PDBsum entry 1til

Transcription

PDB id: 1til

Contents

Protein chains

141 a.a. *

117 a.a. *

Ligands

ATP ×3

Metals

_MG ×3

Waters ×155

* Residue conservation analysis

PDB id:

1til

Name:

Transcription

Title:

Crystal structures of the adp and atp bound forms of the bacillus anti-sigma factor spoiiab in complex with the anti-anti-sigma spoiiaa:poised for phosphorylation complex with atp, crystal form ii

Structure:

Anti-sigma f factor. Chain: a, c, e. Synonym: stage ii sporulation protein ab. Engineered: yes. Mutation: yes. Anti-sigma f factor antagonist. Chain: b, d, f. Synonym: stage ii sporulation protein aa. Engineered: yes.

Source:

Geobacillus stearothermophilus. Organism_taxid: 1422. Gene: spoiiab. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: spoiiaa.

Biol. unit:

Hexamer (from PDB file)

Resolution:

2.70Å R-factor: 0.234 R-free: 0.265

Authors:

S.Masuda,K.S.Murakami,S.Wang,C.A.Olson,J.Donigan,F.Leon,S.A.Darst, E.A.Campbell

Key ref:

S.Masuda et al. (2004). Crystal structures of the ADP and ATP bound forms of the Bacillus anti-sigma factor SpoIIAB in complex with the anti-anti-sigma SpoIIAA. J Mol Biol, 340, 941-956. PubMed id: 15236958 DOI: 10.1016/j.jmb.2004.05.040

Date:

02-Jun-04 Release date: 15-Jun-04

Protein chains

O32727  (SP2AB_GEOSE) -  Anti-sigma F factor from Geobacillus stearothermophilus

Seq: 146 a.a.

Struc: 141 a.a.*

Protein chains

O32726  (SP2AA_GEOSE) -  Anti-sigma F factor antagonist from Geobacillus stearothermophilus

Seq: 116 a.a.

Struc: 117 a.a.*

* PDB and UniProt seqs differ at 18 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, C, E: E.C.2.7.11.1 - non-specific serine/threonine protein kinase.
• Reaction:
  1. L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H⁺
  2. L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H⁺

L-seryl-[protein] (Bound ligand (Het Group name = ATP) corresponds exactly) + ATP = O-phospho-L-seryl-[protein] + ADP + H(+)

L-threonyl-[protein] (Bound ligand (Het Group name = ATP) corresponds exactly) + ATP = O-phospho-L-threonyl-[protein] + ADP + H(+)

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

reference

DOI no: 10.1016/j.jmb.2004.05.040

J Mol Biol 340:941-956 (2004)

PubMed id: 15236958

Crystal structures of the ADP and ATP bound forms of the Bacillus anti-sigma factor SpoIIAB in complex with the anti-anti-sigma SpoIIAA.

S.Masuda, K.S.Murakami, S.Wang, C.Anders Olson, J.Donigian, F.Leon, S.A.Darst, E.A.Campbell.

ABSTRACT

Cell type-specific transcription during Bacillus sporulation is established by sigma(F), the activity of which is controlled by a regulatory circuit involving the anti-sigma factor and serine kinase SpoIIAB, and the anti-anti-sigma SpoIIAA. When ATP is present in the nucleotide-binding site of SpoIIAB, SpoIIAA is phosphorylated, followed by dissociation. The nucleotide-binding site of SpoIIAB is left bound to ADP. SpoIIAB(ADP) can bind an unphosphorylated molecule of SpoIIAA as a stable binding partner. Thus, in this circuit, SpoIIAA plays a dual role as a substrate of the SpoIIAB kinase activity, as well as a tight binding inhibitor. Crystal structures of both the pre-phosphorylation complex and the inhibitory complex, SpoIIAB(ATP) and SpoIIAB(ADP) bound to SpoIIAA, respectively, have been determined. The structural differences between the two forms are subtle and confined to interactions with the phosphoryl groups of the nucleotides. The structures reveal details of the SpoIIAA:SpoIIAB interactions and how phosphorylated SpoIIAA dissociates from SpoIIAB(ADP). Finally, the results confirm and expand upon the docking model for SpoIIAA function as an anti-anti-sigma in releasing sigma(F) from SpoIIAB.

Selected figure(s)

Figure 7.
Figure 7. Steric clash of AA and sF on AB. The AA:AB(ATP) complex is shown, viewed parallel with the dimer 2-fold axis, as in Figure 2 (top), along with the corresponding position of sF from the sF:AB(ADP) complex.11 AA and sF are shown as orange and red a-carbon backbone worms, respectively. AB is shown as a molecular surface. AB1 is colored cyan, AB2 is colored green, except the surface of AB interacting with AA (4 Å cutoff), is colored orange and the surface interacting with sF is colored pink. The surface interacting with both binding partners (overlap) is colored purple. Residues of AB noted as important for docking and induced release are colored red and labeled, and the corresponding residues on AA are drawn as stick. These pairs include AB-Arg20:AA-Glu21, AB-Ile112:AA-Leu90, AB-ATP:AA-Ser58, AB-Glu104:AA-Arg67. Note that the clash occurs in the area of AB-Arg20 between AA and sF as previously predicted.[11.]

Figure 9.
Figure 9. Model of docking during induced release. Cartoon illustrating the mechanism of displacement of sF from AB by AA. AB1 and AB2 are colored cyan and green, respectively. sF is colored pink and AA in orange. Residues important for docking and displacement are labeled in step 1. The model is as follows: (1) AB1 of sF:AB[2] is the targeted molecule for docking as its surface is more accessible to AA. In particular, AB-Arg20, a residue critical for the AA:AB interaction exposed. (2) AA docks onto its initial docking sites on AB1 (represented by AB-Glu104 and AB-Ile112). (3) AA docks into a secondary which is represented by AA-Asp23 interacting with AB-Arg20. Upon the second docking, a clash occurs between sF and AA (circled in black and represented by AA-Glu21 and sF-Asp148). (4) The clash leads to the dissociation of sF from AB(ADP). AA then slips into its final docking conformation that is amenable to phosphorylation (represented by AA turning yellow and Ser58 turning red). (5) P-AA dissociates from AB(ADP) due to steric and electrostatic clashes. (6) Unphosphorylated AAs interact with AB1 as an IC and AB2 as a target for phosphorylation.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 340, 941-956) copyright 2004.

Figures were selected by the author.