5MR0

Thermophilic archaeal branched-chain amino acid transaminases from Geoglobus acetivorans and Archaeoglobus fulgidus: biochemical and structural characterisation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Thermostable Branched-Chain Amino Acid Transaminases From the ArchaeaGeoglobus acetivoransandArchaeoglobus fulgidus: Biochemical and Structural Characterization.

Isupov, M.N.Boyko, K.M.Sutter, J.M.James, P.Sayer, C.Schmidt, M.Schonheit, P.Nikolaeva, A.Y.Stekhanova, T.N.Mardanov, A.V.Ravin, N.V.Bezsudnova, E.Y.Popov, V.O.Littlechild, J.A.

(2019) Front Bioeng Biotechnol 7: 7-7

  • DOI: https://doi.org/10.3389/fbioe.2019.00007
  • Primary Citation of Related Structures:  
    5CM0, 5E25, 5MQZ, 5MR0

  • PubMed Abstract: 

    Two new thermophilic branched chain amino acid transaminases have been identified within the genomes of different hyper-thermophilic archaea, Geoglobus acetivorans , and Archaeoglobus fulgidus . These enzymes belong to the class IV of transaminases as defined by their structural fold. The enzymes have been cloned and over-expressed in Escherichia coli and the recombinant enzymes have been characterized both biochemically and structurally. Both enzymes showed high thermostability with optimal temperature for activity at 80 and 85°C, respectively. They retain good activity after exposure to 50% of the organic solvents, ethanol, methanol, DMSO and acetonitrile. The enzymes show a low activity to ( R )-methylbenzylamine but no activity to ( S )-methylbenzylamine. Both enzymes have been crystallized and their structures solved in the internal aldimine form, to 1.9 Å resolution for the Geoglobus enzyme and 2.0 Å for the Archaeoglobus enzyme. Also the Geoglobus enzyme structure has been determined in complex with the amino acceptor α-ketoglutarate and the Archaeoglobus enzyme in complex with the inhibitor gabaculine. These two complexes have helped to determine the conformation of the enzymes during enzymatic turnover and have increased understanding of their substrate specificity. A comparison has been made with another ( R ) selective class IV transaminase from the fungus Nectria haematococca which was previously studied in complex with gabaculine. The subtle structural differences between these enzymes has provided insight regarding their different substrate specificities.


  • Organizational Affiliation

    Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative branched-chain-amino-acid aminotransferase
A, B, C, D, E
290Archaeoglobus fulgidus DSM 4304Mutation(s): 0 
Gene Names: ilvEAF_0933
EC: 2.6.1.42
UniProt
Find proteins for O29329 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore O29329 
Go to UniProtKB:  O29329
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO29329
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Putative branched-chain-amino-acid aminotransferase290Archaeoglobus fulgidus DSM 4304Mutation(s): 0 
Gene Names: ilvEAF_0933
EC: 2.6.1.42
UniProt
Find proteins for O29329 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore O29329 
Go to UniProtKB:  O29329
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO29329
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PXG
Query on PXG

Download Ideal Coordinates CCD File 
CA [auth E],
G [auth A],
L [auth B],
R [auth C],
Z [auth D]
3-[O-PHOSPHONOPYRIDOXYL]--AMINO-BENZOIC ACID
C15 H17 N2 O7 P
WSOQXCGRIUHULI-UHFFFAOYSA-N
TAM
Query on TAM

Download Ideal Coordinates CCD File 
Q [auth B],
X [auth C]
TRIS(HYDROXYETHYL)AMINOMETHANE
C7 H17 N O3
GKODZWOPPOTFGA-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
BA [auth D]
J [auth A]
K [auth A]
N [auth B]
O [auth B]
BA [auth D],
J [auth A],
K [auth A],
N [auth B],
O [auth B],
P [auth B],
U [auth C],
V [auth C],
W [auth C]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
Y [auth C]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth D]
DA [auth E]
EA [auth E]
FA [auth F]
H [auth A]
AA [auth D],
DA [auth E],
EA [auth E],
FA [auth F],
H [auth A],
I [auth A],
M [auth B],
S [auth C],
T [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LLP
Query on LLP
F
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.21α = 90
b = 140.23β = 90
c = 168.32γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/L002035/1

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2019-07-31
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description