4V4E | pdb_00004v4e

Crystal Structure of Pyrogallol-Phloroglucinol Transhydroxylase from Pelobacter acidigallici complexed with inhibitor 1,2,4,5-tetrahydroxy-benzene

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
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)
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)
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)
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)
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)
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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	TAFII55_N	e4v4eA1	A: alpha bundles	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: TAFII55_N	ECOD (develop294)
W	Adeno_Penton_B	e4v4eW2	A: alpha bundles	X: Type III secretion system domain-like	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Antibiotic binding domain of TipA-like multidrug resistance regulators	F: Adeno_Penton_B	ECOD (develop294)
W	YkuD	e4v4eW3	A: alpha bundles	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: YkuD	ECOD (develop294)
U	Adeno_Penton_B	e4v4eU2	A: alpha bundles	X: Type III secretion system domain-like	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Antibiotic binding domain of TipA-like multidrug resistance regulators	F: Adeno_Penton_B	ECOD (develop294)
U	YkuD	e4v4eU3	A: alpha bundles	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: YkuD	ECOD (develop294)
S	Adeno_Penton_B	e4v4eS2	A: alpha bundles	X: Type III secretion system domain-like	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Antibiotic binding domain of TipA-like multidrug resistance regulators	F: Adeno_Penton_B	ECOD (develop294)
S	YkuD	e4v4eS3	A: alpha bundles	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: YkuD	ECOD (develop294)
Q	Adeno_Penton_B	e4v4eQ2	A: alpha bundles	X: Type III secretion system domain-like	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Antibiotic binding domain of TipA-like multidrug resistance regulators	F: Adeno_Penton_B	ECOD (develop294)
Q	YkuD	e4v4eQ3	A: alpha bundles	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: YkuD	ECOD (develop294)
O	Adeno_Penton_B	e4v4eO2	A: alpha bundles	X: Type III secretion system domain-like	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Antibiotic binding domain of TipA-like multidrug resistance regulators	F: Adeno_Penton_B	ECOD (develop294)
O	YkuD	e4v4eO3	A: alpha bundles	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: YkuD	ECOD (develop294)
M	Molydop_binding	e4v4eM1	A: alpha bundles	X: ssDNA-binding transcriptional regulator domain-like	H: ssDNA-binding transcriptional regulator domain	T: ssDNA-binding transcriptional regulator domain	F: Molydop_binding	ECOD (develop294)
M	Molybdopterin	e4v4eM2	A: alpha bundles	X: ssDNA-binding transcriptional regulator domain-like	H: ssDNA-binding transcriptional regulator domain	T: ssDNA-binding transcriptional regulator domain	F: Molybdopterin	ECOD (develop294)
K	Adeno_Penton_B	e4v4eK2	A: alpha bundles	X: Type III secretion system domain-like	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Antibiotic binding domain of TipA-like multidrug resistance regulators	F: Adeno_Penton_B	ECOD (develop294)
K	YkuD	e4v4eK3	A: alpha bundles	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: YkuD	ECOD (develop294)
I	TAFII55_N	e4v4eI1	A: alpha bundles	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: TAFII55_N	ECOD (develop294)
G	TAFII55_N	e4v4eG1	A: alpha bundles	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: TAFII55_N	ECOD (develop294)
E	Adeno_Penton_B	e4v4eE2	A: alpha bundles	X: Type III secretion system domain-like	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Antibiotic binding domain of TipA-like multidrug resistance regulators	F: Adeno_Penton_B	ECOD (develop294)
E	LRR_8	e4v4eE3	A: alpha bundles	X: Hsp90 co-chaperone CDC37 middle domain	H: Lysozyme-like	T: Lysozyme-like	F: LRR_8	ECOD (develop294)
C	Adeno_Penton_B	e4v4eC2	A: alpha bundles	X: Type III secretion system domain-like	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Antibiotic binding domain of TipA-like multidrug resistance regulators	F: Adeno_Penton_B	ECOD (develop294)
C	YkuD	e4v4eC3	A: alpha bundles	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: YkuD	ECOD (develop294)
B	Adeno_Penton_B	e4v4eB1	A: alpha bundles	X: Type III secretion system domain-like	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Antibiotic binding domain of TipA-like multidrug resistance regulators	F: Adeno_Penton_B	ECOD (develop294)
L	Adeno_Penton_B	e4v4eL1	A: alpha bundles	X: Type III secretion system domain-like	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Antibiotic binding domain of TipA-like multidrug resistance regulators	F: Adeno_Penton_B	ECOD (develop294)
P	Adeno_Penton_B	e4v4eP1	A: alpha bundles	X: Type III secretion system domain-like	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Antibiotic binding domain of TipA-like multidrug resistance regulators	F: Adeno_Penton_B	ECOD (develop294)
X	Adeno_Penton_B	e4v4eX1	A: alpha bundles	X: Type III secretion system domain-like	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Antibiotic binding domain of TipA-like multidrug resistance regulators	F: Adeno_Penton_B	ECOD (develop294)
V	Adeno_Penton_B	e4v4eV1	A: alpha bundles	X: Type III secretion system domain-like	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Antibiotic binding domain of TipA-like multidrug resistance regulators	F: Adeno_Penton_B	ECOD (develop294)
T	Adeno_Penton_B	e4v4eT1	A: alpha bundles	X: Type III secretion system domain-like	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Antibiotic binding domain of TipA-like multidrug resistance regulators	F: Adeno_Penton_B	ECOD (develop294)
R	Adeno_Penton_B	e4v4eR1	A: alpha bundles	X: Type III secretion system domain-like	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Antibiotic binding domain of TipA-like multidrug resistance regulators	F: Adeno_Penton_B	ECOD (develop294)
N	Adeno_Penton_B	e4v4eN1	A: alpha bundles	X: Type III secretion system domain-like	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Antibiotic binding domain of TipA-like multidrug resistance regulators	F: Adeno_Penton_B	ECOD (develop294)
J	Adeno_Penton_B	e4v4eJ1	A: alpha bundles	X: Type III secretion system domain-like	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Antibiotic binding domain of TipA-like multidrug resistance regulators	F: Adeno_Penton_B	ECOD (develop294)
H	Adeno_Penton_B	e4v4eH1	A: alpha bundles	X: Type III secretion system domain-like	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Antibiotic binding domain of TipA-like multidrug resistance regulators	F: Adeno_Penton_B	ECOD (develop294)
F	Adeno_Penton_B	e4v4eF1	A: alpha bundles	X: Type III secretion system domain-like	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Antibiotic binding domain of TipA-like multidrug resistance regulators	F: Adeno_Penton_B	ECOD (develop294)
D	Adeno_Penton_B	e4v4eD1	A: alpha bundles	X: Type III secretion system domain-like	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Antibiotic binding domain of TipA-like multidrug resistance regulators	F: Adeno_Penton_B	ECOD (develop294)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G, I A, C, E, G, I, K, M, O, Q, S, U, W	Pyrogallol hydroxytransferase large subunit	cation binding transition metal ion binding molybdenum ion binding ion binding binding metal ion binding small molecule binding molybdopterin cofactor binding oxidoreductase activity pyrogallol hydroxytransferase activity catalytic activity electron transfer activity	cellular respiration energy derivation by oxidation of organic compounds metabolic process cellular process generation of precursor metabolites and energy anaerobic respiration	cellular anatomical structure outer membrane-bounded periplasmic space cell envelope periplasmic space
B, D, F, H, J B, D, F, H, J, L, N, P, R, T, V, X	Pyrogallol hydroxytransferase small subunit	oxidoreductase activity pyrogallol hydroxytransferase activity catalytic activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G, I A, C, E, G, I, K, M, O, Q, S, U, W	IPR050612	Prokaryotic Molybdopterin Oxidoreductases	Family
A, C, E, G, I A, C, E, G, I, K, M, O, Q, S, U, W	IPR006657	Molybdopterin dinucleotide-binding domain	Domain
A, C, E, G, I A, C, E, G, I, K, M, O, Q, S, U, W	IPR049032	Pyrogallol hydroxytransferase large subunit-like, N-terminal domain	Domain
A, C, E, G, I A, C, E, G, I, K, M, O, Q, S, U, W	IPR006656	Molybdopterin oxidoreductase	Domain
A, C, E, G, I A, C, E, G, I, K, M, O, Q, S, U, W	IPR009010	Aspartate decarboxylase-like domain superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L, N, P, R, T, V, X	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L, N, P, R, T, V, X	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
B, D, F, H, J B, D, F, H, J, L, N, P, R, T, V, X	IPR050954	Electron transfer iron-sulfur cluster-binding protein	Family

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	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.	Defined by 3 residues: HIS:A-144ASP:A-174TYR:A-404 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.97.1.2 (PDB Primary Data) Search M-CSA Motif + EC 1.97.1.2

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

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