Structure of the human ATP citrate lyase holoenzyme in complex with citrate, coenzyme A and Mg.ADP
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
| Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
|---|---|---|---|---|---|
| A | SCOP2B Superfamily | Glutathione synthetase ATP-binding domain-like | 8053676 | 3000094 | SCOP2B (2022-06-29) |
| A | SCOP2B Superfamily | Succinyl-CoA synthetase domain-like | 8053666 | 3000003 | SCOP2B (2022-06-29) |
| A | SCOP2B Superfamily | CoA-binding Rossmann-fold domain | 8053670 | 3000049 | SCOP2B (2022-06-29) |
| A | SCOP2B Superfamily | Succinyl-CoA synthetase domain-like | 8053668 | 3000003 | SCOP2B (2022-06-29) |
| B | SCOP2B Superfamily | Succinyl-CoA synthetase domain-like | 8053668 | 3000003 | SCOP2B (2022-06-29) |
| B | SCOP2B Superfamily | CoA-binding Rossmann-fold domain | 8053670 | 3000049 | SCOP2B (2022-06-29) |
| B | SCOP2B Superfamily | Succinyl-CoA synthetase domain-like | 8053666 | 3000003 | SCOP2B (2022-06-29) |
| B | SCOP2B Superfamily | Glutathione synthetase ATP-binding domain-like | 8053676 | 3000094 | SCOP2B (2022-06-29) |
| C | SCOP2B Superfamily | Succinyl-CoA synthetase domain-like | 8053668 | 3000003 | SCOP2B (2022-06-29) |
| C | SCOP2B Superfamily | CoA-binding Rossmann-fold domain | 8053670 | 3000049 | SCOP2B (2022-06-29) |
| C | SCOP2B Superfamily | Glutathione synthetase ATP-binding domain-like | 8053676 | 3000094 | SCOP2B (2022-06-29) |
| C | SCOP2B Superfamily | Succinyl-CoA synthetase domain-like | 8053666 | 3000003 | SCOP2B (2022-06-29) |
| D | SCOP2B Superfamily | Succinyl-CoA synthetase domain-like | 8053666 | 3000003 | SCOP2B (2022-06-29) |
| D | SCOP2B Superfamily | Succinyl-CoA synthetase domain-like | 8053668 | 3000003 | SCOP2B (2022-06-29) |
| D | SCOP2B Superfamily | CoA-binding Rossmann-fold domain | 8053670 | 3000049 | SCOP2B (2022-06-29) |
| D | SCOP2B Superfamily | Glutathione synthetase ATP-binding domain-like | 8053676 | 3000094 | SCOP2B (2022-06-29) |
| E | SCOP2B Superfamily | Succinyl-CoA synthetase domain-like | 8053668 | 3000003 | SCOP2B (2022-06-29) |
| E | SCOP2B Superfamily | Glutathione synthetase ATP-binding domain-like | 8053676 | 3000094 | SCOP2B (2022-06-29) |
| E | SCOP2B Superfamily | Succinyl-CoA synthetase domain-like | 8053666 | 3000003 | SCOP2B (2022-06-29) |
| E | SCOP2B Superfamily | CoA-binding Rossmann-fold domain | 8053670 | 3000049 | SCOP2B (2022-06-29) |
| F | SCOP2B Superfamily | Succinyl-CoA synthetase domain-like | 8053666 | 3000003 | SCOP2B (2022-06-29) |
| F | SCOP2B Superfamily | Succinyl-CoA synthetase domain-like | 8053668 | 3000003 | SCOP2B (2022-06-29) |
| F | SCOP2B Superfamily | CoA-binding Rossmann-fold domain | 8053670 | 3000049 | SCOP2B (2022-06-29) |
| F | SCOP2B Superfamily | Glutathione synthetase ATP-binding domain-like | 8053676 | 3000094 | SCOP2B (2022-06-29) |
| H | SCOP2B Superfamily | CoA-binding Rossmann-fold domain | 8053670 | 3000049 | SCOP2B (2022-06-29) |
| H | SCOP2B Superfamily | Succinyl-CoA synthetase domain-like | 8053666 | 3000003 | SCOP2B (2022-06-29) |
| H | SCOP2B Superfamily | Succinyl-CoA synthetase domain-like | 8053668 | 3000003 | SCOP2B (2022-06-29) |
| H | SCOP2B Superfamily | Glutathione synthetase ATP-binding domain-like | 8053676 | 3000094 | SCOP2B (2022-06-29) |
| G | SCOP2B Superfamily | Succinyl-CoA synthetase domain-like | 8053668 | 3000003 | SCOP2B (2022-06-29) |
| G | SCOP2B Superfamily | Succinyl-CoA synthetase domain-like | 8053666 | 3000003 | SCOP2B (2022-06-29) |
| G | SCOP2B Superfamily | CoA-binding Rossmann-fold domain | 8053670 | 3000049 | SCOP2B (2022-06-29) |
| G | SCOP2B Superfamily | Glutathione synthetase ATP-binding domain-like | 8053676 | 3000094 | SCOP2B (2022-06-29) |
Domain Annotation: ECOD Classification ECOD Database Homepage
| Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
|---|---|---|---|---|---|---|---|---|
| A | Citrate_synt | e6hxhA4 | A: alpha complex topology | X: Citrate synthase-like | H: Citrate synthase (From Topology) | T: Citrate synthase | F: Citrate_synt | ECOD (1.6) |
| A | ATP-grasp_2 | e6hxhA1 | A: a+b complex topology | X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology) | H: Protein kinase/SAICAR synthase/ATP-grasp | T: ATP-grasp | F: ATP-grasp_2 | ECOD (1.6) |
| A | CoA_binding | e6hxhA5 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Rossmann-related | T: NAD(P)-binding Rossmann-fold domains | F: CoA_binding | ECOD (1.6) |
| A | Succ_CoA_lig | e6hxhA2 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Succinyl-CoA synthetase domains (From Topology) | T: Succinyl-CoA synthetase domains | F: Succ_CoA_lig | ECOD (1.6) |
| A | Citrate_bind | e6hxhA3 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Succinyl-CoA synthetase domains (From Topology) | T: Succinyl-CoA synthetase domains | F: Citrate_bind | ECOD (1.6) |
| B | Citrate_synt | e6hxhB4 | A: alpha complex topology | X: Citrate synthase-like | H: Citrate synthase (From Topology) | T: Citrate synthase | F: Citrate_synt | ECOD (1.6) |
| B | ATP-grasp_2 | e6hxhB1 | A: a+b complex topology | X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology) | H: Protein kinase/SAICAR synthase/ATP-grasp | T: ATP-grasp | F: ATP-grasp_2 | ECOD (1.6) |
| B | CoA_binding | e6hxhB5 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Rossmann-related | T: NAD(P)-binding Rossmann-fold domains | F: CoA_binding | ECOD (1.6) |
| B | Succ_CoA_lig | e6hxhB2 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Succinyl-CoA synthetase domains (From Topology) | T: Succinyl-CoA synthetase domains | F: Succ_CoA_lig | ECOD (1.6) |
| B | Citrate_bind | e6hxhB3 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Succinyl-CoA synthetase domains (From Topology) | T: Succinyl-CoA synthetase domains | F: Citrate_bind | ECOD (1.6) |
| C | Citrate_synt | e6hxhC4 | A: alpha complex topology | X: Citrate synthase-like | H: Citrate synthase (From Topology) | T: Citrate synthase | F: Citrate_synt | ECOD (1.6) |
| C | ATP-grasp_2 | e6hxhC1 | A: a+b complex topology | X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology) | H: Protein kinase/SAICAR synthase/ATP-grasp | T: ATP-grasp | F: ATP-grasp_2 | ECOD (1.6) |
| C | CoA_binding | e6hxhC5 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Rossmann-related | T: NAD(P)-binding Rossmann-fold domains | F: CoA_binding | ECOD (1.6) |
| C | Succ_CoA_lig | e6hxhC2 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Succinyl-CoA synthetase domains (From Topology) | T: Succinyl-CoA synthetase domains | F: Succ_CoA_lig | ECOD (1.6) |
| C | Citrate_bind | e6hxhC3 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Succinyl-CoA synthetase domains (From Topology) | T: Succinyl-CoA synthetase domains | F: Citrate_bind | ECOD (1.6) |
| D | Citrate_synt | e6hxhD4 | A: alpha complex topology | X: Citrate synthase-like | H: Citrate synthase (From Topology) | T: Citrate synthase | F: Citrate_synt | ECOD (1.6) |
| D | ATP-grasp_2 | e6hxhD1 | A: a+b complex topology | X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology) | H: Protein kinase/SAICAR synthase/ATP-grasp | T: ATP-grasp | F: ATP-grasp_2 | ECOD (1.6) |
| D | CoA_binding | e6hxhD5 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Rossmann-related | T: NAD(P)-binding Rossmann-fold domains | F: CoA_binding | ECOD (1.6) |
| D | Succ_CoA_lig | e6hxhD2 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Succinyl-CoA synthetase domains (From Topology) | T: Succinyl-CoA synthetase domains | F: Succ_CoA_lig | ECOD (1.6) |
| D | Citrate_bind | e6hxhD3 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Succinyl-CoA synthetase domains (From Topology) | T: Succinyl-CoA synthetase domains | F: Citrate_bind | ECOD (1.6) |
| E | Citrate_synt | e6hxhE4 | A: alpha complex topology | X: Citrate synthase-like | H: Citrate synthase (From Topology) | T: Citrate synthase | F: Citrate_synt | ECOD (1.6) |
| E | ATP-grasp_2 | e6hxhE1 | A: a+b complex topology | X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology) | H: Protein kinase/SAICAR synthase/ATP-grasp | T: ATP-grasp | F: ATP-grasp_2 | ECOD (1.6) |
| E | CoA_binding | e6hxhE5 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Rossmann-related | T: NAD(P)-binding Rossmann-fold domains | F: CoA_binding | ECOD (1.6) |
| E | Succ_CoA_lig | e6hxhE2 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Succinyl-CoA synthetase domains (From Topology) | T: Succinyl-CoA synthetase domains | F: Succ_CoA_lig | ECOD (1.6) |
| E | Citrate_bind | e6hxhE3 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Succinyl-CoA synthetase domains (From Topology) | T: Succinyl-CoA synthetase domains | F: Citrate_bind | ECOD (1.6) |
| F | Citrate_synt | e6hxhF4 | A: alpha complex topology | X: Citrate synthase-like | H: Citrate synthase (From Topology) | T: Citrate synthase | F: Citrate_synt | ECOD (1.6) |
| F | ATP-grasp_2 | e6hxhF1 | A: a+b complex topology | X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology) | H: Protein kinase/SAICAR synthase/ATP-grasp | T: ATP-grasp | F: ATP-grasp_2 | ECOD (1.6) |
| F | CoA_binding | e6hxhF5 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Rossmann-related | T: NAD(P)-binding Rossmann-fold domains | F: CoA_binding | ECOD (1.6) |
| F | Succ_CoA_lig | e6hxhF2 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Succinyl-CoA synthetase domains (From Topology) | T: Succinyl-CoA synthetase domains | F: Succ_CoA_lig | ECOD (1.6) |
| F | Citrate_bind | e6hxhF3 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Succinyl-CoA synthetase domains (From Topology) | T: Succinyl-CoA synthetase domains | F: Citrate_bind | ECOD (1.6) |
| H | Citrate_synt | e6hxhH4 | A: alpha complex topology | X: Citrate synthase-like | H: Citrate synthase (From Topology) | T: Citrate synthase | F: Citrate_synt | ECOD (1.6) |
| H | ATP-grasp_2 | e6hxhH1 | A: a+b complex topology | X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology) | H: Protein kinase/SAICAR synthase/ATP-grasp | T: ATP-grasp | F: ATP-grasp_2 | ECOD (1.6) |
| H | CoA_binding | e6hxhH5 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Rossmann-related | T: NAD(P)-binding Rossmann-fold domains | F: CoA_binding | ECOD (1.6) |
| H | Succ_CoA_lig | e6hxhH2 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Succinyl-CoA synthetase domains (From Topology) | T: Succinyl-CoA synthetase domains | F: Succ_CoA_lig | ECOD (1.6) |
| H | Citrate_bind | e6hxhH3 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Succinyl-CoA synthetase domains (From Topology) | T: Succinyl-CoA synthetase domains | F: Citrate_bind | ECOD (1.6) |
| G | Citrate_synt | e6hxhG4 | A: alpha complex topology | X: Citrate synthase-like | H: Citrate synthase (From Topology) | T: Citrate synthase | F: Citrate_synt | ECOD (1.6) |
| G | ATP-grasp_2 | e6hxhG1 | A: a+b complex topology | X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology) | H: Protein kinase/SAICAR synthase/ATP-grasp | T: ATP-grasp | F: ATP-grasp_2 | ECOD (1.6) |
| G | CoA_binding | e6hxhG5 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Rossmann-related | T: NAD(P)-binding Rossmann-fold domains | F: CoA_binding | ECOD (1.6) |
| G | Succ_CoA_lig | e6hxhG2 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Succinyl-CoA synthetase domains (From Topology) | T: Succinyl-CoA synthetase domains | F: Succ_CoA_lig | ECOD (1.6) |
| G | Citrate_bind | e6hxhG3 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Succinyl-CoA synthetase domains (From Topology) | T: Succinyl-CoA synthetase domains | F: Citrate_bind | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
| Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
|---|---|---|---|---|---|---|
| A | 3.40.50.261 | Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | Succinyl-CoA synthetase domains | CATH (utative) |
| B | 3.40.50.261 | Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | Succinyl-CoA synthetase domains | CATH (utative) |
| C | 3.40.50.261 | Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | Succinyl-CoA synthetase domains | CATH (utative) |
| D | 3.40.50.261 | Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | Succinyl-CoA synthetase domains | CATH (utative) |
| E | 3.40.50.261 | Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | Succinyl-CoA synthetase domains | CATH (utative) |
| F | 3.40.50.261 | Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | Succinyl-CoA synthetase domains | CATH (utative) |
| H | 3.40.50.261 | Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | Succinyl-CoA synthetase domains | CATH (utative) |
| G | 3.40.50.261 | Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | Succinyl-CoA synthetase domains | CATH (utative) |
Protein Family Annotation Pfam Database Homepage
| Chains | Accession | Name | Description | Comments | Source |
|---|---|---|---|---|---|
| PF02629 | CoA binding domain (CoA_binding) | CoA binding domain | This domain has a Rossmann fold and is found in a number of proteins including succinyl CoA synthetases, malate and ATP-citrate ligases. | Domain | |
| PF00549 | CoA-ligase (Ligase_CoA) | CoA-ligase | This family includes the CoA ligases Succinyl-CoA synthetase alpha and beta chains, malate CoA ligase and ATP-citrate lyase. Some members of the family utilise ATP others use GTP. | Domain | |
| PF16114 | ATP citrate lyase citrate-binding (Citrate_bind) | ATP citrate lyase citrate-binding | This is the citrate-binding domain of ATP citrate lyase. This domain has a Rossmann fold [1]. | Domain | |
| PF00285 | Citrate synthase, C-terminal domain (Citrate_synt) | Citrate synthase, C-terminal domain | This is the long, C-terminal part of the enzyme. | Domain | |
| PF24948 | ATP-citrate synthase ATP-grasp domain (Citrate_synth_N) | ATP-citrate synthase ATP-grasp domain | The ATP-citrate synthase family is responsible for the synthesis of cytosolic acetyl-CoA, a crucial substrate for de novo lipid synthesis, including cholesterol and fatty acids. In animals, these enzymes typically have a homomeric structure, whereas ... | Domain |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
| Chains | Accession | Name | Type |
|---|---|---|---|
| IPR032263 | ATP-citrate synthase, citrate-binding domain | Domain | |
| IPR016102 | Succinyl-CoA synthetase-like | Homologous Superfamily | |
| IPR017440 | ATP-citrate lyase/succinyl-CoA ligase, active site | Active Site | |
| IPR016143 | Citrate synthase-like, small alpha subdomain | Homologous Superfamily | |
| IPR017866 | Succinyl-CoA synthetase, beta subunit, conserved site | Conserved Site | |
| IPR003781 | CoA-binding | Domain | |
| IPR036969 | Citrate synthase superfamily | Homologous Superfamily | |
| IPR005811 | ATP-citrate synthase/succinyl-CoA ligase, C-terminal domain | Domain | |
| IPR056749 | ATP-citrate synthase, ATP-grasp domain | Domain | |
| IPR014608 | ATP-citrate synthase | Family | |
| IPR033847 | ATP-citrate lyase/succinyl-CoA ligase, conserved site | Conserved Site | |
| IPR036291 | NAD(P)-binding domain superfamily | Homologous Superfamily | |
| IPR002020 | Citrate synthase | Family |














