1MI8

2.0 Angstrom crystal structure of a DnaB intein from Synechocystis sp. PCC 6803

Summary for 1MI8

• Entry DOI: 10.2210/pdb1mi8/pdb
• Descriptor: DnaB intein (2 entities in total)
• Functional Keywords: all beta-strands, hydrolase
• Biological source: Synechocystis sp.; More
• Total number of polymer chains: 1
• Total formula weight: 17600.17

Authors

Ding, Y.,Chen, X.,Ferrandon, S.,Xu, M.,Rao, Z. (deposition date: 2002-08-22, release date: 2003-08-19, Last modification date: 2024-05-29)

Primary citation

Ding, Y.,Xu, M.Q.,Ghosh, I.,Chen, X.,Ferrandon, S.,Lesage, G.,Rao, Z.
Crystal structure of mini-intein reveals a conserved catalytic module involved in side chain cyclization of asparagine during protein splicing
J.Biol.Chem., 278:39133-39142, 2003

PubMed Abstract: We have determined the crystal structure of a 154-residue intein derived from the dnaB gene of Synechocystis sp. strain PCC6803 and refined it to a 2.0-A resolution. The x-ray structure suggests that this intein possesses two catalytic sites that appear to be separately responsible for splicing and cleavage of the N- and C-terminal scissile bonds. The conserved intein block F residues are the important components of a catalytic site for side chain cyclization of the last intein residue, Asn-154. The data suggest that the imidazole ring of His-143 is involved in the activation of the side chain Ndelta atom of Asn-154, leading to a nucleophilic attack on the carbonyl carbon of Asn-154. Substitution of His-143 with Ala or Gln resulted in the inhibition of C-terminal cleavage. His-153, Asp-136, and a water molecule appear to constitute an oxyanion binding site by contacting the carbonyl oxygen of Asn-154 to stabilize the transition state. The structure and mutagenesis data also support that the close contact between the hydroxyl groups of Thr-138 and Ser-155, whose side chain participates in an S --> O acyl shift, plays an important role in the nucleophile orientation. Our structural modeling suggests that this catalytic module is conserved in the C-terminal subdomains of inteins from diverse organisms.

PubMed: 12878593
DOI: 10.1074/jbc.M306197200

Experimental method

X-RAY DIFFRACTION (2 Å)