4XB6
Structure of the E. coli C-P lyase core complex
External Resource: Annotation
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Chains | Domain Info | Class | Fold | Superfamily | Family | Domain | Species | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
B | d4xb6b_ | Alpha and beta proteins (a/b) | PLP-dependent transferase-like | PhnH-like | PhnH-like | automated matches | (Escherichia coli str. K-12 substr. MG1655 ) [TaxId: 511145 ], | SCOPe (2.08) |
F | d4xb6f_ | Alpha and beta proteins (a/b) | PLP-dependent transferase-like | PhnH-like | PhnH-like | automated matches | (Escherichia coli str. K-12 substr. MG1655 ) [TaxId: 511145 ], | SCOPe (2.08) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | PF06754 | e4xb6A1 | A: a+b two layers | X: C-P lyase subunit PhnG (From Topology) | H: C-P lyase subunit PhnG (From Topology) | T: C-P lyase subunit PhnG | F: PF06754 | ECOD (1.6) |
E | PF06754 | e4xb6E1 | A: a+b two layers | X: C-P lyase subunit PhnG (From Topology) | H: C-P lyase subunit PhnG (From Topology) | T: C-P lyase subunit PhnG | F: PF06754 | ECOD (1.6) |
B | PF05845 | e4xb6B1 | A: a/b three-layered sandwiches | X: PhnH-like (From Topology) | H: PhnH-like (From Topology) | T: PhnH-like | F: PF05845 | ECOD (1.6) |
F | PF05845 | e4xb6F1 | A: a/b three-layered sandwiches | X: PhnH-like (From Topology) | H: PhnH-like (From Topology) | T: PhnH-like | F: PF05845 | ECOD (1.6) |
C | PF05861 | e4xb6C2 | A: alpha arrays | X: RuvA-C | H: C-P lyase subunit PhnI N-terminal domain (From Topology) | T: C-P lyase subunit PhnI N-terminal domain | F: PF05861 | ECOD (1.6) |
C | PF05861 | e4xb6C1 | A: a+b two layers | X: C-P lyase subunit PhnG (From Topology) | H: C-P lyase subunit PhnG (From Topology) | T: C-P lyase subunit PhnG | F: PF05861 | ECOD (1.6) |
G | PF05861 | e4xb6G2 | A: alpha arrays | X: RuvA-C | H: C-P lyase subunit PhnI N-terminal domain (From Topology) | T: C-P lyase subunit PhnI N-terminal domain | F: PF05861 | ECOD (1.6) |
G | PF05861 | e4xb6G1 | A: a+b two layers | X: C-P lyase subunit PhnG (From Topology) | H: C-P lyase subunit PhnG (From Topology) | T: C-P lyase subunit PhnG | F: PF05861 | ECOD (1.6) |
D | PF06007 | e4xb6D1 | A: a/b three-layered sandwiches | X: PhnH-like (From Topology) | H: PhnH-like (From Topology) | T: PhnH-like | F: PF06007 | ECOD (1.6) |
D | PF06007 | e4xb6D2 | A: few secondary structure elements | X: C-P lyase subunit PhnJ C-terminal Zn-binding domain (From Topology) | H: C-P lyase subunit PhnJ C-terminal Zn-binding domain (From Topology) | T: C-P lyase subunit PhnJ C-terminal Zn-binding domain | F: PF06007 | ECOD (1.6) |
H | PF06007 | e4xb6H2 | A: a/b three-layered sandwiches | X: PhnH-like (From Topology) | H: PhnH-like (From Topology) | T: PhnH-like | F: PF06007 | ECOD (1.6) |
H | PF06007 | e4xb6H1 | A: few secondary structure elements | X: C-P lyase subunit PhnJ C-terminal Zn-binding domain (From Topology) | H: C-P lyase subunit PhnJ C-terminal Zn-binding domain (From Topology) | T: C-P lyase subunit PhnJ C-terminal Zn-binding domain | F: PF06007 | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
B | 3.40.50.11310 | Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | Bacterial phosphonate metabolism protein PhnH | CATH (4.3.0) |
F | 3.40.50.11310 | Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | Bacterial phosphonate metabolism protein PhnH | CATH (4.3.0) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF06754 | Phosphonate metabolism protein PhnG (PhnG) | Phosphonate metabolism protein PhnG | - | Family | |
PF05845 | Bacterial phosphonate metabolism protein (PhnH) (PhnH) | Bacterial phosphonate metabolism protein (PhnH) | - | Family | |
PF05861 | Bacterial phosphonate metabolism protein (PhnI) (PhnI) | Bacterial phosphonate metabolism protein (PhnI) | - | Family | |
PF06007 | Phosphonate metabolism protein PhnJ (PhnJ) | Phosphonate metabolism protein PhnJ | - | Family |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR009609 | Phosphonate metabolism PhnG | Family | |
IPR038058 | PhnH-like superfamily | Homologous Superfamily | |
IPR008772 | Bacterial phosphonate metabolism, PhnH | Family | |
IPR008773 | Phosphonate metabolism protein PhnI | Family | |
IPR010306 | Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase | Family |
Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage
Chains | Enzyme Name | Description | Catalytic Residues |
---|---|---|---|
alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase M-CSA #949 | This radical SAM (AdoMet) enzyme is part of the C-P lyase complex, which is responsible for processing phophonates into usable phosphate. The enzyme from the bacterium Escherichia coli can act on additional alpha-D-ribose phosphonate substrates with different substituents attached to the phosphonate phosphorus (e.g. alpha-D-ribose-1- (N-(phosphonomethyl)glycine)-5-phosphate and alpha-D-ribose-1-(2-N- acetamidomethylphosphonate)-5-phosphate). | Defined by 5 residues: GLY:D-32CYS:D-241CYS:D-244CYS:D-266CYS:D-272 | EC: 4.7.1.1 (PDB Primary Data) |