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Catalytic Site Atlas

CSA LITERATURE entry for 1dd8

E.C. namebeta-ketoacyl-acyl-carrier-protein synthase I
SpeciesEscherichia coli (Bacteria)
E.C. Number (IntEnz) 2.3.1.41
CSA Homologues of 1dd8There are 46 Homologs
CSA Entries With UniProtID P0A953
CSA Entries With EC Number 2.3.1.41
PDBe Entry 1dd8
PDBSum Entry 1dd8
MACiE Entry M0292

Literature Report

IntroductionBeta-ketoacyl-acyl carrier protein synthase (KAS) I catalyses the Claisen condensation between acyl-ACP and malonyl-ACP to produce free acyl carrier protein (ACP), 3-oxoacyl ACP, and CO2. KAS I fuctions, together with KAS II and KAS III, to synthesise C16 and C18 fatty acids in plant plastids: KAS III is specific for the first step of the elongation and uses a CoA-activated primer substrate, while KAS I extends C4 to C16 in six rounds of elongation using an ACP substrate. KAS II then carries out an additional step to yield C18. In E. coli, KAS I is essential for the construction of the unsaturated fatty acids characterising E. coli membrane lipids.
MechansimThe catalysed reaction occurs in three steps. First, Cys 163 acts as a nucleophile to attack the carbonyl group of acyl ACP in a transesterification reaction that releases ACP and forms a Cys 163-linked thioester. The tetrahedral intermediate in this reaction is stabilised by an oxyanion hole composed of the backbone NH groups of Cys 163 and Phe 392. The nucleophilic nature of Cys 163 is enhanced by the positive end of an alpha-helix dipole.
In the second step, His 298 deprotonates the carboxyl group of malonyl ACP to initiate the decarboxylation of this substrate with formation of an enolate intermediate. Accumulation of negative charge on the thioester carbonyl of malonyl CoA during formation of the enolate is stabilised by a hydrogen bond from His 333. The pKa of His 298 is modified by Lys 328 (acting indirectly via a hydroxide ion) and by a C-H...O hydrogen bond from the backbone oxygen of Phe 390.
In the final step, the enolate produced from malonyl ACP attacks the Cys 163-linked thioester in a Claisen condensation reaction. This forms the product 3-oxoacyl-ACP and regenerates free Cys 163. The tetrahedral intermediate formed during the attack is stabilised by the oxyanion hole of Cys 163 and Phe 392.
Reaction

Catalytic Sites for 1dd8

Annotated By Reference To The Literature - Site 5 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
PheA392392macie:mainChainAmideBackbone NH forms part of oxyanion hole that stabilises the tetrahedral intermediate that results from attack on the acyl-ACP carbonyl by the side chain of Cys 163 and later by the malonyl-ACP derived enolate.
LysA328328macie:sideChainIndirectly modifies the pKa of His 298 by stabilising a hydroxide ion that interacts with the N-delta of His 298.
HisA298298macie:sideChainDeprotonates the carboxyl group of malonyl ACP to initiate the decarboxylation reaction. Backbone oxygen forms a C-H...O hydrogen bond to C-epsilon of His 298 which modifies the pKa of the imidazole ring.
HisA298298macie:mainChainCarbonylDeprotonates the carboxyl group of malonyl ACP to initiate the decarboxylation reaction. Backbone oxygen forms a C-H...O hydrogen bond to C-epsilon of His 298 which modifies the pKa of the imidazole ring.
HisA333333macie:sideChainDonates a hydrogen bond to the thioester carbonyl of maloyl-ACP, stabilising accumulation of negative charge on this atom during formation of the enolate intermediate.
PheA390390macie:mainChainCarbonylModifies the pKa of His 298 by forming a C-H...O hydrogen bond from its backbone oxygen to C-epsilon of His 298.
CysA163163macie:sideChainAttacks the thioester carbonyl of acyl ACP to form an enzyme-linked acyl thioester in a transesterification reaction. Backbone NH forms part of oxyanion hole that stabilises the tetrahedral intermediate that results from attack by the side chain of Cys 163 and later by the malonyl-ACP derived enolate.
CysA163163macie:mainChainAmideAttacks the thioester carbonyl of acyl ACP to form an enzyme-linked acyl thioester in a transesterification reaction. Backbone NH forms part of oxyanion hole that stabilises the tetrahedral intermediate that results from attack by the side chain of Cys 163 and later by the malonyl-ACP derived enolate.

Annotated By Reference To The Literature - Site 6 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
PheB392392macie:mainChainAmideBackbone NH forms part of oxyanion hole that stabilises the tetrahedral intermediate that results from attack on the acyl-ACP carbonyl by the side chain of Cys 163 and later by the malonyl-ACP derived enolate.
LysB328328macie:sideChainIndirectly modifies the pKa of His 298 by stabilising a hydroxide ion that interacts with the N-delta of His 298.
HisB298298macie:sideChainDeprotonates the carboxyl group of malonyl ACP to initiate the decarboxylation reaction. Backbone oxygen forms a C-H...O hydrogen bond to C-epsilon of His 298 which modifies the pKa of the imidazole ring.
HisB298298macie:mainChainCarbonylDeprotonates the carboxyl group of malonyl ACP to initiate the decarboxylation reaction. Backbone oxygen forms a C-H...O hydrogen bond to C-epsilon of His 298 which modifies the pKa of the imidazole ring.
HisB333333macie:sideChainDonates a hydrogen bond to the thioester carbonyl of maloyl-ACP, stabilising accumulation of negative charge on this atom during formation of the enolate intermediate.
PheB390390macie:mainChainCarbonylModifies the pKa of His 298 by forming a C-H...O hydrogen bond from its backbone oxygen to C-epsilon of His 298.
CysB163163macie:sideChainAttacks the thioester carbonyl of acyl ACP to form an enzyme-linked acyl thioester in a transesterification reaction. Backbone NH forms part of oxyanion hole that stabilises the tetrahedral intermediate that results from attack by the side chain of Cys 163 and later by the malonyl-ACP derived enolate.
CysB163163macie:mainChainAmideAttacks the thioester carbonyl of acyl ACP to form an enzyme-linked acyl thioester in a transesterification reaction. Backbone NH forms part of oxyanion hole that stabilises the tetrahedral intermediate that results from attack by the side chain of Cys 163 and later by the malonyl-ACP derived enolate.

Annotated By Reference To The Literature - Site 7 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
PheC392392macie:mainChainAmideBackbone NH forms part of oxyanion hole that stabilises the tetrahedral intermediate that results from attack on the acyl-ACP carbonyl by the side chain of Cys 163 and later by the malonyl-ACP derived enolate.
LysC328328macie:sideChainIndirectly modifies the pKa of His 298 by stabilising a hydroxide ion that interacts with the N-delta of His 298.
HisC298298macie:sideChainDeprotonates the carboxyl group of malonyl ACP to initiate the decarboxylation reaction. Backbone oxygen forms a C-H...O hydrogen bond to C-epsilon of His 298 which modifies the pKa of the imidazole ring.
HisC298298macie:mainChainCarbonylDeprotonates the carboxyl group of malonyl ACP to initiate the decarboxylation reaction. Backbone oxygen forms a C-H...O hydrogen bond to C-epsilon of His 298 which modifies the pKa of the imidazole ring.
HisC333333macie:sideChainDonates a hydrogen bond to the thioester carbonyl of maloyl-ACP, stabilising accumulation of negative charge on this atom during formation of the enolate intermediate.
PheC390390macie:mainChainCarbonylModifies the pKa of His 298 by forming a C-H...O hydrogen bond from its backbone oxygen to C-epsilon of His 298.
CysC163163macie:sideChainAttacks the thioester carbonyl of acyl ACP to form an enzyme-linked acyl thioester in a transesterification reaction. Backbone NH forms part of oxyanion hole that stabilises the tetrahedral intermediate that results from attack by the side chain of Cys 163 and later by the malonyl-ACP derived enolate.
CysC163163macie:mainChainAmideAttacks the thioester carbonyl of acyl ACP to form an enzyme-linked acyl thioester in a transesterification reaction. Backbone NH forms part of oxyanion hole that stabilises the tetrahedral intermediate that results from attack by the side chain of Cys 163 and later by the malonyl-ACP derived enolate.

Annotated By Reference To The Literature - Site 8 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
PheD392392macie:mainChainAmideBackbone NH forms part of oxyanion hole that stabilises the tetrahedral intermediate that results from attack on the acyl-ACP carbonyl by the side chain of Cys 163 and later by the malonyl-ACP derived enolate.
LysD328328macie:sideChainIndirectly modifies the pKa of His 298 by stabilising a hydroxide ion that interacts with the N-delta of His 298.
HisD298298macie:sideChainDeprotonates the carboxyl group of malonyl ACP to initiate the decarboxylation reaction. Backbone oxygen forms a C-H...O hydrogen bond to C-epsilon of His 298 which modifies the pKa of the imidazole ring.
HisD298298macie:mainChainCarbonylDeprotonates the carboxyl group of malonyl ACP to initiate the decarboxylation reaction. Backbone oxygen forms a C-H...O hydrogen bond to C-epsilon of His 298 which modifies the pKa of the imidazole ring.
HisD333333macie:sideChainDonates a hydrogen bond to the thioester carbonyl of maloyl-ACP, stabilising accumulation of negative charge on this atom during formation of the enolate intermediate.
PheD390390macie:mainChainCarbonylModifies the pKa of His 298 by forming a C-H...O hydrogen bond from its backbone oxygen to C-epsilon of His 298.
CysD163163macie:sideChainAttacks the thioester carbonyl of acyl ACP to form an enzyme-linked acyl thioester in a transesterification reaction. Backbone NH forms part of oxyanion hole that stabilises the tetrahedral intermediate that results from attack by the side chain of Cys 163 and later by the malonyl-ACP derived enolate.
CysD163163macie:mainChainAmideAttacks the thioester carbonyl of acyl ACP to form an enzyme-linked acyl thioester in a transesterification reaction. Backbone NH forms part of oxyanion hole that stabilises the tetrahedral intermediate that results from attack by the side chain of Cys 163 and later by the malonyl-ACP derived enolate.

Literature References

Notes:
Olsen JG
Structures of beta-ketoacyl-acyl carrier protein synthase I complexed with fatty acids elucidate its catalytic machinery.
Structure 2001 9 233-243
PubMed: 11286890
McGuire KA
beta-Ketoacyl-[acyl carrier protein] synthase I of Escherichia coli: aspects of the condensation mechanism revealed by analyses of mutations in the active site pocket.
Biochemistry 2001 40 9836-9845
PubMed: 11502177
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