PDBsum entry 1nqd

Hydrolase

PDB id: 1nqd

Contents

Protein chains

111 a.a. *

114 a.a. *

Metals

_CA ×4

Waters ×313

* Residue conservation analysis

PDB id:

1nqd

Name:

Hydrolase

Title:

Crystal structure of clostridium histolyticum colg collagenase collagen-binding domain 3b at 1.65 angstrom resolution in presence of calcium

Structure:

Class 1 collagenase. Chain: a, b. Fragment: collagen-binding domain. Engineered: yes

Source:

Clostridium histolyticum. Organism_taxid: 1498. Gene: colg. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Dimer (from PQS)

Resolution:

1.65Å R-factor: 0.191 R-free: 0.260

Authors:

J.J.Wilson,O.Matsushita,A.Okabe,J.Sakon

Key ref:

J.J.Wilson et al. (2003). A bacterial collagen-binding domain with novel calcium-binding motif controls domain orientation. EMBO J, 22, 1743-1752. PubMed id: 12682007 DOI: 10.1093/emboj/cdg172

Date:

21-Jan-03 Release date: 15-Apr-03

Protein chain

Q9X721  (COLG_HATHI) -  Collagenase ColG from Hathewaya histolytica

Seq: 1118 a.a.

Struc: 111 a.a.

Protein chain

Q9X721  (COLG_HATHI) -  Collagenase ColG from Hathewaya histolytica

Seq: 1118 a.a.

Struc: 114 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B: E.C.3.4.24.3 - microbial collagenase.
• Reaction: Digestion of native collagen in the triple helical region at Xaa-|-Gly bonds. With synthetic peptides, a preference is shown for Gly at P3 and P1'; Pro and Ala at P2 and P2'; and hydroxyproline, Ala or Arg at P3'.
• Cofactor: Zn(2+)

DOI no: 10.1093/emboj/cdg172

EMBO J 22:1743-1752 (2003)

PubMed id: 12682007

A bacterial collagen-binding domain with novel calcium-binding motif controls domain orientation.

J.J.Wilson, O.Matsushita, A.Okabe, J.Sakon.

ABSTRACT

The crystal structure of a collagen-binding domain (CBD) with an N-terminal domain linker from Clostridium histolyticum class I collagenase was determined at 1.00 A resolution in the absence of calcium (1NQJ) and at 1.65 A resolution in the presence of calcium (1NQD). The mature enzyme is composed of four domains: a metalloprotease domain, a spacing domain and two CBDs. A 12-residue-long linker is found at the N-terminus of each CBD. In the absence of calcium, the CBD reveals a beta-sheet sandwich fold with the linker adopting an alpha-helix. The addition of calcium unwinds the linker and anchors it to the distal side of the sandwich as a new beta-strand. The conformational change of the linker upon calcium binding is confirmed by changes in the Stokes and hydrodynamic radii as measured by size exclusion chromatography and by dynamic light scattering with and without calcium. Furthermore, extensive mutagenesis of conserved surface residues and collagen-binding studies allow us to identify the collagen-binding surface of the protein and propose likely collagen-protein binding models.

Selected figure(s)

Figure 2.
Figure 2 CBD in the presence and absence of calcium. (A) In the high resolution apo-CBD structure, no calcium was observed, and the N-terminus residues 895 -908 adopted an -helix conformation (colored red) in one molecule of the ASU. (B) In the holo-CBD structure, two Ca^2+ ions were found (colored orange), and the N-terminus residues 890 -908 continued the -sheet on the back face of the protein. Residues N963 -N966 were not resolved. The tyrosine-rich surface is at the left and the back face is at the right of each molecule.

Figure 4.
Figure 4 Stereo diagram of the dual-calcium-binding site. Holo-CBD is shown with coordinated Ca^2+ ions (orange spheres). Calcium-binding residues are in 'ball-and-stick' rendering. The orientation is similar to that of Figure 2. The calcium on the right is coordinated to ligands with near square antiprismatic geometry while the one on the left is coordinated to them with near pentagonal bipyramidal geometry. This figure was prepared using Molscript (Kraulis, 1991).

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2003, 22, 1743-1752) copyright 2003.

Figures were selected by the author.