Crystal structure of the heterodimeric nitrate reductase from Rhodobacter sphaeroides
External Resource: Annotation
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
P | SCOP2B Superfamily | Di-heme elbow motif | 8089678 | 3000145 | SCOP2B (2022-06-29) |
N | SCOP2B Superfamily | Di-heme elbow motif | 8089678 | 3000145 | SCOP2B (2022-06-29) |
L | SCOP2B Superfamily | Di-heme elbow motif | 8089678 | 3000145 | SCOP2B (2022-06-29) |
J | SCOP2B Superfamily | Di-heme elbow motif | 8089678 | 3000145 | SCOP2B (2022-06-29) |
H | SCOP2B Superfamily | Di-heme elbow motif | 8089678 | 3000145 | SCOP2B (2022-06-29) |
F | SCOP2B Superfamily | Di-heme elbow motif | 8089678 | 3000145 | SCOP2B (2022-06-29) |
D | SCOP2B Superfamily | Di-heme elbow motif | 8089678 | 3000145 | SCOP2B (2022-06-29) |
B | SCOP2 Family | NapB-like | 8089677 | 4000355 | SCOP2 (2022-06-29) |
B | SCOP2 Superfamily | Di-heme elbow motif | 8089678 | 3000145 | SCOP2 (2022-06-29) |
O | SCOP2B Superfamily | ADC-like | 8037499 | 3001132 | SCOP2B (2022-06-29) |
O | SCOP2B Superfamily | Formate dehydrogenase/DMSO reductase, domains 1-3 | 8037500 | 3001453 | SCOP2B (2022-06-29) |
M | SCOP2B Superfamily | ADC-like | 8037499 | 3001132 | SCOP2B (2022-06-29) |
M | SCOP2B Superfamily | Formate dehydrogenase/DMSO reductase, domains 1-3 | 8037500 | 3001453 | SCOP2B (2022-06-29) |
K | SCOP2B Superfamily | ADC-like | 8037499 | 3001132 | SCOP2B (2022-06-29) |
K | SCOP2B Superfamily | Formate dehydrogenase/DMSO reductase, domains 1-3 | 8037500 | 3001453 | SCOP2B (2022-06-29) |
I | SCOP2B Superfamily | ADC-like | 8037499 | 3001132 | SCOP2B (2022-06-29) |
I | SCOP2B Superfamily | Formate dehydrogenase/DMSO reductase, domains 1-3 | 8037500 | 3001453 | SCOP2B (2022-06-29) |
G | SCOP2B Superfamily | Formate dehydrogenase/DMSO reductase, domains 1-3 | 8037500 | 3001453 | SCOP2B (2022-06-29) |
G | SCOP2B Superfamily | ADC-like | 8037499 | 3001132 | SCOP2B (2022-06-29) |
E | SCOP2B Superfamily | ADC-like | 8037499 | 3001132 | SCOP2B (2022-06-29) |
E | SCOP2B Superfamily | Formate dehydrogenase/DMSO reductase, domains 1-3 | 8037500 | 3001453 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | ADC-like | 8037499 | 3001132 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | Formate dehydrogenase/DMSO reductase, domains 1-3 | 8037500 | 3001453 | SCOP2B (2022-06-29) |
A | SCOP2 Family | Formate dehydrogenase/DMSO reductase, C-terminal domain | 8025120 | 4002360 | SCOP2 (2022-06-29) |
A | SCOP2 Family | Formate dehydrogenase/DMSO reductase, domains 1-3 | 8025121 | 4000801 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | ADC-like | 8037499 | 3001132 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | Formate dehydrogenase/DMSO reductase, domains 1-3 | 8037500 | 3001453 | SCOP2 (2022-06-29) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
P | NapB | e1ogyP1 | A: few secondary structure elements | X: Multiheme cytochromes | H: Di-heme elbow motif (From Topology) | T: Di-heme elbow motif | F: NapB | ECOD (1.6) |
N | NapB | e1ogyN1 | A: few secondary structure elements | X: Multiheme cytochromes | H: Di-heme elbow motif (From Topology) | T: Di-heme elbow motif | F: NapB | ECOD (1.6) |
L | NapB | e1ogyL1 | A: few secondary structure elements | X: Multiheme cytochromes | H: Di-heme elbow motif (From Topology) | T: Di-heme elbow motif | F: NapB | ECOD (1.6) |
J | NapB | e1ogyJ1 | A: few secondary structure elements | X: Multiheme cytochromes | H: Di-heme elbow motif (From Topology) | T: Di-heme elbow motif | F: NapB | ECOD (1.6) |
H | NapB | e1ogyH1 | A: few secondary structure elements | X: Multiheme cytochromes | H: Di-heme elbow motif (From Topology) | T: Di-heme elbow motif | F: NapB | ECOD (1.6) |
F | NapB | e1ogyF1 | A: few secondary structure elements | X: Multiheme cytochromes | H: Di-heme elbow motif (From Topology) | T: Di-heme elbow motif | F: NapB | ECOD (1.6) |
D | NapB | e1ogyD1 | A: few secondary structure elements | X: Multiheme cytochromes | H: Di-heme elbow motif (From Topology) | T: Di-heme elbow motif | F: NapB | ECOD (1.6) |
B | NapB | e1ogyB1 | A: few secondary structure elements | X: Multiheme cytochromes | H: Di-heme elbow motif (From Topology) | T: Di-heme elbow motif | F: NapB | ECOD (1.6) |
O | Molydop_binding | e1ogyO1 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: Molydop_binding | ECOD (1.6) |
O | Molybdop_Fe4S4 | e1ogyO4 | 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) |
O | Molybdopterin_2nd | e1ogyO2 | 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) |
O | Molybdopterin_1st_1 | e1ogyO3 | 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) |
M | Molydop_binding | e1ogyM1 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: Molydop_binding | ECOD (1.6) |
M | Molybdop_Fe4S4 | e1ogyM4 | 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) |
M | Molybdopterin_2nd | e1ogyM2 | 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) |
M | Molybdopterin_1st_1 | e1ogyM3 | 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) |
K | Molydop_binding | e1ogyK1 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: Molydop_binding | ECOD (1.6) |
K | Molybdop_Fe4S4 | e1ogyK4 | 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) |
K | Molybdopterin_2nd | e1ogyK2 | 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) |
K | Molybdopterin_1st_1 | e1ogyK3 | 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) |
I | Molydop_binding | e1ogyI1 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: Molydop_binding | ECOD (1.6) |
I | Molybdop_Fe4S4 | e1ogyI4 | 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) |
I | Molybdopterin_2nd | e1ogyI2 | 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) |
I | Molybdopterin_1st_1 | e1ogyI3 | 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) |
G | Molydop_binding | e1ogyG1 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: Molydop_binding | ECOD (1.6) |
G | Molybdop_Fe4S4 | e1ogyG4 | 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) |
G | Molybdopterin_2nd | e1ogyG2 | 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) |
G | Molybdopterin_1st_1 | e1ogyG3 | 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) |
E | Molydop_binding | e1ogyE1 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: Molydop_binding | ECOD (1.6) |
E | Molybdop_Fe4S4 | e1ogyE4 | 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) |
E | Molybdopterin_2nd | e1ogyE2 | 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) |
E | Molybdopterin_1st_1 | e1ogyE3 | 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) |
C | Molydop_binding | e1ogyC1 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: Molydop_binding | ECOD (1.6) |
C | Molybdop_Fe4S4 | e1ogyC4 | 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) |
C | Molybdopterin_2nd | e1ogyC2 | 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) |
C | Molybdopterin_1st_1 | e1ogyC3 | 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) |
A | Molydop_binding | e1ogyA1 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: Molydop_binding | ECOD (1.6) |
A | Molybdop_Fe4S4 | e1ogyA3 | 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 | e1ogyA5 | 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 | e1ogyA4 | 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
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 entire s ... | 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 | Domain |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage
Chains | Enzyme Name | Description | Catalytic Residues |
---|---|---|---|
nitrate reductase M-CSA #276 | Nitrate reductase is a molybdenum-bis(molybdopterin guanine dinucleotide) dependent enzyme. It catalyses the reduction of nitrate to nitrite and water. The protein associates with NapB, a soluble haem-containing protein and NapC, a membrane-bound cytochrome c. The periplasmic nitrate reductases are not involved in the assimilation of nitrogen, and are not directly involved in the formation of electrochemical gradients (i.e. respiration) either. Rather, the purpose of this enzyme is either dissimilatory (i.e. to dispose of excess reductive equivalents) or indirectly respiratory by virtue of the consumption of electrons derived from NADH via the proton translocating NADH dehydrogenase. | Defined by 6 residues: LYS:E-56CYS:E-152MET:E-153MET:E-346GLY:E-383GLN:E-384 | EC: 1.7.99.4 (PDB Primary Data) EC: 1.9.6.1 (UniProt) |