5U22 | pdb_00005u22

Structure of N2152 from Neocallimastix frontalis

• PDB DOI: https://doi.org/10.2210/pdb5U22/pdb

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


• Deposited: 2016-11-29 Released: 2017-06-14 
• Deposition Author(s): Jones, D.R., Abbott, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.194 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Literature

Discovery and characterization of family 39 glycoside hydrolases from rumen anaerobic fungi with polyspecific activity on rare arabinosyl substrates.

Jones, D.R., Uddin, M.S., Gruninger, R.J., Pham, T.T.M., Thomas, D., Boraston, A.B., Briggs, J., Pluvinage, B., McAllister, T.A., Forster, R.J., Tsang, A., Selinger, L.B., Abbott, D.W.

(2017) J Biological Chem 292: 12606-12620

• PubMed: 28588026 
• DOI: https://doi.org/10.1074/jbc.M117.789008
• Primary Citation Related Structures: 
  5U22


• PubMed Abstract: 
  

  Enzyme activities that improve digestion of recalcitrant plant cell wall polysaccharides may offer solutions for sustainable industries. To this end, anaerobic fungi in the rumen have been identified as a promising source of novel carbohydrate active enzymes (CAZymes) that modify plant cell wall polysaccharides and other complex glycans. Many CAZymes share insufficient sequence identity to characterized proteins from other microbial ecosystems to infer their function; thus presenting challenges to their identification. In this study, four rumen fungal genes ( nf2152 , nf2215 , nf2523 , and pr2455 ) were identified that encode family 39 glycoside hydrolases (GH39s), and have conserved structural features with GH51s. Two recombinant proteins, NF2152 and NF2523, were characterized using a variety of biochemical and structural techniques, and were determined to have distinct catalytic activities. NF2152 releases a single product, β1,2-arabinobiose (Ara ₂ ) from sugar beet arabinan (SBA), and β1,2-Ara ₂ and α-1,2-galactoarabinose (Gal-Ara) from rye arabinoxylan (RAX). NF2523 exclusively releases α-1,2-Gal-Ara from RAX, which represents the first description of a galacto-(α-1,2)-arabinosidase. Both β-1,2-Ara ₂ and α-1,2-Gal-Ara are disaccharides not previously described within SBA and RAX. In this regard, the enzymes studied here may represent valuable new biocatalytic tools for investigating the structures of rare arabinosyl-containing glycans, and potentially for facilitating their modification in industrial applications.

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Organizational Affiliation: 
• Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada.
Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada; Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta T1K 6T5, Canada.
Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec H4B 1R6, Canada.
Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada.
School of Biology, Ridley Building 2, Newcastle University, Claremont Road, Newcastle upon Tyne NE1 7RU, United Kingdom.
Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta T1K 6T5, Canada.
Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada; Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta T1K 6T5, Canada. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 49.5 kDa 
• Atom Count: 3,536 
• Modeled Residue Count: 403 
• Deposited Residue Count: 423 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N2152	A	423	Neocallimastix frontalis	Mutation(s): 0
UniProt
Find proteins for A0A247D6Y4 (Neocallimastix frontalis) Explore A0A247D6Y4  Go to UniProtKB:  A0A247D6Y4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTB	B [auth A]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N
IOD	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
EDO	C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.194 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.986	α = 90
b = 104.793	β = 110.06
c = 49.445	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data collection
HKL-3000	data scaling
SHELX	phasing
PDB_EXTRACT	data extraction
HKL-3000	data reduction
SHELXD	phasing
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-14 
Deposition Author(s): Jones, D.R., Abbott, D.W.

Revision History  

• Version 1.0: 2017-06-14
  Type: Initial release
  
• Version 1.1: 2017-08-09
  Changes: Database references
• Version 1.2: 2017-11-01
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references