PDBsum entry: 1yk9

Lyase

PDB id: 1yk9

Contents

Protein chain

184 a.a. *

Waters ×71

* Residue conservation analysis

PDB id:

1yk9

Name:

Lyase

Title:

Crystal structure of a mutant form of the mycobacterial adenylyl cyclase rv1625c

Structure:

Adenylate cyclase. Chain: a. Fragment: rv1625c catalytic domain. Synonym: atp pyrophosphate-lyase, adenylyl cyclase. Engineered: yes. Mutation: yes

Source:

Mycobacterium tuberculosis. Organism_taxid: 1773. Gene: rv1625c. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Resolution:

2.70Å R-factor: 0.205 R-free: 0.245

Authors:

A.D.Ketkar,A.R.Shenoy,U.A.Ramagopal,S.S.Visweswariah, K.Suguna,Tb Structural Genomics Consortium (Tbsgc)

Key ref:

A.D.Ketkar et al. (2006). A Structural Basis for the Role of Nucleotide Specifying Residues in Regulating the Oligomerization of the Rv1625c Adenylyl Cyclase from M.tuberculosis. J Mol Biol, 356, 904-916. PubMed id: 16403515 DOI: 10.1016/j.jmb.2005.12.017

Date:

17-Jan-05 Release date: 24-Jan-06

Protein chain

P0A4Y0  (CYA1_MYCTU) -  Adenylate cyclase

Seq: 443 a.a.

Struc: 184 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.4.6.1.1 - Adenylate cyclase.
• Reaction: ATP = 3',5'-cyclic AMP + diphosphate
• Cofactor: Pyridoxal 5'-phosphate

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

 Gene Ontology (GO) functional annotation 

• Biological process: cyclic nucleotide biosynthetic process (1 term)
• Biochemical function: phosphorus-oxygen lyase activity (1 term)

reference

DOI no: 10.1016/j.jmb.2005.12.017

J Mol Biol 356:904-916 (2006)

PubMed id: 16403515

A Structural Basis for the Role of Nucleotide Specifying Residues in Regulating the Oligomerization of the Rv1625c Adenylyl Cyclase from M.tuberculosis.

A.D.Ketkar, A.R.Shenoy, U.A.Ramagopal, S.S.Visweswariah, K.Suguna.

ABSTRACT

The Rv1625c Class III adenylyl cyclase from Mycobacterium tuberculosis is a homodimeric enzyme with two catalytic centers at the dimer interface, and shows sequence similarity with the mammalian adenylyl and guanylyl cyclases. Mutation of the substrate-specifying residues in the catalytic domain of Rv1625c, either independently or together, to those present in guanylyl cyclases not only failed to confer guanylyl cyclase activity to the protein, but also severely abrogated the adenylyl cyclase activity of the enzyme. Biochemical analysis revealed alterations in the behavior of the mutants on ion-exchange chromatography, indicating differences in the surface-exposed charge upon mutation of substrate-specifying residues. The mutant proteins showed alterations in oligomeric status as compared to the wild-type enzyme, and differing abilities to heterodimerize with the wild-type protein. The crystal structure of a mutant has been solved to a resolution of 2.7A. On the basis of the structure, and additional biochemical studies, we provide possible reasons for the altered properties of the mutant proteins, as well as highlight unique structural features of the Rv1625c adenylyl cyclase.

Selected figure(s)

Figure 5.
Figure 5. (a) Stereoview of the modeled "homodimer" of KFD->ERC. For clarity, the two subunits of the KFD->ERC homodimer are shown in different colors, viz. blue and cyan. Residues showing steric clashes are shown as stick models. Corresponding residues of the two subunits are colored differently (red and yellow) for clarity. For details, see the text. (b) Zoomed stereoview of the KFD->ERC homodimer. The residues showing steric clashes are labeled in red in one subunit.

Figure 8.
Figure 8. Conformational changes at the active site of KFD->ERC. Comparison of the active site of KFD->ERC and that of VC1-IIC2 dimer of mAC. VC1 chain is shown in red ribbon, IIC2 chain in magenta, while the superimposed KFD->ERC homodimer model is shown in blue cartoon representation. The mutated residues in KFD->ERC are shown as sticks, and are labeled (left half of the Figure). The corresponding residues from the IIC2 chain are also shown as sticks and are labeled. The two metal-binding aspartate residues (D256 and D300) of KFD->ERC are indicated as sticks, and the corresponding aspartate residues from VC1 (D396, D440) are shown for comparison (right half of the Figure). The ATP-analog, dideoxyadenosine-5'-triphosphate is shown in yellow. The two metal ions, Mg2+ and Mn2+, are shown as green spheres. The interactions between the three mutated residues of KFD->ERC are indicated by broken lines, and the corresponding distances (in Å) are given.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 356, 904-916) copyright 2006.

Figures were selected by an automated process.