110011

• PubMed: 38649133 
• DOI: https://doi.org/10.1016/j.abb.2024.110011
• Primary Citation Related Structures: 
  8RAF, 8RAI


• PubMed Abstract: 
  

  Structure-function relationships are key to understanding enzyme mechanisms, controlling enzyme activities, and designing biocatalysts. Here, we investigate the functions of arginine residues in the active sites of pyridoxal-5'-phosphate (PLP)-dependent non-canonical d-amino acid transaminases, focusing on the analysis of a transaminase from Haliscomenobacter hydrossis. Our results show that the tandem of arginine residues R28* and R90, which form the conserved R-[RK] motif in non-canonical d-amino acid transaminases, not only facilitates effective substrate binding but also regulates the catalytic properties of PLP. Non-covalent interactions between residues R28*, R90, and Y147 strengthen the hydrogen bond between Y147 and PLP, thereby maintaining the reactivity of the cofactor. Next, the R90 residue contributes to the stability of the holoenzyme. Finally, the R90I substitution induces structural changes that lead to substrate promiscuity, as evidenced by the effective binding of substrates with and without the α-carboxylate group. This study sheds light on the structural determinants of the activity of non-canonical d-amino acid transaminases. Understanding the structural basis of the active site plasticity in the non-canonical transaminase from H. hydrossis, which is characterized by effective conversion of d-amino acids and α-keto acids, may help to tailor it for industrial applications.

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Organizational Affiliation: 
• Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071, Moscow, Russia. Electronic address: [e-mail].
Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071, Moscow, Russia.
N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Ave. 47, 119334, Moscow, Russia.
Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071, Moscow, Russia; Department of Biology, Lomonosov Moscow State University, Leninskie Gory 1, bld. 12, 119991, Moscow, Russia.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 32.52 kDa 
• Atom Count: 2,482 
• Modeled Residue Count: 281 
• Deposited Residue Count: 283 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminotransferase class IV	A	283	Haliscomenobacter hydrossis DSM 1100	Mutation(s): 1  Gene Names: Halhy_2446 EC: 2.6.1.42
UniProt
Find proteins for F4KWH0 (Haliscomenobacter hydrossis (strain ATCC 27775 / DSM 1100 / LMG 10767 / O)) Explore F4KWH0  Go to UniProtKB:  F4KWH0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP (Subject of Investigation/LOI)	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.392	α = 90
b = 72.627	β = 100.8
c = 52.244	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
CrysalisPro	data reduction
REFMAC	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-12-27 
Deposition Author(s): Matyuta, I.O., Bakunova, A.K., Minyaev, M.E., Popov, V.O., Bezsudnova, E.Y., Boyko, K.M.

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Funding Organization	Location	Grant Number
Russian Science Foundation	Russian Federation	23-74-30004

Revision History  

• Version 1.0: 2023-12-27
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Database references
• Version 1.2: 2024-05-08
  Changes: Database references