5Z73 | pdb_00005z73

Crystal structure of alkaline/neutral invertase InvB from Anabaena sp. PCC 7120

• PDB DOI: https://doi.org/10.2210/pdb5Z73/pdb

• Classification: HYDROLASE
• Organism(s): Nostoc sp. PCC 7120 = FACHB-418
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-01-27 Released: 2018-05-30 
• Deposition Author(s): Xie, J., Hu, H.X., Cai, K., Yang, F., Jiang, Y.L., Chen, Y., Zhou, C.Z.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.228 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Literature

Structural and enzymatic analyses of Anabaena heterocyst-specific alkaline invertase InvB.

Xie, J., Hu, H.X., Cai, K., Xia, L.Y., Yang, F., Jiang, Y.L., Chen, Y., Zhou, C.Z.

(2018) FEBS Lett 592: 1589-1601

• PubMed: 29578606 
• DOI: https://doi.org/10.1002/1873-3468.13041
• Primary Citation Related Structures: 
  5Z73, 5Z74


• PubMed Abstract: 
  

  Anabaena sp. PCC 7120 encodes two alkaline/neutral invertases, namely InvA and InvB. Following our recently reported InvA structure, here we report the crystal structure of the heterocyst-specific InvB. Despite sharing an overall structure similar to InvA, InvB possesses a much higher catalytic activity. Structural comparisons of the catalytic pockets reveal that Arg430 of InvB adopts a different conformation, which may facilitate the deprotonation of the catalytic residue Glu415. We propose that the higher activity may be responsible for the vital role of InvB in heterocyst development and nitrogen fixation. Furthermore, phylogenetic analysis combined with activity assays also suggests the role of this highly conserved arginine in plants and cyanobacteria, as well as some proteobacteria living in highly extreme environments.

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Organizational Affiliation: 
• Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
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: 105.31 kDa 
• Atom Count: 7,206 
• Modeled Residue Count: 860 
• Deposited Residue Count: 914 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alr0819 protein	A, B	457	Nostoc sp. PCC 7120 = FACHB-418	Mutation(s): 0  Gene Names: invB, alr0819 EC: 3.2.1.26
UniProt
Find proteins for Q8YYM9 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)) Explore Q8YYM9  Go to UniProtKB:  Q8YYM9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.228 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.637	α = 90
b = 82.384	β = 118.86
c = 94.829	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-05-30 
Deposition Author(s): Xie, J., Hu, H.X., Cai, K., Yang, F., Jiang, Y.L., Chen, Y., Zhou, C.Z.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31630001

Revision History  

• Version 1.0: 2018-05-30
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Database references, Structure summary