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Catalytic Site Atlas Version 2.2.12
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CSA entry for 1l0o
Original Entry
Title:
Protein binding
Compound:
Anti-sigma f factor
Mutant:
No
UniProt/Swiss-Prot:
O32727-SP22_BACST
O32728-O32728
EC Class:
2.7.1.37
Other CSA Entries:
Overview of all sites for 1l0o
Homologues of 1l0o
Entries for UniProt/Swiss-Prot: O32727
Entries for UniProt/Swiss-Prot: O32728
Entries for EC: 2.7.1.37
Other Databases:
PDB entry: 1l0o
PDBsum entry: 1l0o
UniProt/Swiss-Prot: O32727
UniProt/Swiss-Prot: O32728
IntEnz entry: 2.7.1.37
Literature Report:
Introduction:
The control of sporulation in some bacteria is controlled by sigma factors, one of which is sigma-F which triggers the cascade of gene expression in the forespore compartment of the sporulating cell. Control of sigma-F is by the SpoII proteins: SpoIIAB, which binds to sigma-F and thereby inactivates it; SpoIIAA, a non-enzymatic protein which is phosphorylated by SpoIIAB, thus inducing release of sigma-F; and SpoIIE, a phosphatase which returns SpoII-P to the dephosphorylated state.

SpoIIAB has the same ATP-binding domain as other members of the GHKL superfamily. It phosphorylates the Ser 58 residue of SpoIIAA, using up ATP.
Mechanism:
The basic mechanism is inline displacement of ADP, by attack of the SpoIIAA Ser 58 on the gamma-phosphate of ATP. Various residues and an Mg cofactor aid the reaction:

Mg2+ (bound by Asn 50) coordinates all three phosphate groups of ATP. This stabilises the transition state by reducing charge build-up.

Arg 105 is in the correct position to stabilise the transition state by hydrogen bonding to two oxygens of the gamma-phosphate group.

Glu 46 hydrogen bonds to, and polarises, the SpoIIAA Ser 58 hydroxyl, making it nucleophilic enough to attack ATP.

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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
GLUA 46 46Sidechain
ElectrostaticSubstrate
Glu 46 hydrogen bonds to, and polarises, the SpoIIAA Ser 58 hydroxyl, making it nucleophilic enough to attack ATP.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11955433 Current protein Conservation of residue
PubMed ID 11955433 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 11955433 Current protein Structural similarity to homologue of known mechanism

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ARGA 105 105Sidechain
ElectrostaticTransition state
Arg 105 stabilises the transition state by hydrogen bonding to two oxygens of the gamma-phosphate group.
Evidence from paper Evidence concerns Evidence type
PubMed ID 15236958 Related protein: UniProt P10728 Conservation of residue
PubMed ID 15236958 Related protein: UniProt P10728 Mutagenesis of residue
PubMed ID 15236958 Related protein: UniProt P10728 Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
MGA 602 0
ElectrostaticTransition state
Mg2+ (bound by Asn 50) coordinates all three phosphate groups of ATP. This stabilises the transition state by reducing charge build-up.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11955433 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 11955433 Current protein Conservation of residue
PubMed ID 11955433 Current protein Ligand is essential for catalysis
Notes:

References:
1
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 and K. S. Murakami and S. Wang and C. Anders Olson and J. Donigian and F. Leon and S. A. Darst and E. A. Campbell
J Mol Biol 340, (5) 941-56, (2004).
15236958
2
Crystal structure of the Bacillus stearothermophilus anti-sigma factor SpoIIAB with the sporulation sigma factor sigmaF.
E. A. Campbell and S. Masuda and J. L. Sun and O. Muzzin and C. A. Olson and S. Wang and S. A. Darst
Cell 108, (6) 795-807, (2002).
11955433
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