PDBsum entry 3ghm

Hydrolase

PDB id: 3ghm

Contents

Protein chain

369 a.a. *

Ligands

NAG-NAG

FUC-BGC

NAG

Waters ×29

* Residue conservation analysis

PDB id:

3ghm

Name:

Hydrolase

Title:

Crystal structure of the exosite-containing fragment of human adamts13 (form-1)

Structure:

A disintegrin and metalloproteinase with thrombospondin motifs 13. Chain: a. Fragment: dtcs domains. Synonym: adamts-13, adam-ts 13, adam-ts13, von willebrand factor- cleaving protease, vwf-cleaving protease, vwf-cp. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: adamts13. Expressed in: cricetulus griseus. Expression_system_taxid: 10029. Expression_system_cell_line: cho cells.

Resolution:

2.60Å R-factor: 0.243 R-free: 0.289

Authors:

M.Akiyama,S.Takeda,K.Kokame,J.Takagi,T.Miyata

Key ref:

M.Akiyama et al. (2009). Crystal structures of the noncatalytic domains of ADAMTS13 reveal multiple discontinuous exosites for von Willebrand factor. Proc Natl Acad Sci U S A, 106, 19274-19279. PubMed id: 19880749 DOI: 10.1073/pnas.0909755106

Date:

04-Mar-09 Release date: 27-Oct-09

Protein chain

Q76LX8  (ATS13_HUMAN) -  A disintegrin and metalloproteinase with thrombospondin motifs 13 from Homo sapiens

Seq: 1427 a.a.

Struc: 369 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.4.24.87 - Adamts13 endopeptidase.

DOI no: 10.1073/pnas.0909755106

Proc Natl Acad Sci U S A 106:19274-19279 (2009)

PubMed id: 19880749

Crystal structures of the noncatalytic domains of ADAMTS13 reveal multiple discontinuous exosites for von Willebrand factor.

M.Akiyama, S.Takeda, K.Kokame, J.Takagi, T.Miyata.

ABSTRACT

ADAMTS13 specifically cleaves plasma von Willebrand factor (VWF) and thereby controls VWF-mediated platelet thrombus formation. Severe deficiencies in ADAMTS13 can cause life-threatening thrombotic thrombocytopenic purpura. Here, we determined 2 crystal structures of ADAMTS13-DTCS (residues 287-685), an exosite-containing human ADAMTS13 fragment, at 2.6-A and 2.8-A resolution. The structures revealed folding similarities between the disintegrin-like (D) domain and the N-terminal portion of the cysteine-rich domain (designated the C(A) domain). The spacer (S) domain forms a globular functional unit with a 10-stranded beta-sandwich fold that has multiple interaction sites with the C(A) domain. We expressed 25 structure-based mutants of ADAMTS13-MDTCS (residues 75-685) and measured their enzymatic activity. We identified 3 VWF-binding exosites on the linearly aligned discontinuous surfaces of the D, C(A), and S domains traversing the W-shaped molecule. Since the MDTCS domains are conserved among ADAMTS family proteins, the structural framework of the multiple enzyme-substrate interactions identified in the ADAMTS13-VWF system provides the basis for a common substrate recognition mode in this class of proteinases.

Selected figure(s)

Figure 1.
Structure of ADAMTS13-DTCS. (A) Schematic representation of the domain structures of full-length ADAMTS13 and ADAMTS13-DTCS. (B) Ribbon structure of ADAMTS13-DTCS (form-1) in stereo. Domains are colored as in A. Strands in the S domain are numbered.

Figure 4.
ADAMTS13-VWF interactions. (A) Folded and unfolded structures of the VWF A2 domain. The VWF A2 domain adopts a Rossman fold with a central 6-stranded β-sheet surrounded by 5 α-helices (shown as “A2 folded”) (28). The scissile peptide bond (Tyr-1605-Met-1606) is buried within the protein core under static conditions. The C-terminal region (residues 1,596–1,668, corresponding to VWF73) (31) of the A2 domain must be unfolded to expose the scissile bond and the exosite-binding regions under shear-stress conditions (shown as A2 unfolded). (B) ADAMTS13-MDTCS-VWF binding model. The molecular surface of the ADAMTS13-MDTCS model is shown in gray and the bound zinc ion is shown in yellow. Residues that mediate VWF binding are depicted as in Fig. 3C, and the exosites and the catalytic cleft are indicated by red and yellow dotted ellipsoids, respectively. The dotted green line represents a VWF molecule (residues 1,596–1,668) bound to ADAMTS-MDTCS. (C) Close-up view of the α6 helix and surrounding residues in the VWF A2 domain. Hydrophobic residues are indicated with red letters. Systematic charge-to-alanine substitutions revealed that the D1653A and D1663A mutations (cyan) reduced the substrate cleavage, the E1655A mutation (orange) slightly increased cleavage, and the R1659A, E1660A, and R1668A mutations (gray) had no significant effect (34).

Figures were selected by an automated process.