PDBsum entry 1tej

Protein binding

PDB id

1tej

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Contents

			Protein chains

					62 a.a. *


					63 a.a. *

			Waters ×161

* Residue conservation analysis

PDB id:

1tej

Links

Name:

Protein binding

Title:

Crystal structure of a disintegrin heterodimer at 1.9 a resolution.

Structure:

Disintegrin chain a. Chain: a. Disintegrin chain b. Chain: b

Source:

Echis carinatus. Saw-scaled viper. Organism_taxid: 40353. Organism_taxid: 40353

Biol. unit:

Tetramer (from PQS)

Resolution:

1.90Å

R-factor:

0.215

R-free:

0.253

Authors:

S.Bilgrami,P.Kaur,S.Yadav,M.Perbandt,C.Betzel,T.P.Singh

Key ref:

S.Bilgrami et al. (2005). Crystal structure of the disintegrin heterodimer from saw-scaled viper (Echis carinatus) at 1.9 A resolution. Biochemistry, 44, 11058-11066. PubMed id: 16101289 DOI: 10.1021/bi050849y

Date:

25-May-04

Release date:

15-Jun-04

PROCHECK

	Headers

	References

Protein chain

P0C6B4 (DIDLA_ECHCA) - Disintegrin schistatin-like subunit A from Echis carinatus

Seq: Struc:					62 a.a. 62 a.a.

Protein chain

P0C6B5 (DIDLB_ECHCA) - Disintegrin schistatin-like subunit B from Echis carinatus

Seq: Struc:					63 a.a. 63 a.a.

Key:

PfamA domain

Secondary structure

CATH domain

DOI no: 10.1021/bi050849y	Biochemistry 44:11058-11066 (2005)
PubMed id: 16101289

Crystal structure of the disintegrin heterodimer from saw-scaled viper (Echis carinatus) at 1.9 A resolution.
S.Bilgrami, S.Yadav, P.Kaur, S.Sharma, M.Perbandt, C.Betzel, T.P.Singh.

ABSTRACT

Disintegrins constitute a family of potent polypeptide inhibitors of integrins. Integrins are transmembrane heterodimeric molecules involved in cell-cell and cell-extracellular matrix interactions. They are involved in many diseases such as cancer and thrombosis. Thus, disintegrins have a great potential as anticancer and antithrombotic agents. A novel heterodimeric disintegrin was isolated from the venom of saw-scaled viper (Echis carinatus) and was crystallized. The crystals diffracted to 1.9 A resolution and belonged to space group P4(3)2(1)2. The data indicated the presence of a pseudosymmetry. The structure was solved by applying origin shifts to the disintegrin homodimer schistatin solved in space group I4(1)22 with similar cell dimensions. The structure refined to the final R(cryst)/R(free) factors of 0.213/0.253. The notable differences are observed between the loops, (Gln39-Asp48) containing the important Arg42-Gly43-Asp44, of the present heterodimer and schistatin. These differences are presumably due to the presence of two glycines at positions 43 and 46 that allow the molecule to adopt variable conformations. A comparative analysis of the surface-charge distributions of various disintegrins showed that the charge distribution on monomeric disintegrins occurred uniformly over the whole surface of the molecule, while in the dimeric disintegrins, the charge is distributed only on one face. Such a feature may be important in the binding of two integrins to a single dimeric disintegrin. The phylogenetic analysis developed on the basis of amino acid sequence and three-dimensional structures indicates that the protein diversification and evolution presumably took place from the medium disintegrins and both the dimeric and short disintegrins evolved from them.

Literature references that cite this PDB file's key reference

PubMed id

Reference

18391413

N.Moiseeva, R.Bau, S.D.Swenson, F.S.Markland, J.Y.Choe, Z.J.Liu, and M.Allaire (2008).
Structure of acostatin, a dimeric disintegrin from Southern copperhead (Agkistrodon contortrix contortrix), at 1.7 A resolution.

Acta Crystallogr D Biol Crystallogr, 64, 466-470.

PDB code:

3c05

17177090

A.Bazaa, P.Juárez, N.Marrakchi, Z.Bel Lasfer, M.El Ayeb, R.A.Harrison, J.J.Calvete, and L.Sanz (2007).
Loss of introns along the evolutionary diversification pathway of snake venom disintegrins evidenced by sequence analysis of genomic DNA from Macrovipera lebetina transmediterranea and Echis ocellatus.

J Mol Evol, 64, 261-271.

16786436

P.Juárez, S.C.Wagstaff, J.Oliver, L.Sanz, R.A.Harrison, and J.J.Calvete (2006).
Molecular cloning of disintegrin-like transcript BA-5A from a Bitis arietans venom gland cDNA library: a putative intermediate in the evolution of the long-chain disintegrin bitistatin.

J Mol Evol, 63, 142-152.

16830094

P.Juárez, S.C.Wagstaff, L.Sanz, R.A.Harrison, and J.J.Calvete (2006).
Molecular cloning of Echis ocellatus disintegrins reveals non-venom-secreted proteins and a pathway for the evolution of ocellatusin.

J Mol Evol, 63, 183-193.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.