5DDS

Crystal structure of aminotransferase CrmG from Actinoalloteichus sp. WH1-2216-6 in complex with PLP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Biochemical and Structural Insights into the Aminotransferase CrmG in Caerulomycin Biosynthesis

Zhu, Y.Xu, J.Mei, X.Feng, Z.Zhang, L.Zhang, Q.Zhang, G.Zhu, W.Liu, J.Zhang, C.

(2016) Acs Chem.Biol. 11: 943-952

  • DOI: 10.1021/acschembio.5b00984
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Caerulomycin A (CRM A 1) belongs to a family of natural products containing a 2,2'-bipyridyl ring core structure and is currently under development as a potent novel immunosuppressive agent. Herein, we report the functional characterization, kinetic ...

    Caerulomycin A (CRM A 1) belongs to a family of natural products containing a 2,2'-bipyridyl ring core structure and is currently under development as a potent novel immunosuppressive agent. Herein, we report the functional characterization, kinetic analysis, substrate specificity, and structure insights of an aminotransferase CrmG in 1 biosynthesis. The aminotransferase CrmG was confirmed to catalyze a key transamination reaction to convert an aldehyde group to an amino group in the 1 biosynthetic pathway, preferring l-glutamate and l-glutamine as the amino donor substrates. The crystal structures of CrmG in complex with the cofactor 5'-pyridoxal phosphate (PLP) or 5'-pyridoxamine phosphate (PMP) or the acceptor substrate were determined to adopt a canonical fold-type I of PLP-dependent enzymes with a unique small additional domain. The structure guided site-directed mutagenesis identified key amino acid residues for substrate binding and catalytic activities, thus providing insights into the transamination mechanism of CrmG.


    Organizational Affiliation

    Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China , Qingdao 266003, China.,CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road, Guangzhou 510301, China.,Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou 510530, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CrmG
A, B, C, D
523Actinoalloteichus sp. WH1-2216-6Mutation(s): 0 
Find proteins for H8Y6N2 (Actinoalloteichus sp. WH1-2216-6)
Go to UniProtKB:  H8Y6N2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download SDF File 
Download CCD File 
D
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A, B, C, D
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.215 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 84.078α = 106.71
b = 84.210β = 109.16
c = 88.949γ = 95.03
Software Package:
Software NamePurpose
PHENIXphasing
Aimlessdata reduction
Aimlessdata scaling
MOSFLMdata collection
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-08-25 
  • Released Date: 2016-08-10 
  • Deposition Author(s): Xu, J., Feng, Z., Liu, J.

Funding OrganizationLocationGrant Number
National Science Foundation of ChinaChina31500638
Natural Science Foundation of Guangdong ProvinceChina2014A030310356

Revision History 

  • Version 1.0: 2016-08-10
    Type: Initial release