Crystal structure of MarH, an epimerase for biosynthesis of Maremycins in Streptomyces, under 400 mM Zinc acetate

Experimental Data Snapshot

  • Resolution: 1.58 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


Structural basis of the mechanism of beta-methyl epimerization by enzyme MarH.

Liu, B.Hou, Y.Wang, X.Ma, X.Fang, S.Huang, T.Chen, Y.Bai, Z.Lin, S.Zhang, R.Hu, K.

(2019) Org Biomol Chem 17: 9605-9614

  • DOI: https://doi.org/10.1039/c9ob01996k
  • Primary Citation of Related Structures:  
    6J4B, 6J4C

  • PubMed Abstract: 

    Diverse derivatives of amino acids with different steric configurations are important biosynthetic building blocks. In biology, epimerization is an important way to generate steric diversity. MarH catalyzes the epimerization of the β-position of (3R)-β-methyl-indolepyruvate (MeInPy), forming (3S)-β-MeInPy. Both compounds are derivatives of l-tryptophan (l-Trp) and are important precursors of bioactive natural products. Here, we report the crystal structures of MarH and the NMR structure of its complex with l-Trp, an analogue of its native substrate, (3R)-β-MeInPy. Structural analysis and mutagenesis studies indicated that His25 acts as a base to remove H β and generate a planar carbanion intermediate, which is then putatively reprotonated on the opposite face by a water molecule to form (3S)-β-MeInPy in a stereospecific manner. The details of β-site isomerization at the atomic level provide deeper insights into the epimerization mechanism of MarH and will facilitate further enzyme design to extend the substrate scope.

  • Organizational Affiliation

    Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China. kaifenghu@mail.kib.ac.cn and University of Chinese Academy of Sciences, Beijing, 100049, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cupin superfamily protein126Streptomyces sp. B9173Mutation(s): 0 
Gene Names: marH
Find proteins for X2D812 (Streptomyces sp. B9173)
Explore X2D812 
Go to UniProtKB:  X2D812
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupX2D812
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
C3 H8 O3
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A]
Query on ACY

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth A]
C2 H4 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.58 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.627α = 90
b = 43.627β = 90
c = 99.973γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Basic Research Program of China (973 Program)China2017YFA0505800
National Basic Research Program of China (973 Program)China2017YFA0504300
National Natural Science Foundation of ChinaChina31570720

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references, Derived calculations