5DDS

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

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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: https://doi.org/10.1021/acschembio.5b00984
  • Primary Citation of Related Structures:  
    5DDS, 5DDU, 5DDW

  • 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 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

    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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CrmG
A, B, C, D
523Actinoalloteichus sp. WH1-2216-6Mutation(s): 0 
UniProt
Find proteins for H8Y6N2 (Actinoalloteichus sp. WH1-2216-6)
Explore H8Y6N2 
Go to UniProtKB:  H8Y6N2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH8Y6N2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
J [auth D]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACY
Query on ACY

Download Ideal Coordinates CCD File 
K [auth D]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.078α = 106.71
b = 84.21β = 109.16
c = 88.949γ = 95.03
Software Package:
Software NamePurpose
MOSFLMdata collection
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Aimlessdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

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