4FUS | pdb_00004fus

The X-ray structure of Hahella chejuensis family 48 glycosyl hydrolase

• PDB DOI: https://doi.org/10.2210/pdb4FUS/pdb

• Classification: HYDROLASE
• Organism(s): Hahella chejuensis KCTC 2396
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-06-28 Released: 2012-10-17 
• Deposition Author(s): Alahuhta, P.M., Lunin, V.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.205 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

Sequence, structure, and evolution of cellulases in glycoside hydrolase family 48.

Sukharnikov, L.O., Alahuhta, M., Brunecky, R., Upadhyay, A., Himmel, M.E., Lunin, V.V., Zhulin, I.B.

(2012) J Biological Chem 287: 41068-41077

• PubMed: 23055526 
• DOI: https://doi.org/10.1074/jbc.M112.405720
• Primary Citation Related Structures: 
  4FUS


• PubMed Abstract: 
  

  Currently, the cost of cellulase enzymes remains a key economic impediment to commercialization of biofuels. Enzymes from glycoside hydrolase family 48 (GH48) are a critical component of numerous natural lignocellulose-degrading systems. Although computational mining of large genomic data sets is a promising new approach for identifying novel cellulolytic activities, current computational methods are unable to distinguish between cellulases and enzymes with different substrate specificities that belong to the same protein family. We show that by using a robust computational approach supported by experimental studies, cellulases and non-cellulases can be effectively identified within a given protein family. Phylogenetic analysis of GH48 showed non-monophyletic distribution, an indication of horizontal gene transfer. Enzymatic function of GH48 proteins coded by horizontally transferred genes was verified experimentally, which confirmed that these proteins are cellulases. Computational and structural studies of GH48 enzymes identified structural elements that define cellulases and can be used to computationally distinguish them from non-cellulases. We propose that the structural element that can be used for in silico discrimination between cellulases and non-cellulases belonging to GH48 is an ω-loop located on the surface of the molecule and characterized by highly conserved rare amino acids. These markers were used to screen metagenomics data for "true" cellulases.

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Organizational Affiliation: 
• BioEnergy Science Center, University of Tennessee, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 80.08 kDa 
• Atom Count: 5,837 
• Modeled Residue Count: 635 
• Deposited Residue Count: 695 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RTX toxins and related Ca2+-binding protein	A	695	Hahella chejuensis KCTC 2396	Mutation(s): 0  Gene Names: HCH_02465 EC: 3.2.1.4
UniProt
Find proteins for Q2SJA2 (Hahella chejuensis (strain KCTC 2396)) Explore Q2SJA2  Go to UniProtKB:  Q2SJA2

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan: G84824ZO GlyCosmos: G84824ZO

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4	I [auth A], J [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	K [auth A], L [auth A], M [auth A], N [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	AA [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	BA [auth A], CA [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OHI	A	L-PEPTIDE LINKING	C6 H7 N3 O3		HIS

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900005	B	beta-cellobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.205 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.69	α = 90
b = 78.389	β = 98.94
c = 67.075	γ = 90

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
MOLREP	phasing
REFMAC	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-17 
Deposition Author(s): Alahuhta, P.M., Lunin, V.V.

Revision History  

• Version 1.0: 2012-10-17
  Type: Initial release
  
• Version 1.1: 2012-12-19
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-09-13
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2023-12-06
  Changes: Data collection