Biological Assembly 1  

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 189402.66 
• Atom Count: 7149 
• Residue Count: 1722 
• Unique protein chains: 1

4PPM

Crystal structure of PigE: a transaminase involved in the biosynthesis of 2-methyl-3-n-amyl-pyrrole (MAP) from Serratia sp. FS14

• DOI: 10.2210/pdb4PPM/pdb

• Classification: TRANSFERASE
• Organism(s): Serratia sp. (strain FS14)
• Expression System: Escherichia coli


• Deposited: 2014-02-27 Released: 2015-01-14 
• Deposition Author(s): Lou, X.D., Ran, T.T., Xu, D.Q., Wang, W.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.272 
• R-Value Work: 0.238 

Literature

Crystal structure of the catalytic domain of PigE: a transaminase involved in the biosynthesis of 2-methyl-3-n-amyl-pyrrole (MAP) from Serratia sp. FS14

Lou, X.D., Ran, T.T., Han, N., Gao, Y., He, J., Tang, L., Xu, D.Q., Wang, W.W.

(2014) Biochem.Biophys.Res.Commun. 447: 178-183

• PubMed: 24704447 
• DOI: 10.1016/j.bbrc.2014.03.125


• PubMed Abstract: 
  

Prodigiosin, a tripyrrole red pigment synthesized by Serratia and some other microbes through a bifurcated biosynthesis pathway, MBC (4-methoxy-2,2'-bipyrrole-5-carbaldehyde) and MAP (2-methyl-3-n-amyl-pyrrole) are synthesized separately and then condensed by PigC to form prodigiosin. MAP is synthesized sequentially by PigD, PigE and PigB. PigE catalyzes the transamination of an amino group to the aldehyde group of 3-acetyloctanal, resulting in an aminoketone, which spontaneously cyclizes to form H2MAP. Here we report the crystal structure of the catalytic domain of PigE which involved in the biosynthesis of prodigiosin precursor MAP for the first time to a resolution of 2.3Å with a homodimer in the asymmetric unit. The monomer of PigE catalytic domain is composed of three domains with PLP as cofactor: a small N-terminal domain connecting the catalytic domain with the front part of PigE, a large PLP-binding domain and a C-terminal domain. The residues from both monomers build the PLP binding site at the interface of the dimer which resembles the other PLP-dependent enzymes. Structural comparison of PigE with Thermus thermophilus AcOAT showed a higher hydrophobic and smaller active site of PigE, these differences may be the reason for substrate specificity.

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Organizational Affiliation: 

Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Aminotransferase	A, B	861	Serratia sp. (strain FS14)	Mutation(s): 0  Gene Names: pigE EC: 2.6.1.-
Find proteins for A0A0J9X1Q5 (Serratia sp. (strain FS14)) Go to UniProtKB:  A0A0J9X1Q5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MG	A, B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
PLP	A, B	PYRIDOXAL-5'-PHOSPHATE VITAMIN B6 Phosphate C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.272 
• R-Value Work: 0.238 
• Space Group: P 3 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 228.100	α = 90.00
b = 228.100	β = 90.00
c = 67.100	γ = 120.00

Software Package:

Software Name	Purpose
Blu-Ice	data collection
BALBES	phasing
XDS	data reduction
XDS	data scaling
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-02-27 
• Released Date: 2015-01-14 
• Deposition Author(s): Lou, X.D., Ran, T.T., Xu, D.Q., Wang, W.W.

Revision History 

• Version 1.0: 2015-01-14
  Type: Initial release