Crystal Structure of Pyrogallol-Phloroglucinol Transhydroxylase from Pelobacter acidigallici complexed with inhibitor 1,2,4,5-tetrahydroxy-benzene
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
| Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
|---|---|---|---|---|---|
| B | SCOP2B Superfamily | Cna B-type domain-like | 8041466 | 3000862 | SCOP2B (2022-06-29) |
| B | SCOP2B Superfamily | 4Fe-4S ferredoxins | 8041469 | 3000020 | SCOP2B (2022-06-29) |
| X | SCOP2B Superfamily | Cna B-type domain-like | 8041466 | 3000862 | SCOP2B (2022-06-29) |
| X | SCOP2B Superfamily | 4Fe-4S ferredoxins | 8041469 | 3000020 | SCOP2B (2022-06-29) |
| V | SCOP2B Superfamily | Cna B-type domain-like | 8041466 | 3000862 | SCOP2B (2022-06-29) |
| V | SCOP2B Superfamily | 4Fe-4S ferredoxins | 8041469 | 3000020 | SCOP2B (2022-06-29) |
| T | SCOP2B Superfamily | Cna B-type domain-like | 8041466 | 3000862 | SCOP2B (2022-06-29) |
| T | SCOP2B Superfamily | 4Fe-4S ferredoxins | 8041469 | 3000020 | SCOP2B (2022-06-29) |
| R | SCOP2B Superfamily | Cna B-type domain-like | 8041466 | 3000862 | SCOP2B (2022-06-29) |
| R | SCOP2B Superfamily | 4Fe-4S ferredoxins | 8041469 | 3000020 | SCOP2B (2022-06-29) |
| P | SCOP2B Superfamily | 4Fe-4S ferredoxins | 8041469 | 3000020 | SCOP2B (2022-06-29) |
| P | SCOP2B Superfamily | Cna B-type domain-like | 8041466 | 3000862 | SCOP2B (2022-06-29) |
| N | SCOP2 Family | Cna B-type domain-like | 8029087 | 4002132 | SCOP2 (2022-06-29) |
| N | SCOP2 Family | Ferredoxin domains from multidomain proteins | 8029090 | 4000021 | SCOP2 (2022-06-29) |
| N | SCOP2 Superfamily | Cna B-type domain-like | 8041466 | 3000862 | SCOP2 (2022-06-29) |
| N | SCOP2 Superfamily | 4Fe-4S ferredoxins | 8041469 | 3000020 | SCOP2 (2022-06-29) |
| L | SCOP2B Superfamily | 4Fe-4S ferredoxins | 8041469 | 3000020 | SCOP2B (2022-06-29) |
| L | SCOP2B Superfamily | Cna B-type domain-like | 8041466 | 3000862 | SCOP2B (2022-06-29) |
| J | SCOP2B Superfamily | 4Fe-4S ferredoxins | 8041469 | 3000020 | SCOP2B (2022-06-29) |
| J | SCOP2B Superfamily | Cna B-type domain-like | 8041466 | 3000862 | SCOP2B (2022-06-29) |
| H | SCOP2B Superfamily | 4Fe-4S ferredoxins | 8041469 | 3000020 | SCOP2B (2022-06-29) |
| H | SCOP2B Superfamily | Cna B-type domain-like | 8041466 | 3000862 | SCOP2B (2022-06-29) |
| F | SCOP2B Superfamily | Cna B-type domain-like | 8041466 | 3000862 | SCOP2B (2022-06-29) |
| F | SCOP2B Superfamily | 4Fe-4S ferredoxins | 8041469 | 3000020 | SCOP2B (2022-06-29) |
| D | SCOP2B Superfamily | Cna B-type domain-like | 8041466 | 3000862 | SCOP2B (2022-06-29) |
| D | SCOP2B Superfamily | 4Fe-4S ferredoxins | 8041469 | 3000020 | SCOP2B (2022-06-29) |
| A | SCOP2B Superfamily | Formate dehydrogenase/DMSO reductase, domains 1-3 | 8041464 | 3001453 | SCOP2B (2022-06-29) |
| A | SCOP2B Superfamily | ADC-like | 8041462 | 3001132 | SCOP2B (2022-06-29) |
| W | SCOP2B Superfamily | ADC-like | 8041462 | 3001132 | SCOP2B (2022-06-29) |
| W | SCOP2B Superfamily | Formate dehydrogenase/DMSO reductase, domains 1-3 | 8041464 | 3001453 | SCOP2B (2022-06-29) |
| U | SCOP2B Superfamily | ADC-like | 8041462 | 3001132 | SCOP2B (2022-06-29) |
| U | SCOP2B Superfamily | Formate dehydrogenase/DMSO reductase, domains 1-3 | 8041464 | 3001453 | SCOP2B (2022-06-29) |
| S | SCOP2B Superfamily | Formate dehydrogenase/DMSO reductase, domains 1-3 | 8041464 | 3001453 | SCOP2B (2022-06-29) |
| S | SCOP2B Superfamily | ADC-like | 8041462 | 3001132 | SCOP2B (2022-06-29) |
| Q | SCOP2B Superfamily | Formate dehydrogenase/DMSO reductase, domains 1-3 | 8041464 | 3001453 | SCOP2B (2022-06-29) |
| Q | SCOP2B Superfamily | ADC-like | 8041462 | 3001132 | SCOP2B (2022-06-29) |
| O | SCOP2B Superfamily | ADC-like | 8041462 | 3001132 | SCOP2B (2022-06-29) |
| O | SCOP2B Superfamily | Formate dehydrogenase/DMSO reductase, domains 1-3 | 8041464 | 3001453 | SCOP2B (2022-06-29) |
| M | SCOP2 Family | Formate dehydrogenase/DMSO reductase, C-terminal domain | 8029083 | 4002360 | SCOP2 (2022-06-29) |
| M | SCOP2 Family | Formate dehydrogenase/DMSO reductase, domains 1-3 | 8029085 | 4000801 | SCOP2 (2022-06-29) |
| M | SCOP2 Superfamily | ADC-like | 8041462 | 3001132 | SCOP2 (2022-06-29) |
| M | SCOP2 Superfamily | Formate dehydrogenase/DMSO reductase, domains 1-3 | 8041464 | 3001453 | SCOP2 (2022-06-29) |
| K | SCOP2B Superfamily | ADC-like | 8041462 | 3001132 | SCOP2B (2022-06-29) |
| K | SCOP2B Superfamily | Formate dehydrogenase/DMSO reductase, domains 1-3 | 8041464 | 3001453 | SCOP2B (2022-06-29) |
| I | SCOP2B Superfamily | ADC-like | 8041462 | 3001132 | SCOP2B (2022-06-29) |
| I | SCOP2B Superfamily | Formate dehydrogenase/DMSO reductase, domains 1-3 | 8041464 | 3001453 | SCOP2B (2022-06-29) |
| G | SCOP2B Superfamily | ADC-like | 8041462 | 3001132 | SCOP2B (2022-06-29) |
| G | SCOP2B Superfamily | Formate dehydrogenase/DMSO reductase, domains 1-3 | 8041464 | 3001453 | SCOP2B (2022-06-29) |
| E | SCOP2B Superfamily | ADC-like | 8041462 | 3001132 | SCOP2B (2022-06-29) |
| E | SCOP2B Superfamily | Formate dehydrogenase/DMSO reductase, domains 1-3 | 8041464 | 3001453 | SCOP2B (2022-06-29) |
| C | SCOP2B Superfamily | Formate dehydrogenase/DMSO reductase, domains 1-3 | 8041464 | 3001453 | SCOP2B (2022-06-29) |
| C | SCOP2B Superfamily | ADC-like | 8041462 | 3001132 | 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) |
|---|---|---|---|---|---|---|---|---|
| B | P22_portal | e4v4eB1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| X | P22_portal | e4v4eX1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| V | P22_portal | e4v4eV1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| T | P22_portal | e4v4eT1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| R | P22_portal | e4v4eR1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| P | P22_portal | e4v4eP1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| N | P22_portal | e4v4eN1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| L | P22_portal | e4v4eL1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| J | P22_portal | e4v4eJ1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| H | P22_portal | e4v4eH1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| F | P22_portal | e4v4eF1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| D | P22_portal | e4v4eD1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| A | TAFII55_N | e4v4eA1 | A: alpha arrays | X: omega toxin-like | H: HTH | T: Three-helical HTH | F: TAFII55_N | ECOD (v295) |
| W | P22_portal | e4v4eW2 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| W | YkuD | e4v4eW3 | A: alpha arrays | X: Cytidine deaminase-like | H: KorB C-terminal domain | T: KorB C-terminal domain | F: YkuD | ECOD (v295) |
| U | P22_portal | e4v4eU2 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| U | YkuD | e4v4eU3 | A: alpha arrays | X: Cytidine deaminase-like | H: KorB C-terminal domain | T: KorB C-terminal domain | F: YkuD | ECOD (v295) |
| S | P22_portal | e4v4eS2 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| S | YkuD | e4v4eS3 | A: alpha arrays | X: Cytidine deaminase-like | H: KorB C-terminal domain | T: KorB C-terminal domain | F: YkuD | ECOD (v295) |
| Q | P22_portal | e4v4eQ2 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| Q | YkuD | e4v4eQ3 | A: alpha arrays | X: Cytidine deaminase-like | H: KorB C-terminal domain | T: KorB C-terminal domain | F: YkuD | ECOD (v295) |
| O | P22_portal | e4v4eO2 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| O | YkuD | e4v4eO3 | A: alpha arrays | X: Cytidine deaminase-like | H: KorB C-terminal domain | T: KorB C-terminal domain | F: YkuD | ECOD (v295) |
| M | Molydop_binding | e4v4eM1 | A: alpha arrays | X: ssDNA-binding transcriptional regulator domain-like | H: ssDNA-binding transcriptional regulator domain | T: ssDNA-binding transcriptional regulator domain | F: Molydop_binding | ECOD (v295) |
| M | Molybdopterin | e4v4eM2 | A: alpha arrays | X: ssDNA-binding transcriptional regulator domain-like | H: ssDNA-binding transcriptional regulator domain | T: ssDNA-binding transcriptional regulator domain | F: Molybdopterin | ECOD (v295) |
| K | P22_portal | e4v4eK2 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| K | YkuD | e4v4eK3 | A: alpha arrays | X: Cytidine deaminase-like | H: KorB C-terminal domain | T: KorB C-terminal domain | F: YkuD | ECOD (v295) |
| I | TAFII55_N | e4v4eI1 | A: alpha arrays | X: omega toxin-like | H: HTH | T: Three-helical HTH | F: TAFII55_N | ECOD (v295) |
| G | TAFII55_N | e4v4eG1 | A: alpha arrays | X: omega toxin-like | H: HTH | T: Three-helical HTH | F: TAFII55_N | ECOD (v295) |
| E | P22_portal | e4v4eE2 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| E | LRR_8 | e4v4eE3 | A: alpha arrays | X: Hsp90 co-chaperone CDC37 middle domain | H: Lysozyme-like | T: Lysozyme-like | F: LRR_8 | ECOD (v295) |
| C | P22_portal | e4v4eC2 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| C | YkuD | e4v4eC3 | A: alpha arrays | X: Cytidine deaminase-like | H: KorB C-terminal domain | T: KorB C-terminal domain | F: YkuD | ECOD (v295) |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
| Chains | Polymer | Molecular Function | Biological Process | Cellular Component |
|---|---|---|---|---|
| Pyrogallol hydroxytransferase small subunit | - | - | ||
| Pyrogallol hydroxytransferase large subunit |
InterPro: Protein Family Classification InterPro Database Homepage
| Chains | Accession | Name | Type |
|---|---|---|---|
| IPR013783 | Immunoglobulin-like fold | Homologous Superfamily | |
| IPR017896 | 4Fe-4S ferredoxin-type, iron-sulphur binding domain | Domain | |
| IPR050954 | Electron transfer iron-sulfur cluster-binding protein | Family | |
| IPR050612 | Prokaryotic Molybdopterin Oxidoreductases | Family | |
| IPR006657 | Molybdopterin dinucleotide-binding domain | Domain | |
| IPR049032 | Pyrogallol hydroxytransferase large subunit-like, N-terminal domain | Domain | |
| IPR006656 | Molybdopterin oxidoreductase | Domain | |
| IPR009010 | Aspartate decarboxylase-like domain superfamily | Homologous Superfamily |
Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage
| Chains | Enzyme Name | Description | Catalytic Residues |
|---|---|---|---|
| pyrogallol hydroxytransferase M-CSA #146 | The Mo enzyme pyrogallol-phloroglucinol transhydroxylase (TH) from the anaerobic microorganism Pelobacter acidigallici catalyses the conversion of pyrogallol to phloroglucinol. Such trihydroxybenzenes and their derivatives represent important building blocks of plant polymers. The overall reaction appears as transfer of the 2-hydroxy group of 1,2,3,5-tetrahydroxybenzene to the C5 position of pyrogallol (systematic name 1,2,3-trihydroxybenzene). This converts pyrogallol into 1,2,3,5-tetrahydroxybenzene, and 1,2,3,5-tetrahydroxybenzene into phloroglucinol (systematic name 1,3,5-trihydroxybenzene). Therefore, the net reaction consumes no 1,2,3,5-tetrahydroxybenzene. TH is cytoplasmic and consists of a large alpha subunit and a small beta subunit. The beta subunit contains several Fe-S clusters, which have no known function and may be evolutionary relics. This subunit also has a fibronectin-like domain which can be used for membrane association. The alpha subunit contain the Mo-binding site (with Mo coordinated to two molybdopterin guanine dinucleotide (MGD) cofactors) and the catalytic active site. Like other members of the DMSO-reducing enzyme family, Mo cycles between +4 and +6 oxidation states for catalytic activity. | EC: 1.97.1.2 (PDB Primary Data) |














