PDBsum entry 4cbo

Hydrolase

PDB id: 4cbo

Contents

Protein chains

228 a.a.

Ligands

GOL ×2

Waters ×261

PDB id:

4cbo

Name:

Hydrolase

Title:

Crystal structure of complement factor d mutant r202a after ensemble refinement

Structure:

Complement factor d. Chain: a, b. Fragment: residues 26-253. Synonym: adipsin, c3 convertase activator, properdin factor d. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: hek293

Resolution:

1.80Å R-factor: 0.166 R-free: 0.212

Ensemble:

77 models

Authors:

F.Forneris,B.T.Burnley,P.Gros

Key ref:

F.Forneris et al. (2014). Ensemble refinement shows conformational flexibility in crystal structures of human complement factor D. Acta Crystallogr D Biol Crystallogr, 70, 733-743. PubMed id: 24598742 DOI: 10.1107/S1399004713032549

Date:

15-Oct-13 Release date: 18-Dec-13

Protein chains

P00746  (CFAD_HUMAN) -  Complement factor D from Homo sapiens

Seq: 253 a.a.

Struc: 228 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.3.4.21.46 - complement factor D.
• Reaction: Cleaves component factor B (Arg-|-Lys) when in complex with C3b or with cobra venom factor (CVF).

DOI no: 10.1107/S1399004713032549

Acta Crystallogr D Biol Crystallogr 70:733-743 (2014)

PubMed id: 24598742

Ensemble refinement shows conformational flexibility in crystal structures of human complement factor D.

F.Forneris, B.T.Burnley, P.Gros.

ABSTRACT

Human factor D (FD) is a self-inhibited thrombin-like serine proteinase that is critical for amplification of the complement immune response. FD is activated by its substrate through interactions outside the active site. The substrate-binding, or `exosite', region displays a well defined and rigid conformation in FD. In contrast, remarkable flexibility is observed in thrombin and related proteinases, in which Na(+) and ligand binding is implied in allosteric regulation of enzymatic activity through protein dynamics. Here, ensemble refinement (ER) of FD and thrombin crystal structures is used to evaluate structure and dynamics simultaneously. A comparison with previously published NMR data for thrombin supports the ER analysis. The R202A FD variant has enhanced activity towards artificial peptides and simultaneously displays active and inactive conformations of the active site. ER revealed pronounced disorder in the exosite loops for this FD variant, reminiscent of thrombin in the absence of the stabilizing Na(+) ion. These data indicate that FD exhibits conformational dynamics like thrombin, but unlike in thrombin a mechanism has evolved in FD that locks the unbound native state into an ordered inactive conformation via the self-inhibitory loop. Thus, ensemble refinement of X-ray crystal structures may represent an approach alternative to spectroscopy to explore protein dynamics in atomic detail.