2JIR
A New Catalytic Mechanism of Periplasmic Nitrate Reductase from Desulfovibrio desulfuricans ATCC 27774 from Crystallographic and EPR Data and based on detailed analysis of the sixth ligand
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Chains | Domain Info | Class | Fold | Superfamily | Family | Domain | Species | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | d2jira1 | All beta proteins | Double psi beta-barrel | ADC-like | Formate dehydrogenase/DMSO reductase, C-terminal domain | Periplasmic nitrate reductase alpha chain, NapA | (Desulfovibrio desulfuricans ) [TaxId: 876 ], | SCOPe (2.08) |
A | d2jira2 | Alpha and beta proteins (a/b) | Formate dehydrogenase/DMSO reductase, domains 1-3 | Formate dehydrogenase/DMSO reductase, domains 1-3 | Formate dehydrogenase/DMSO reductase, domains 1-3 | Periplasmic nitrate reductase alpha chain | (Desulfovibrio desulfuricans ) [TaxId: 876 ], | SCOPe (2.08) |
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | Molydop_binding | e2jirA1 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: Molydop_binding | ECOD (1.6) |
A | Molybdop_Fe4S4 | e2jirA4 | A: a+b two layers | X: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology) | H: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology) | T: Formate dehydrogenase/DMSO reductase, domain 1 | F: Molybdop_Fe4S4 | ECOD (1.6) |
A | Molybdopterin_2nd | e2jirA2 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology) | T: Formate dehydrogenase/DMSO reductase, domains 2 and 3 | F: Molybdopterin_2nd | ECOD (1.6) |
A | Molybdopterin_1st_1 | e2jirA3 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology) | T: Formate dehydrogenase/DMSO reductase, domains 2 and 3 | F: Molybdopterin_1st_1 | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
A | 2.20.25.90 | Mainly Beta | Single Sheet | N-terminal domain of TfIIb | ADC-like domains | CATH (4.3.0) |
A | 3.40.50.740 | Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | CATH (4.3.0) | |
A | 3.40.228.10 | Alpha Beta | 3-Layer(aba) Sandwich | Dimethylsulfoxide Reductase | domain 2 | CATH (4.3.0) |
A | 2.40.40.20 | Mainly Beta | Beta Barrel | Barwin-like endoglucanases | CATH (4.3.0) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF01568 | Molydopterin dinucleotide binding domain (Molydop_binding) | Molydopterin dinucleotide binding domain | This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entir ... | Domain | |
PF04879 | Molybdopterin oxidoreductase Fe4S4 domain (Molybdop_Fe4S4) | Molybdopterin oxidoreductase Fe4S4 domain | This domain is found in formate dehydrogenase H for which the structure is known. This first domain (residues 1 to 60) of PDB:1aa6 is an Fe4S4 cluster just below the protein surface [1]. | Domain | |
PF00384 | Molybdopterin oxidoreductase (Molybdopterin) | Molybdopterin oxidoreductase | - | Family |