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Catalytic Site Atlas

CSA LITERATURE entry for 1n2c

E.C. namenitrogenase
SpeciesAzotobacter vinelandii (Bacteria)
E.C. Number (IntEnz) 1.18.6.1
CSA Homologues of 1n2c
CSA Entries With UniProtID P07328
CSA Entries With EC Number 1.18.6.1
PDBe Entry 1n2c
PDBSum Entry 1n2c
MACiE Entry M0212

Literature Report

IntroductionThe nitrogenase complex from Azotobacter vinelandii catalyses the reduction of atmospheric nitrogen to ammonia, coupled to the hydrolysis of ATP and the oxidation of ferrodoxin. The complex consists of the heterotetramer of the FeMo protein, with one homodimer of Fe protein associated with each of the two alpha-beta subunits. The FeMo protein contains the FeMo-cofactor which contains a Fe7MoS9.homocitrate cofactor (FeMo-co) which is thought to contain a nitrogen atom, and the P-cluster containing an [8Fe-7S] cluster. The Fe protein contains a [4Fe-4S] cubane cluster and catalyses the hydrolysis of ATP and transfers an electron to the FeMo protein. This protein then catalyses the reaction of dinitrogen to ammonia.
Nitrogenase is very biologically important because it reduces inert dinitrogen into a form which organisms can use in synthesis. Only a small subset of organisms can catalyse this reaction while all organisms require reduced nitrogen. This reaction is of industrial interest because enzymatic nitrogen fixation occurs under very mild conditions, while the industrial Haber-Bosch process must be run at high temperatures and pressures.

MechansimThe Fe protein and the FeMo protein must associate before catalytic reactions can occur. Once associated, Asp129 from the Fe protein removes a proton from water and hydroxide acts as the nucleophile in the hydrolysis of ATP to ADP and phosphate. This causes a conformational change that enables the transfer of an electron from the [4Fe-4S] cluster of the Fe protein to the P-cluster and then the FeMo-co of the FeMo protein. The protein complex then dissociates and the Fe protein is reduced by an external molecule of reduced ferrodoxin. For each molecule of ammonia produced, this cycle of ATP hydrolysis and electron transfer to the FeMo protein must occur eight times.
The pathway of electron transfer to the FeMo-co is poorly understood, though the electron is thought to pass through the homocitrate ligand before being transferred to the active face of the cluster. This allows S3B to be protonated, with the proton source thought to be a water chain. The proton is then transferred to a different atom in the complex, thought to be iron, and S3B accepts another proton. Dihydrogen is then released and two more protons are transferred to the cluster from the bulk solvent. Dinitrogen can then bind to an iron in an end-on fashion, and then bind to another iron in a similar fashion. There is proton transfer to one and then the other of the nitrogens. This is followed by an intramolecular nucleophilic substitution, leaving a nitrogen bridging the two irons and bonded to an NH3+ group. There is then N-N bond cleavage (mechanism unclear) to release one molecule of ammonia and to leave the remaining nitrogen bonded to two irons and two protons. A substitution reaction occurs that leads to the cleavage of one Fe-N bond, followed by proton transfer to the nitrogen. There is then a second nucleophilic substitution to release the second molecule of ammonia.

Catalytic Sites for 1n2c

Annotated By Reference To The Literature - Site 5 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
LysF1516macie:sideChainLys15 stabilises the terminal phosphate group during ATP hydrolysis.
LysF4142macie:sideChainLys41 stabilises the terminal phosphate group during ATP hydrolysis.
HisA195195macie:sideChainForms a hydrogen bond with S2B of the FeMo-co during the resting state and acts as an activator.
CysA6262macie:sideChainCys62 is thought to form part of the electron transfer pathway between the P-cluster and the FeMo-co
AlaA6565macie:sideChainAla65 is thought to form part of the electron transfer pathway between the P-cluster and the FeMo-co.
ArgA9696macie:sideChainForms a hydrogen bond with S5A of the FeMo-co during the resting state and acts as an activator.
ValB157157macie:sideChainVal157 is thought to act as an electron donor/acceptor in the transfer of an electron from the Fe protein to the P-cluster of the FeMo protein.
CysB153153macie:sideChainCys153 is thought to act as an electron donor/acceptor in the transfer of an electron from the Fe protein to the P-cluster of the FeMo protein.
LysE1011macie:sideChainLys10 can stabilise the terminal phosphate group of ATP during hydrolysis.
AspE129130macie:sideChainAsp129 acts as a general base for water attack on the terminal phosphate group of ATP. It also stabilises the terminal phosphate group during the reaction.

Annotated By Reference To The Literature - Site 6 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
HisC195195macie:sideChainError
CysC6262macie:sideChainError
ArgC9696macie:sideChainError
AlaC6565macie:sideChainError

Annotated By Reference To The Literature - Site 7 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
LysF1516macie:sideChainLys15 stabilises the terminal phosphate group during ATP hydrolysis.
LysF4142macie:sideChainLys41 stabilises the terminal phosphate group during ATP hydrolysis.
HisA195195macie:sideChainForms a hydrogen bond with S2B of the FeMo-co during the resting state and acts as an activator.
CysA6262macie:sideChainCys62 is thought to form part of the electron transfer pathway between the P-cluster and the FeMo-co
AlaA6565macie:sideChainAla65 is thought to form part of the electron transfer pathway between the P-cluster and the FeMo-co.
ArgA9696macie:sideChainForms a hydrogen bond with S5A of the FeMo-co during the resting state and acts as an activator.
ValB157157macie:sideChainVal157 is thought to act as an electron donor/acceptor in the transfer of an electron from the Fe protein to the P-cluster of the FeMo protein.
CysB153153macie:sideChainCys153 is thought to act as an electron donor/acceptor in the transfer of an electron from the Fe protein to the P-cluster of the FeMo protein.
LysE1011macie:sideChainLys10 can stabilise the terminal phosphate group of ATP during hydrolysis.
AspE129130macie:sideChainAsp129 acts as a general base for water attack on the terminal phosphate group of ATP. It also stabilises the terminal phosphate group during the reaction.

Annotated By Reference To The Literature - Site 8 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
ValD157157macie:sideChainError
CysD153153macie:sideChainError

Annotated By Reference To The Literature - Site 9 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
CysA154154macie:sideChainError
LeuA158158macie:sideChainError

Annotated By Reference To The Literature - Site 10 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
CysC154154macie:sideChainError
LeuC158158macie:sideChainError

Annotated By Reference To The Literature - Site 11 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
LysF1516macie:sideChainLys15 stabilises the terminal phosphate group during ATP hydrolysis.
LysF4142macie:sideChainLys41 stabilises the terminal phosphate group during ATP hydrolysis.
HisA195195macie:sideChainForms a hydrogen bond with S2B of the FeMo-co during the resting state and acts as an activator.
CysA6262macie:sideChainCys62 is thought to form part of the electron transfer pathway between the P-cluster and the FeMo-co
AlaA6565macie:sideChainAla65 is thought to form part of the electron transfer pathway between the P-cluster and the FeMo-co.
ArgA9696macie:sideChainForms a hydrogen bond with S5A of the FeMo-co during the resting state and acts as an activator.
ValB157157macie:sideChainVal157 is thought to act as an electron donor/acceptor in the transfer of an electron from the Fe protein to the P-cluster of the FeMo protein.
CysB153153macie:sideChainCys153 is thought to act as an electron donor/acceptor in the transfer of an electron from the Fe protein to the P-cluster of the FeMo protein.
LysE1011macie:sideChainLys10 can stabilise the terminal phosphate group of ATP during hydrolysis.
AspE129130macie:sideChainAsp129 acts as a general base for water attack on the terminal phosphate group of ATP. It also stabilises the terminal phosphate group during the reaction.

Annotated By Reference To The Literature - Site 12 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
LysF1011macie:sideChainError
AspF129130macie:sideChainError

Annotated By Reference To The Literature - Site 13 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
LysG1011macie:sideChainError
AspG129130macie:sideChainError

Annotated By Reference To The Literature - Site 14 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
LysH1011macie:sideChainError
AspH129130macie:sideChainError

Annotated By Reference To The Literature - Site 15 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
LysF1516macie:sideChainLys15 stabilises the terminal phosphate group during ATP hydrolysis.
LysF4142macie:sideChainLys41 stabilises the terminal phosphate group during ATP hydrolysis.
HisA195195macie:sideChainForms a hydrogen bond with S2B of the FeMo-co during the resting state and acts as an activator.
CysA6262macie:sideChainCys62 is thought to form part of the electron transfer pathway between the P-cluster and the FeMo-co
AlaA6565macie:sideChainAla65 is thought to form part of the electron transfer pathway between the P-cluster and the FeMo-co.
ArgA9696macie:sideChainForms a hydrogen bond with S5A of the FeMo-co during the resting state and acts as an activator.
ValB157157macie:sideChainVal157 is thought to act as an electron donor/acceptor in the transfer of an electron from the Fe protein to the P-cluster of the FeMo protein.
CysB153153macie:sideChainCys153 is thought to act as an electron donor/acceptor in the transfer of an electron from the Fe protein to the P-cluster of the FeMo protein.
LysE1011macie:sideChainLys10 can stabilise the terminal phosphate group of ATP during hydrolysis.
AspE129130macie:sideChainAsp129 acts as a general base for water attack on the terminal phosphate group of ATP. It also stabilises the terminal phosphate group during the reaction.

Annotated By Reference To The Literature - Site 16 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
LysE1516macie:sideChainError
LysE4142macie:sideChainError

Annotated By Reference To The Literature - Site 17 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
LysG1516macie:sideChainError
LysG4142macie:sideChainError

Annotated By Reference To The Literature - Site 18 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
LysH1516macie:sideChainError
LysH4142macie:sideChainError

Literature References

Notes:
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