PDBsum entry: 1cjk

Lyase/lyase/signaling protein

PDB id: 1cjk

Contents

Protein chains

189 a.a. *

190 a.a. *

330 a.a. *

Ligands

FOK

TAT

MES

GSP

Metals

_MG ×2

_MN

_CL

Waters ×34

* Residue conservation analysis

PDB id:

1cjk

Name:

Lyase/lyase/signaling protein

Title:

Complex of gs-alpha with the catalytic domains of mammalian cyclase: complex with adenosine 5'-(alpha thio)-triphosphat mg, and mn

Structure:

Adenylate cyclase, type v. Chain: a. Fragment: c1a domain of adenylyl cyclase. Synonym: protein vc1. Engineered: yes. Mutation: yes. Adenylate cyclase, type ii. Chain: b. Fragment: c2a domain of adenylyl cyclase.

Source:

Canis lupus familiaris. Dog. Organism_taxid: 9615. Strain: familiaris. Tissue: cardiac muscle. Cellular_location: cytoplasm. Gene: adenylyl cyclase type v. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Hexamer (from PQS)

Resolution:

3.00Å R-factor: 0.220 R-free: 0.266

Authors:

J.J.G.Tesmer,S.R.Sprang

Key ref:

J.J.Tesmer et al. (1999). Two-metal-Ion catalysis in adenylyl cyclase. Science, 285, 756-760. PubMed id: 10427002 DOI: 10.1126/science.285.5428.756

Date:

16-Apr-99 Release date: 31-Aug-99

Protein chain

P30803  (ADCY5_CANFA) -  Adenylate cyclase type 5

Seq: 1265 a.a.

Struc: 189 a.a.*

Protein chain

P26769  (ADCY2_RAT) -  Adenylate cyclase type 2

Seq: 1090 a.a.

Struc: 190 a.a.

Protein chain

P04896  (GNAS2_BOVIN) -  Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

Seq: 394 a.a.

Struc: 330 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chains A, B: E.C.4.6.1.1 - Adenylate cyclase.
• Reaction: ATP = 3',5'-cyclic AMP + diphosphate

ATP (Bound ligand (Het Group name = TAT) matches with 93.75% similarity) = 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 

• Cellular component: membrane (5 terms)
• Biological process: intracellular signal transduction (25 terms)
• Biochemical function: nucleotide binding (10 terms)

reference

DOI no: 10.1126/science.285.5428.756

Science 285:756-760 (1999)

PubMed id: 10427002

Two-metal-Ion catalysis in adenylyl cyclase.

J.J.Tesmer, R.K.Sunahara, R.A.Johnson, G.Gosselin, A.G.Gilman, S.R.Sprang.

ABSTRACT

Adenylyl cyclase (AC) converts adenosine triphosphate (ATP) to cyclic adenosine monophosphate, a ubiquitous second messenger that regulates many cellular functions. Recent structural studies have revealed much about the structure and function of mammalian AC but have not fully defined its active site or catalytic mechanism. Four crystal structures were determined of the catalytic domains of AC in complex with two different ATP analogs and various divalent metal ions. These structures provide a model for the enzyme-substrate complex and conclusively demonstrate that two metal ions bind in the active site. The similarity of the active site of AC to those of DNA polymerases suggests that the enzymes catalyze phosphoryl transfer by the same two-metal-ion mechanism and likely have evolved from a common ancestor.

Selected figure(s)

Figure 1.
Fig. 1. Complexes of ATP analog inhibitors with the catalytic core of AC (31). (A) The C[1a]:C[2a] catalytic core of AC viewed along its pseudo-twofold axis toward what is believed to be the cytoplasmic face of the molecule. Forskolin (FSK) and ATP, which bind between the C[1a] (tan) and C[2a] (mauve) domains, are shown as stick models. The switch II helix of G[s] , which forms much of the interface with AC, is depicted as a red rod. (B) Model of ATP bound in the active site. The side chain of N1025 is modeled after its conformation in the AC · ATP S-R[p] · Mn structure (Fig. 1D), whereas all other elements are those of the AC · LddATP · Mn structure (Fig. 1C). Thin black lines depict the coordination of the metal ions. The fifth ligand to metal A is a carboxylate oxygen from D440 and is obscured in this view. Protein and inhibitor residues are drawn as stick models, metals as magenta metallic spheres, and water molecules as red spheres. Carbon atoms are gray, nitrogens blue, oxygens red, phosphorous green, and sulfur yellow. Amino acids are labeled according to their position in canine type V AC for C[1a] and rat type II AC for C[2a]. (C) The left panel portrays the active site of the AC · LddATP · Mn complex. Secondary structure is labeled as previously defined (5). Superimposed is electron density from a 2.8 Å resolution |F[o[Mg]]| |F[c]| omit map (blue wire cage) contoured at 2.5 . Structural elements donated by the C[1a] and C[2a] domains of AC are shown in tan and mauve, respectively. The right panel is a closeup of the triphosphate of the inhibitor. For clarity, the image has been rotated slightly from the view in the left panel. The green and purple wire cages represent electron density contoured at 5 for 3.0 Å |F[o[Zn]]| |F[o[Mg]]| and 2.8 Å |F[o[Mn ]]| |F[o[Mg]]| omit maps, respectively, demonstrating that Zn^2+ preferentially binds at site A and Mn^2+ at site B. The peak height is 8.2 for the Zn^2+ electron density and 11.3 for Mn^2+. |F[o[Mg]]|, |F[o[Mn]]|, and |F[o[Zn]]| are the observed structure factor amplitudes of the AC · LddATP · Mg, AC · LddATP · Mn, and AC · LddATP · Zn data sets, respectively. (D) The active site of AC · ATP S-R[p] · Mn (left) and a closeup view of its thiotriphosphate (right). Superimposed is electron density from a 3.0 Å |F[o]| |F[c]| omit map contoured at 2.5 . A 7 peak marks the position of metal B and is modeled as Mn^2+. A 2 peak marks the position of metal A and is modeled as Mg^2+, although it could also be a weakly bound Mn^2+.

The above figure is reprinted by permission from the AAAs: Science (1999, 285, 756-760) copyright 1999.