NikD
NikD is an unusual amino acid oxidising enzyme that contains covalently bound FAD and catalyses a 4-electron oxidation of piperideine-2-carboxylic acid to picolinate and plays a critical role in the biosynthesis of nikkomycin antibiotics. Nikkomycins are potent antifungal agents that block cell wall formation by inhibiting the biosynthesis of chitin, the second most abundant polysaccharide in nature.
NikD exhibits two unique structural features as compared with other members of the MSOX family of amino acid oxidases:
- nikD contains a mobile cation-binding loop of unknown function that has been shown to bind sodium or potassium ions.
- nikD exhibits two distinct modes for substrate binding, as judged by the open and closed forms of the enzyme·picolinate complex. In the closed form, picolinate is bound parallel with the flavin ring, the indole ring of Trp355 is perpendicular to the flavin ring, and the active site is inaccessible to solvent. This ligand binding mode is compatible with redox catalysis and similar to that observed with MSOX. In the open form, picolinate is bound perpendicular to the flavin ring, Trp355 is stacked atop the flavin ring, and the active site is accessible to solvent. This binding mode is not compatible with redox catalysis or observed with MSOX. However, the coplanar orientation of the flavin and indole rings is required for charge-transfer interaction between FAD and Trp355, a feature observed with solutions of the ligand-free enzyme at weakly alkaline pH
Reference Protein and Structure
- Sequence
-
Q9X9P9
(Sequence Homologues)
(PDB Homologues)
- Biological species
-
Streptomyces tendae (Bacteria)
- PDB
-
2oln
- NikD, an unusual amino acid oxidase essential for nikkomycin biosynthesis: closed form at 1.15 A resolution
(1.15 Å)
- Catalytic CATH Domains
-
3.30.9.10
3.50.50.60
(see all for 2oln)
- Cofactors
- Fadh2(2-) (1)
Enzyme Mechanism
Introduction
The mechanism is proposed to occur by an initial enamine tautomerisation to eliminate the first hydride to FAD. The substrate then undergoes a second tautomerisation and concomitant loss of a proton, regenerating the enamine tautomer. The intermediate then undergoes a second tautomerisation to generate the isomer that is ready for the second hydride elimination to FAD to generate the final product.
Catalytic Residues Roles
| UniProt | PDB* (2oln) | ||
| Trp355 | Trp355A | Trp355 is the intrinsic charge transfer donor. The indole ring of Trp355 is coplanar with or perpendicular to the flavin ring in “open” or “closed” crystalline forms of nikD, respectively. Importantly, a coplanar configuration is required for charge transfer interaction. | electrostatic stabiliser |
| Asp276, Glu101 | Asp276A, Glu101A | Although mutation studies have ruled these residues out as the general acid/base, they are still likely involved in maintaining the correct orientation of the substrate in the active site. | steric role |
| Cys321 | Cys321A | The FAD cofactor is covalently attached to Cys321. This interaction is likely to modulate the redox potential of the cofactor. | covalently attached, alter redox potential |
| Arg53, Lys358 | Arg53A, Lys358A | Involved in holding the substrate in the correct orientation for the reaction to occur. | electrostatic stabiliser |
| Tyr258 | Tyr258A | Tyr258 forms part of an “aromatic cage” that surrounds the ligand ring in the enzyme·picolinate complex. It is unlikely to participate directly in P2C or DHP oxidation, as judged by the location and orientation of the tyrosyl side chain in the open or closed form of the enzyme·picolinate complex. Nevertheless, a conservative mutation at this position appears to promote release of the reactive DHP intermediate and causes a 10−50-fold decrease in steady-state kinetic parameters. | electrostatic stabiliser |
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file;
y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain;
C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.
Chemical Components
hydride transfer, overall reactant used, proton transfer, assisted tautomerisation (not keto-enol), overall product formed, native state of cofactor regenerated, native state of enzyme regeneratedReferences
- Carrell CJ et al. (2007), Structure, 15, 928-941. NikD, an Unusual Amino Acid Oxidase Essential for Nikkomycin Biosynthesis: Structures of Closed and Open Forms at 1.15 and 1.90 Å Resolution. DOI:10.1016/j.str.2007.06.010. PMID:17697998.
- Kommoju PR et al. (2009), Biochemistry, 48, 6951-6962. Probing the Role of Active Site Residues in NikD, an Unusual Amino Acid Oxidase That Catalyzes an Aromatization Reaction Important in Nikkomycin Biosynthesis. DOI:10.1021/bi9006918. PMID:19530706.
- Kommoju PR et al. (2009), Biochemistry, 48, 9542-9555. Factors That Affect Oxygen Activation and Coupling of the Two Redox Cycles in the Aromatization Reaction Catalyzed by NikD, an Unusual Amino Acid Oxidase. DOI:10.1021/bi901056a. PMID:19702312.
- Bruckner RC et al. (2009), Biochemistry, 48, 4455-4465. Spectral and Kinetic Characterization of Intermediates in the Aromatization Reaction Catalyzed by NikD, an Unusual Amino Acid Oxidase. DOI:10.1021/bi900179j. PMID:19354202.
- Bruckner RC et al. (2007), Biochemistry, 46, 819-827. A Mobile Tryptophan Is the Intrinsic Charge Transfer Donor in a Flavoenzyme Essential for Nikkomycin Antibiotic Biosynthesis†. DOI:10.1021/bi062087s. PMID:17223703.
- Venci D et al. (2002), Biochemistry, 41, 15795-15802. Molecular Characterization of NikD, a New Flavoenzyme Important in the Biosynthesis of Nikkomycin Antibiotics†. DOI:10.1021/bi020515y.
Step 1. The enamine tautomer eliminates a hydride ion to the covalently attached FAD cofactor.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Tyr258A | electrostatic stabiliser |
| Trp355A | electrostatic stabiliser |
| Cys321A | alter redox potential, covalently attached |
| Arg53A | electrostatic stabiliser |
| Lys358A | electrostatic stabiliser |
| Glu101A | steric role |
| Asp276A | steric role |
Chemical Components
hydride transfer, overall reactant used
Step 2. The FAD cofactor abstracts a proton from the intermediate to generate the second enamine tautomer.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Arg53A | electrostatic stabiliser |
| Tyr258A | electrostatic stabiliser |
| Trp355A | electrostatic stabiliser |
| Lys358A | electrostatic stabiliser |
| Cys321A | covalently attached, alter redox potential |
| Glu101A | steric role |
| Asp276A | steric role |
Chemical Components
proton transfer, assisted tautomerisation (not keto-enol)
Step 3. The FAD cofactor initiates a second proton transfer to generate the final enamine tautomer required.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Arg53A | electrostatic stabiliser |
| Tyr258A | electrostatic stabiliser |
| Trp355A | electrostatic stabiliser |
| Lys358A | electrostatic stabiliser |
| Cys321A | covalently attached, alter redox potential |
| Glu101A | steric role |
| Asp276A | steric role |
Chemical Components
proton transfer, assisted tautomerisation (not keto-enol)
Step 4. FAD undergoes oxidation to regenerate it for the final hydride transfer.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Glu101A | steric role |
| Asp276A | steric role |
| Arg53A | electrostatic stabiliser |
| Tyr258A | electrostatic stabiliser |
| Trp355A | electrostatic stabiliser |
| Lys358A | electrostatic stabiliser |
| Cys321A | covalently attached, alter redox potential |
Chemical Components
proton transfer, hydride transfer, overall product formed, native state of cofactor regenerated, overall reactant used
Catalytic Residues Roles
| Residue | Roles |
|---|---|
| Glu101A | steric role |
| Asp276A | steric role |
| Arg53A | electrostatic stabiliser |
| Tyr258A | electrostatic stabiliser |
| Trp355A | electrostatic stabiliser |
| Lys358A | electrostatic stabiliser |
| Cys321A | alter redox potential, covalently attached |
Chemical Components
hydride transfer
Step 6. Dioxygen regenerates the cofactor along with the final protonation state of the product.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Glu101A | steric role |
| Asp276A | steric role |
| Arg53A | electrostatic stabiliser |
| Tyr258A | electrostatic stabiliser |
| Trp355A | electrostatic stabiliser |
| Lys358A | electrostatic stabiliser |
| Cys321A | covalently attached, alter redox potential |
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