Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 45.90 kDa 
• Atom Count: 3145 
• Modelled Residue Count: 385 
• Deposited Residue Count: 404 
• Unique protein chains: 1

6J2L

Crystal structure of Bi-functional enzyme

• PDB DOI: 10.2210/pdb6J2L/pdb

• Classification: HYDROLASE
• Organism(s): Shigella flexneri
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-01-01 Released: 2020-01-01 
• Deposition Author(s): Zhang, H., Shang, G., Wang, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 0.248 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 

Literature

Structural analysis of Shigella flexneri bi-functional enzyme HisIE in histidine biosynthesis.

Wang, Y., Zhang, F., Nie, Y., Shang, G., Zhang, H.

(2019) Biochem Biophys Res Commun 516: 540-545

• PubMed: 31235255 
• DOI: 10.1016/j.bbrc.2019.06.099
• Primary Citation of Related Structures:  
  6J22, 6J2L


• PubMed Abstract: 
  

Histidine biosynthesis, which is absent in animals, was shown to be highly conserved among gram-negative bacteria, thus making it an attractive target for antibiotic design. There are many fusion forms of enzymes in the histidine biosynthetic pathway and people still have limited knowledge about their domain organizations and catalytic mechanisms, due to the lack of structural information. Here we report the first crystal structure of Shigella flexneri bi-functional enzyme HisIE (SfHisIE) that functions in the 2nd and 3rd steps in the histidine biosynthetic pathway. This structure shows that HisIE exists as dimers with two loops (fusion loop) connecting the individual dimer of HisE and HisI in its N-terminus and C-terminus respectively. Our mutagenesis study shows mutations in this fusion loop are lethal for bacteria indicating the advantage of gene fusion in Histidine biosynthesis. Structural analysis revealed several highly conserved residues in the putative ligand binding grooves of HisE and HisI, showing an evolutionarily conserved catalytic mechanism shared among gram negative-bacteria.

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Organizational Affiliation: 

Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai, China. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidine biosynthesis bifunctional protein HisIE	A, B	202	Shigella flexneri	Mutation(s): 0  Gene Names: hisI, hisIE, SF2088, S2209 EC: 3.5.4.19 (PDB Primary Data), 3.6.1.31 (PDB Primary Data)
UniProt
Find proteins for P37793 (Shigella flexneri) Explore P37793  Go to UniProtKB:  P37793

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], E [auth A], F [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 0.248 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.05	α = 90
b = 45.23	β = 112.53
c = 65.259	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2019-01-01 
• Released Date: 2020-01-01 
Deposition Author(s): Zhang, H., Shang, G., Wang, Y.

Revision History  

• Version 1.0: 2020-01-01
  Type: Initial release