6SMT

S-enantioselective imine reductase from Mycobacterium smegmatis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.132 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural Characterization of an S -enantioselective Imine Reductase from Mycobacterium Smegmatis .

Meyer, T.Zumbragel, N.Geerds, C.Groger, H.Niemann, H.H.

(2020) Biomolecules 10

  • DOI: https://doi.org/10.3390/biom10081130
  • Primary Citation of Related Structures:  
    6SMT

  • PubMed Abstract: 

    NADPH-dependent imine reductases (IREDs) are enzymes capable of enantioselectively reducing imines to chiral secondary amines, which represent important building blocks in the chemical and pharmaceutical industry. Since their discovery in 2011, many previously unknown IREDs have been identified, biochemically and structurally characterized and categorized into families. However, the catalytic mechanism and guiding principles for substrate specificity and stereoselectivity remain disputed. Herein, we describe the crystal structure of S -IRED- Ms from Mycobacterium smegmatis together with its cofactor NADPH. S -IRED- Ms belongs to the S -enantioselective superfamily 3 (SFam3) and is the first IRED from SFam3 to be structurally described. The data presented provide further evidence for the overall high degree of structural conservation between different IREDs of various superfamilies. We discuss the role of Asp170 in catalysis and the importance of hydrophobic amino acids in the active site for stereospecificity. Moreover, a separate entrance to the active site, potentially functioning according to a gatekeeping mechanism regulating access and, therefore, substrate specificity is described.


  • Organizational Affiliation

    Structural Biochemistry, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
6-phosphogluconate dehydrogenase, NAD-binding
A, B, C, D, E
298Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEG_6341
UniProt
Find proteins for A0R5X0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R5X0 
Go to UniProtKB:  A0R5X0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R5X0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download Ideal Coordinates CCD File 
AA [auth E],
F [auth A],
L [auth B],
P [auth C],
T [auth D]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
2EH
Query on 2EH

Download Ideal Coordinates CCD File 
HA [auth E],
J [auth A],
N [auth B],
S [auth C],
Y [auth D]
(2S)-2-ethylhexan-1-ol
C8 H18 O
YIWUKEYIRIRTPP-QMMMGPOBSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
BA [auth E]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
K [auth A],
O [auth B],
Z [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
GA [auth E],
I [auth A],
R [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT
Query on FMT

Download Ideal Coordinates CCD File 
CA [auth E]
DA [auth E]
EA [auth E]
FA [auth E]
G [auth A]
CA [auth E],
DA [auth E],
EA [auth E],
FA [auth E],
G [auth A],
H [auth A],
M [auth B],
Q [auth C],
U [auth D],
V [auth D],
W [auth D],
X [auth D]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.007α = 90
b = 77.023β = 90.2
c = 194.485γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Federal Ministry for Education and ResearchGermany031A184A

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-12
    Type: Initial release
  • Version 1.1: 2020-08-19
    Changes: Database references
  • Version 1.2: 2020-09-30
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description