PDBsum entry: 1mi8

Hydrolase

PDB id: 1mi8

Contents

Protein chain

141 a.a. *

Waters ×50

* Residue conservation analysis

PDB id:

1mi8

Name:

Hydrolase

Title:

2.0 angstrom crystal structure of a dnab intein from synecho pcc 6803

Structure:

Dnab intein. Chain: a. Synonym: replicative DNA helicase. Engineered: yes. Other_details: tethered dimer linked by lessslqlspeieklsq

Source:

Synechocystis sp.. Organism_taxid: 1148. Strain: pcc 6803. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.00Å R-factor: 0.210 R-free: 0.263

Authors:

Y.Ding,X.Chen,S.Ferrandon,M.Xu,Z.Rao

Key ref:

Y.Ding et al. (2003). Crystal structure of a mini-intein reveals a conserved catalytic module involved in side chain cyclization of asparagine during protein splicing. J Biol Chem, 278, 39133-39142. PubMed id: 12878593 DOI: 10.1074/jbc.M306197200

Date:

22-Aug-02 Release date: 19-Aug-03

Protein chain

Q55418  (DNAB_SYNY3) -  Replicative DNA helicase

Seq: 872 a.a.

Struc: 141 a.a.*

* PDB and UniProt seqs differ at 39 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.6.4.12 - Dna helicase.
• Reaction: ATP + H₂O = ADP + phosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Biological process: intein-mediated protein splicing (1 term)

reference

DOI no: 10.1074/jbc.M306197200

J Biol Chem 278:39133-39142 (2003)

PubMed id: 12878593

Crystal structure of a mini-intein reveals a conserved catalytic module involved in side chain cyclization of asparagine during protein splicing.

Y.Ding, M.Q.Xu, I.Ghosh, X.Chen, S.Ferrandon, G.Lesage, Z.Rao.

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.

Selected figure(s)

Figure 3.
FIG. 3. Diagram of the residues present in the C-terminal catalytic site of the Ssp DnaB intein. Dashed lines indicate hydrogen bonds, and numbers are distances in angstroms. The red arrows indicate the routes of nucleophilic attacks in the splicing pathway. The energy-minimized wild type intein model was used to generate this illustration.

Figure 4.
FIG. 4. A chemical mechanism proposed for splicing of the Ssp DnaB intein. The red arrows indicate the routes of nucleophilic attacks in the splicing pathway. Dashed lines indicate hydrogen bonds. The tetrahedral intermediate formed by an N-S acyl rearrangement at Cys-1 is not shown.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 39133-39142) copyright 2003.

Figures were selected by an automated process.