Introduction to Structural Bioinformatics

Homework Project: 1CEN

By: CHEN WANG

General Information of 1CEN

Polysaccharides fulfill a wide variety of functions in living organism. Some like starch and glycogen, serve mainly to store sugar in plants and animals. Others like cellulose, are structure materials in the cell. Also, Cell wall polysaccharides, act as cell-specific recognition signals.

1CEN is an enzyme belongs to a family of cellulase, which is capable of digesting cellulose.

Protein name:	Cellulase Celc (1,4-beta-D-Glucan-Glucanohydrolase, Endo-1,4-beta-Glucanase C)
Protein Source:	Clostridium Thermocellum
Protein function:	Cellulose Degradation
Protein information:	343 Residues, Molecular Weight and Primary Citation
Experiment:	X-ray diffraction with cellulase (Celc) E140Q, resolution is 2.3A

Experimental Detail in Crystallography

Space Group

Symmetric relationship between the molecules in a crystal lettice, which include translational and rotational symmetry

P21P21P21

Rotate by 180deg around b and shift by b/2.

Unit Cell

The repeating unit of the crystal

dim [Å]:	a	51.40	b	84.33	c	87.50
angles [¯]:	alpha	90.00	beta	90.00	gamma	90.00

Determined by unit cell length and angle.

R-value

The comparison of calculated structure factor with measured structure factor

0.178

The difference between two factors divided by measures factor

Resolution

Calculated from the electron density distribution

2.3A

Molecular detail can be observed

CATH Classification: A Novel Hierarchical Classification of Protein Domain Structure

Class (3)	Derived from secondary structure	Alpha Beta
Architecture (20)	Gross orientation of secondary structure independent of connectivity	Barrel
Topology (20)	Cluster structures according to topological connection and numbers of secondary structure	TIM Barrel
Homologous Super Family (80)	Cluster protein with highly similar structure and function	Glycosidases
Sequence Homologous	Cluster proteins based on their sequences	Cellulose Degradation

SCOP Structure Classification: A structural Classification of Protein Database

For the investigation of sequence and structure, user can navigate through the level of class, folds, superfamily and species to search for structure domains of individual PDB entries

Class	Proteins are grouped by their fold	Alpha and beta proteins (a/b)	mainly parallel beta sheets (beta-alpha-beta units)
Fold	Proteins that have the same major secondary structures in same arrangement with the same topological connections	TIM beta/alpha-barrel	contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678
Superfamily: families	Proteins that have low sequence identities but their structures and functional features suggest a common evolutionary origin	(Trans)glycosidases	Enzymes that catalyze the cleavage of glycosidic bonds between sugar moieties. Glycosidic bonds: covalent bonds formed between sugar molecules.
Family	Proteins are clustered based on: either they have residue identities of 30% or , proteins with low sequence identities but their structures and functions are very similar	Beta-glycanases	Enzymes that catalyze the cleavage of glycosidic bonds of glycans. Glycans: the polymers of glucose.

Secondary Structure Calculation: Determined by Hydrogen Bonding

Calculation with DSSP Algorithm to define secondary structure of 1CEN

Ligand-Protein Complex Structure (1CEN) Apo Structure (1CEO)

Active Site of 1CEN

Arg46, His90, Asn139, Glu140, His198, Tyr200 and Glu280 (in green) participate in a network of hydrogen bonds, which contribute to stability of the active site architecture. These residues are strictly conserved in family 5 cellulases. In this structure, only three of the above residues, His90, Gln140 and Glu280 make direct contacts with the substrate.