PDBsum entry: 1ybt

Hydrolase

PDB id: 1ybt

Contents

Protein chains

167 a.a. *

Waters ×153

* Residue conservation analysis

PDB id:

1ybt

Name:

Hydrolase

Title:

Mycobacterium tuberculosis adenylyl cyclase, rv1900c chd

Structure:

Hydrolase, alpha/beta hydrolase fold family. Chain: a, b, c, d. Fragment: rv1900c chd. Engineered: yes

Source:

Mycobacterium tuberculosis. Organism_taxid: 83331. Strain: cdc1551. Gene: rv1900c. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.31Å R-factor: 0.194 R-free: 0.230

Authors:

S.C.Sinha,M.Wetterer,S.R.Sprang,J.E.Schultz,J.U.Linder

Key ref:

S.C.Sinha et al. (2005). Origin of asymmetry in adenylyl cyclases: structures of Mycobacterium tuberculosis Rv1900c. EMBO J, 24, 663-673. PubMed id: 15678099 DOI: 10.1038/sj.emboj.7600573

Date:

21-Dec-04 Release date: 15-Feb-05

Protein chains

O07732  (O07732_MYCTU) -  PROBABLE LIGNIN PEROXIDASE LIPJ

Seq: 462 a.a.

Struc: 167 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: intracellular signal transduction (2 terms)
• Biochemical function: phosphorus-oxygen lyase activity (1 term)

DOI no: 10.1038/sj.emboj.7600573

EMBO J 24:663-673 (2005)

PubMed id: 15678099

Origin of asymmetry in adenylyl cyclases: structures of Mycobacterium tuberculosis Rv1900c.

S.C.Sinha, M.Wetterer, S.R.Sprang, J.E.Schultz, J.U.Linder.

ABSTRACT

Rv1900c, a Mycobacterium tuberculosis adenylyl cyclase, is composed of an N-terminal alpha/beta-hydrolase domain and a C-terminal cyclase homology domain. It has an unusual 7% guanylyl cyclase side-activity. A canonical substrate-defining lysine and a catalytic asparagine indispensable for mammalian adenylyl cyclase activity correspond to N342 and H402 in Rv1900c. Mutagenic analysis indicates that these residues are dispensable for activity of Rv1900c. Structures of the cyclase homology domain, solved to 2.4 A both with and without an ATP analog, form isologous, but asymmetric homodimers. The noncanonical N342 and H402 do not interact with the substrate. Subunits of the unliganded open dimer move substantially upon binding substrate, forming a closed dimer similar to the mammalian cyclase heterodimers, in which one interfacial active site is occupied and the quasi-dyad-related active site is occluded. This asymmetry indicates that both active sites cannot simultaneously be catalytically active. Such a mechanism of half-of-sites-reactivity suggests that mammalian heterodimeric adenylyl cyclases may have evolved from gene duplication of a primitive prokaryote-type cyclase, followed by loss of function in one active site.

Selected figure(s)

Figure 4.
Figure 4 Rv1900c CHD dimers. (A) Superimposed open and closed Rv1900c CHD homodimers viewed down the pseudo-dyad dimer axis of the open form. Monomers A and B of the open dimer are rendered in gray and violet, respectively, while those of the closed dimer are rendered sage and salmon, respectively. (B) Closed Rv1900c CHD dimer viewed down the pseudo-dyad dimer axis. Subunits are colored as in (A). The location of the occupied active site is indicated by the bound Mn2+ AMPCPP rendered in atomic detail, and colored by atom type (O red, N blue, P orange and Mn2+ black, and C gray) while the unoccupied, dyad-related site is indicated by an AMPCPP molecule represented as a black stick model. (C) View along the dimer dyad axis showing the dimer active sites. Subunits are colored as in (A). Residues that may play a role in substrate binding or catalysis are rendered in atomic detail and colored by atom type (O red, N blue, P orange and Mn2+ black, and C according to protein subunit). Metal coordination is depicted by solid, black lines while dashed, black lines indicate hydrogen bonds.

Figure 5.
Figure 5 The CHD active site. All three figures are viewed in similar orientations and depict the three crystallographically captured states of the Rv1900c CHD active site. Atomic details of residues that may play a role in substrate binding or catalysis are shown. Subunits, atoms and bonds are represented as in Figure 3. (A) Detailed view of the ligand-unoccupied active site of the open dimer. Active site residues are loosely and asymmetrically packed. (B) Detailed view of the Mn2+-AMPCPP-occupied active site of the closed dimer. Potential hydrogen bonds to the oxygen bridging the ATP - and -phosphates (leaving group), which is a nonscissile carbon in AMPCPP, are indicated by dashed, magenta lines. (C) Detailed view of the ligand-unoccupied active site of the closed dimer. Residues that participate in binding substrate are held in inactive conformations by a network of hydrogen bonds.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2005, 24, 663-673) copyright 2005.

Figures were selected by an automated process.