The 1.6 Å structure of Kunitz-type domain from the α3 chain of human type VI collagen

Arnoux, B.; Merigeau, K.; Saludjian, P.; Norris, Fanny; Norris, Kjeld; Bjørn, Søren E.; Olsen, Ole H.; Petersen, Lars C.; Ducruix, A.

doi:10.1016/s0022-2836(05)80110-x

Cited by 26 publications

(36 citation statements)

References 32 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The structure of the C5 fragment was solved at 1.6 ,~, resolution by X-ray crystallography (Arnoux et al, 1995) and more recently its solution structure has been analyzed by NMR . From the P' cleavage side (residues 16-18), the aromatic Phel7 group, which is not conserved in BPTI and APPI, is buried in an hydrophobic pocket composed of Trp34, Tyr35 and Gly36.…”

Section: Comparison With Other Kunitz Fragmentsmentioning

confidence: 99%

“…Because the NMR study demonstrated that C5 is a highly dynamic molecule at room temperature, with multiple conformers which could not be properly located in the 1.6 A resolution X-ray structure (Arnoux et al, 1995), we have measured a new X-ray diffraction data set at room temperature using wiggler beam synchrotron radiation. We refined the structure using SHELXL93 program (Sheldrick, 1993) at 1.2 ,& resolution, which allowed for anisotropic refinement.…”

Section: Comparison With Other Kunitz Fragmentsmentioning

confidence: 99%

“…The protocol initially devised by F. Norris (Arnoux et aL, 1995), was modified in the following way: the pH was changed to 3.3, the temperature was 291 K and the protein concentration was higher (Table 1). Two crystals were used to record data at 291 K using station DW32 (Fourme et al, 1992) at LURE with an incident wavelength close to 0.9 A.…”

Section: Crystal and Crystallographic Data Collectionmentioning

confidence: 99%

“…The last three residues belong to the binding loop corresponding to the P' side of BPTI. It has been postulated (Arnoux et al, 1995) that the absence of antiprotease activity of C5 can be due to a 180 ° rotation of the carbonyl group of Aspl6 and the backbone N atom of Phel7. Phel7 probably does not have alternate conformations because it is buried in a hydrophobic pocket consisting of Trp34, Tyr35, Gly36 and a few backbone C atoms.…”

Section: Comparison With the 16 A Structurementioning

confidence: 99%

“…The first 58 residues of the C-terminus domain of C5 were cloned and expressed in Saccharomyces cerevisae (Arnoux et al, 1995) following conditions described for APPI (Petersen et al, 1994). In terms of sequence ( Fig.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

1.2 Å Refinement of the Kunitz-Type Domain from the α3 Chain of Human Type VI Collagen

Merigeau

Arnoux

Pérahia

et al. 1998

Acta Crystallogr D Biol Cryst

Self Cite

View full text Add to dashboard Cite

The recombinant Kunitz-type domain (C5) of human collagen cr3(VI) chain was previously described at 1.6 ,A resolution at room temperature. By changing the crystallization conditions and using synchrotron radiation, we are able to record diffraction data to 1.2,~ resolution for crystals of the same space group at 291 K. The protein-water-ion model has been refined anisotropically against these new data using the program SHELXL93; the results converged to an R factor of 15.0%, with all data between 7 and 1.2,4,. The final electron-density map reveals a clear chain tracing with a few disordered residues and five residues out of 58 that present alternate conformations. The Cys14-Cys38 bond presents the less frequently observed left-hand conformation (Xl = -60°) • The solvent molecules and a phosphate ion are well ordered with an average B of 38 ~2. The high-resolution structure reveals the N and C termini which were missing from the 1.6 A structure.

show abstract

Section: Comparison With Other Kunitz Fragmentsmentioning

confidence: 99%

Section: Comparison With Other Kunitz Fragmentsmentioning

confidence: 99%

Section: Crystal and Crystallographic Data Collectionmentioning

confidence: 99%

Section: Comparison With the 16 A Structurementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

1.2 Å Refinement of the Kunitz-Type Domain from the α3 Chain of Human Type VI Collagen

Merigeau

Arnoux

Pérahia

et al. 1998

Acta Crystallogr D Biol Cryst

Self Cite

View full text Add to dashboard Cite

show abstract

Protein structure determination using a Riemannian approach

Wei

et al. 2019

FEBS Letters

View full text Add to dashboard Cite

Protein NMR structure determination is one of the most extensively studied problems. Here, we adopt a novel method based on a matrix completion technique – the Riemannian approach – to rebuild the protein structure from the nuclear Overhauser effect distance restraints and the dihedral angle restraints. In comparison with the cyana method, the results generated via the Riemannian approach are more similar to the standard X‐ray crystallographic structures as a result of the simple but powerful internal calculation processing function. In addition, our results demonstrate that the Riemannian approach has a comparable or even better performance than the cyana method on other structural assessment metrics, including the stereochemical quality and restraint violations. The Riemannian approach software is available at: https://github.com/xubiaopeng/Protein_Recon_MCRiemman.

show abstract

Comparative analysis of the noncollagenous NC1 domain of type IV collagen: Identification of structural features important for assembly, function, and pathogenesis

et al. 1998

View full text Add to dashboard Cite

Type IV collagen al-a6 chains have important roles in the assembly of basement membranes and are implicated in the pathogenesis of Goodpasture syndrome, an autoimmune disorder, and Alport syndrome, a hereditary renal disease. We report comparative sequence analyses and structural predictions of the noncollagenous C-terminal globular NCl domain (28 sequences). The inferred tree verified that type IV collagen sequences fall into two groups, a1-like and a2-like, and suggested that vertebrate a3/a4 sequences evolved before a l / a 2 and a5/a6. About one fifth of NCl residues were identified to confer either the a 1 or a 2 group-specificity. These residues accumulate opposite charge in subdomain B of a1 (positive) and a 2 (negative) sequences and may play a role in the stoichiometric chain selection upon type IV collagen assembly. Neural network secondary structure prediction on multiple aligned sequences revealed a subdomain core structure consisting of six hydrophobic P-strands and one short a-helix with a significant hydrophobic moment. The existence of opposite charges in the a-helices may carry implications for intersubdomain interactions. The results provide a rationale for defining the epitope that binds Goodpasture autoantibodies and a framework for understanding how certain NC1 mutations may lead to Alport syndrome. A search algorithm, based entirely on amino acid properties, yielded a possible similarity of NCl to tissue inhibitor of metalloproteinases (TIMP) and prompted an investigation of a possible functional relationship. The results indicate that NCl preparations decrease the activity of matrix metalloproteinases 2 and 3 (MMP-2, MMP-3) toward a peptide substrate, though not to [14C]-gelatin. We suggest that an ancestral NC1 may have been incorporated into type IV collagen as an evolutionarily mobile domain carrying proteinase inhibitor function.

show abstract

The 1.6 Å structure of Kunitz-type domain from the α3 chain of human type VI collagen

Cited by 26 publications

References 32 publications

1.2 Å Refinement of the Kunitz-Type Domain from the α3 Chain of Human Type VI Collagen

1.2 Å Refinement of the Kunitz-Type Domain from the α3 Chain of Human Type VI Collagen

Protein structure determination using a Riemannian approach

Comparative analysis of the noncollagenous NC1 domain of type IV collagen: Identification of structural features important for assembly, function, and pathogenesis

Contact Info

Product

Resources

About