PDBsum entry 2v5c

Hydrolase

PDB id: 2v5c

Contents

Protein chains

584 a.a. *

Ligands

CAC ×5

Metals

_NA ×2

_CA ×4

Waters ×1191

* Residue conservation analysis

PDB id:

2v5c

Name:

Hydrolase

Title:

Family 84 glycoside hydrolase from clostridium perfringens, 2.1 angstrom structure

Structure:

O-glcnacase nagj. Chain: a, b. Fragment: catalytic module, residues 31-624. Synonym: beta-hexosaminidase, hexosaminidase b, gh84, n-acetyl-beta- glucosaminidase, beta-n-acetylhexosaminidase, family 84 glycoside hydrolase. Engineered: yes

Source:

Clostridium perfringens. Organism_taxid: 1502. Atcc: 13124. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

2.10Å R-factor: 0.198 R-free: 0.255

Authors:

E.Ficko-Blean,K.J.Gregg,J.J.Adams,J.H.Hehemann,S.J.Smith,M.Czjzek, A.B.Boraston

Key ref:

E.Ficko-Blean et al. (2009). Portrait of an enzyme, a complete structural analysis of a multimodular {beta}-N-acetylglucosaminidase from Clostridium perfringens. J Biol Chem, 284, 9876-9884. PubMed id: 19193644 DOI: 10.1074/jbc.M808954200

Date:

02-Oct-08 Release date: 27-Jan-09

Protein chains

Q0TR53  (OGA_CLOP1) -  O-GlcNAcase NagJ from Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A)

Seq: 1001 a.a.

Struc: 584 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.1.169 - protein O-GlcNAcase.
• Reaction:
  1. 3-O-(N-acetyl-beta-D-glucosaminyl)-L-seryl-[protein] + H2O = N-acetyl-D-glucosamine + L-seryl-[protein]
  2. 3-O-(N-acetyl-beta-D-glucosaminyl)-L-threonyl-[protein] + H2O = L-threonyl-[protein] + N-acetyl-D-glucosamine

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1074/jbc.M808954200

J Biol Chem 284:9876-9884 (2009)

PubMed id: 19193644

Portrait of an enzyme, a complete structural analysis of a multimodular {beta}-N-acetylglucosaminidase from Clostridium perfringens.

E.Ficko-Blean, K.J.Gregg, J.J.Adams, J.H.Hehemann, M.Czjzek, S.P.Smith, A.B.Boraston.

ABSTRACT

Common features of the extracellular carbohydrate-active virulence factors involved in host-pathogen interactions are their large sizes and modular complexities. This has made them recalcitrant to structural analysis, and therefore our understanding of the significance of modularity in these important proteins is lagging. Clostridium perfringens is a prevalent human pathogen that harbors a wide array of large, extracellular carbohydrate-active enzymes and is an excellent and relevant model system to approach this problem. Here we describe the complete structure of C. perfringens GH84C (NagJ), a 1001-amino acid multimodular homolog of the C. perfringens micro-toxin, which was determined using a combination of small angle x-ray scattering and x-ray crystallography. The resulting structure reveals unprecedented insight into how catalysis, carbohydrate-specific adherence, and the formation of molecular complexes with other enzymes via an ultra-tight protein-protein interaction are spatially coordinated in an enzyme involved in a host-pathogen interaction.

Selected figure(s)

Figure 2.
Structures of GH84C catalytic module and GH84C-CBM32 as determined using x-ray crystallography and SAXS. A and B show the crystal structures of GH84C catalytic module and GH84C-CBM32, respectively, in a ribbon representation. The arrow in B shows the C terminus of the CBM. C shows the GASBOR-generated SAXS envelope of GH84C-CBM32, whereas D shows the modules of GH84C-CBM32 manually fit into the SAXS envelope. E shows the model in D without the SAXS form. F shows the unmodified x-ray crystal structure, shown in B, fit into the SAXS-generated envelope. All of the structures are shown from identical orientations. The N-terminal domain is pictured in light blue, the catalytic TIM barrel is in orange, the helical bundle is in pale green, and the CBM in red.

Figure 4.
Structural features of the Coh-FN3 modular pair. A shows a ribbon representation of the 1.8-Å crystal structure of Coh-FN3. The Coh module is depicted in blue, and FN3 is shown in black. B shows the surface representation of Coh-FN3 colored according to electrostatic potential (red is negative, and blue is positive). The basic patch of FN3 is circled and expanded to show a patch of basic residues.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 9876-9884) copyright 2009.

Figures were selected by an automated process.