PDBsum entry 1wc0

Lyase

PDB id: 1wc0

Contents

Protein chains

199 a.a. *

Ligands

APC ×2

Metals

_CA ×2

Waters ×141

* Residue conservation analysis

PDB id:

1wc0

Name:

Lyase

Title:

Soluble adenylyl cyclase cyac from s. Platensis in complex with alpha, beta-methylene-atp

Structure:

Adenylate cyclase. Chain: a, b. Fragment: catalytic domain, residues 1005-1202. Synonym: soluble adenylyl cyclase cyac. Engineered: yes

Source:

Spirulina platensis. Organism_taxid: 118562. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.40Å R-factor: 0.219 R-free: 0.271

Authors:

C.Steegborn,T.N.Litvin,L.R.Levin,J.Buck,H.Wu

Key ref:

C.Steegborn et al. (2005). Bicarbonate activation of adenylyl cyclase via promotion of catalytic active site closure and metal recruitment. Nat Struct Mol Biol, 12, 32-37. PubMed id: 15619637 DOI: 10.1038/nsmb880

Date:

05-Nov-04 Release date: 20-Dec-04

Protein chains

O32393  (O32393_ARTPT) -  histidine kinase from Arthrospira platensis

Seq: 1202 a.a.

Struc: 199 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.2.7.13.3 - histidine kinase.
• Reaction: ATP + protein L-histidine = ADP + protein N-phospho-L-histidine

ATP + protein L-histidine = ADP (Bound ligand (Het Group name = APC) matches with 61.11% similarity) + protein N-phospho-L-histidine

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

reference

DOI no: 10.1038/nsmb880

Nat Struct Mol Biol 12:32-37 (2005)

PubMed id: 15619637

Bicarbonate activation of adenylyl cyclase via promotion of catalytic active site closure and metal recruitment.

C.Steegborn, T.N.Litvin, L.R.Levin, J.Buck, H.Wu.

ABSTRACT

In an evolutionarily conserved signaling pathway, 'soluble' adenylyl cyclases (sACs) synthesize the ubiquitous second messenger cyclic adenosine 3',5'-monophosphate (cAMP) in response to bicarbonate and calcium signals. Here, we present crystal structures of a cyanobacterial sAC enzyme in complex with ATP analogs, calcium and bicarbonate, which represent distinct catalytic states of the enzyme. The structures reveal that calcium occupies the first ion-binding site and directly mediates nucleotide binding. The single ion-occupied, nucleotide-bound state defines a novel, open adenylyl cyclase state. In contrast, bicarbonate increases the catalytic rate by inducing marked active site closure and recruiting a second, catalytic ion. The phosphates of the bound substrate analogs are rearranged, which would facilitate product formation and release. The mechanisms of calcium and bicarbonate sensing define a reaction pathway involving active site closure and metal recruitment that may be universal for class III cyclases.

Selected figure(s)

Figure 3.
Figure 3. Conformational states and comparison of AC enzymes. (a) Structure-based sequence alignment of bicarbonate responsive sAC enzymes and the G protein -regulated tmAC domains VC[1] and IIC[2] (PDB entry 1AZS). Secondary structure elements of sAC and IIC[2] are indicated on top and bottom, respectively. Ion-binding residues ( ) and residues binding the substrate (^) or the transition state ( ) are labeled (filled and empty symbols label C[1] and C[2] residues, respectively). Thr1139^* and the insertion characteristic for sAC enzymes are indicated ( ). Conserved amino acids are shaded yellow, and residues with conserved physicochemical properties are shaded red. (b) Overlay of the sAC - , -Me-ATP structure (open state, darkest gray, with 1 helix and 7 - 8 loop in blue), the sAC -Rp-ATP S complex (partially closed, middle gray and red), and the bicarbonate-soaked Rp-ATP S structure (closed, lightest gray and yellow). Structures were superimposed on sAC - , -Me-ATP by optimizing positional agreement for residues 1014 -1018, 1056 -1065, 1117 -1126 and 1143 -1167 in both subunits. (c) sAC active site in complex with Rp-ATP S and two magnesium ions, with the two monomers colored red and blue, respectively. The dashed lines indicate the octahedral coordination of the ions through the ATP analog, protein residues and one and two water molecules (gold spheres), respectively. The 2F[o] - F[c] omit electron density for the ligands was contoured at 1.1 . In its tmAC complex, P of Rp-ATP S was modeled differently but with limited electron density for the ribose and its link to the P 16, and we speculate that this density might also be interpretable with the inhibitor conformation observed here for its sAC complex.

Figure 4.
Figure 4. Model for catalysis by class III nucleotidyl cyclases. The model for catalysis (bottom pathway) is based on the conformational changes observed with the sAC -substrate analog complexes (top). The arrows at 1 and 7 - 8 indicate the movements undergone by these protein parts. The individual catalytic states (open, intermediate and closed) are extrapolated from the different sAC structures presented in the text, with the protein conformation of the sAC -Rp-ATP S complex being a speculative approximate intermediate state.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2005, 12, 32-37) copyright 2005.

Figures were selected by an automated process.