4UHP | pdb_00004uhp

Crystal structure of the pyocin AP41 DNase-Immunity complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
H	d4uhph1	All alpha proteins	Acyl carrier protein-like	Colicin E immunity proteins	automated matches	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
H	d4uhph2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
F	d4uhpf1	All alpha proteins	Acyl carrier protein-like	Colicin E immunity proteins	automated matches	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
F	d4uhpf2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
D	d4uhpd_	All alpha proteins	Acyl carrier protein-like	Colicin E immunity proteins	automated matches	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
B	d4uhpb_	All alpha proteins	Acyl carrier protein-like	Colicin E immunity proteins	automated matches	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
G	d4uhpg_	Alpha and beta proteins (a+b)	His-Me finger endonucleases	His-Me finger endonucleases	automated matches	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
E	d4uhpe_	Alpha and beta proteins (a+b)	His-Me finger endonucleases	His-Me finger endonucleases	automated matches	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
C	d4uhpc_	Alpha and beta proteins (a+b)	His-Me finger endonucleases	His-Me finger endonucleases	automated matches	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
A	d4uhpa_	Alpha and beta proteins (a+b)	His-Me finger endonucleases	His-Me finger endonucleases	automated matches	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	Colicin E immunity proteins	8074108	3001814	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Colicin E immunity proteins	8074108	3001814	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Colicin E immunity proteins	8074108	3001814	SCOP2B (2022-06-29)
B	SCOP2 Family	Colicin E immunity proteins	8074107	4000862	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Colicin E immunity proteins	8074108	3001814	SCOP2 (2022-06-29)
G	SCOP2B Superfamily	His-Me finger endonucleases	8074116	3001893	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	His-Me finger endonucleases	8074116	3001893	SCOP2B (2022-06-29)
C	SCOP2 Family	HNH-motif	8074115	4000889	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	His-Me finger endonucleases	8074116	3001893	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	His-Me finger endonucleases	8074116	3001893	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)
H	Colicin_Pyocin	e4uhpH1	A: alpha bundles	X: ACP-like	H: Colicin E immunity proteins (From Topology)	T: Colicin E immunity proteins	F: Colicin_Pyocin	ECOD (1.6)
F	Colicin_Pyocin	e4uhpF1	A: alpha bundles	X: ACP-like	H: Colicin E immunity proteins (From Topology)	T: Colicin E immunity proteins	F: Colicin_Pyocin	ECOD (1.6)
D	Colicin_Pyocin	e4uhpD1	A: alpha bundles	X: ACP-like	H: Colicin E immunity proteins (From Topology)	T: Colicin E immunity proteins	F: Colicin_Pyocin	ECOD (1.6)
B	Colicin_Pyocin	e4uhpB1	A: alpha bundles	X: ACP-like	H: Colicin E immunity proteins (From Topology)	T: Colicin E immunity proteins	F: Colicin_Pyocin	ECOD (1.6)
G	LHH	e4uhpG1	A: few secondary structure elements	X: His-Me finger endonucleases (From Homology)	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: LHH	ECOD (1.6)
E	LHH	e4uhpE1	A: few secondary structure elements	X: His-Me finger endonucleases (From Homology)	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: LHH	ECOD (1.6)
C	LHH	e4uhpC1	A: few secondary structure elements	X: His-Me finger endonucleases (From Homology)	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: LHH	ECOD (1.6)
A	LHH	e4uhpA1	A: few secondary structure elements	X: His-Me finger endonucleases (From Homology)	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: LHH	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	1.10.1200.20	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)
F	1.10.1200.20	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)
D	1.10.1200.20	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)
B	1.10.1200.20	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)
G	3.90.540.10	Alpha Beta	Alpha-Beta Complex	Colicin E7 immunity protein	Chain B, fragment: Endonuclease domain	CATH (4.3.0)
E	3.90.540.10	Alpha Beta	Alpha-Beta Complex	Colicin E7 immunity protein	Chain B, fragment: Endonuclease domain	CATH (4.3.0)
C	3.90.540.10	Alpha Beta	Alpha-Beta Complex	Colicin E7 immunity protein	Chain B, fragment: Endonuclease domain	CATH (4.3.0)
A	3.90.540.10	Alpha Beta	Alpha-Beta Complex	Colicin E7 immunity protein	Chain B, fragment: Endonuclease domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H	PF01320	Colicin immunity protein / pyocin immunity protein (Colicin_Pyocin)	Colicin immunity protein / pyocin immunity protein		Domain
A, C, E, G	PF21431	Colicin/Pyocin-S2, DNase domain (Col-Pyo_DNase)	Colicin/Pyocin-S2, DNase domain	This entry represents the DNAse domain from colicin/pyocin bacteriocins, such as pyocin-S2 from Pseudomonas aeruginosa and colicin E7/E9 from E. coli. This domain has an alpha/beta fold containing a Zn2+ ion binding site [1-5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H	BACTERIOCIN IMMUNITY PROTEIN	binding toxic substance binding	metabolic process cellular process bacteriocin immunity toxin metabolic process secondary metabolic process	-
A, C, E, G	LARGE COMPONENT OF PYOCIN AP41	hydrolase activity catalytic activity protein binding binding signaling receptor binding endonuclease activity nuclease activity catalytic activity, acting on a nucleic acid	defense response to bacterium biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus cellular process cytolysis disruption of cell in another organism disruption of anatomical structure in another organism defense response to bacterium biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus cellular process cytolysis disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H	IPR000290	Colicin immunity protein/pyocin immunity protein	Family
B, D, F, H	IPR035900	Colicin E immunity protein superfamily	Homologous Superfamily
A, C, E, G	IPR016128	Pyosin/cloacin translocation domain	Domain
A, C, E, G	IPR036302	Pyosin/cloacin translocation domain superfamily	Homologous Superfamily
A, C, E, G	IPR037146	Colicin/pyocin, DNase domain superfamily	Homologous Superfamily
A, C, E, G	IPR003060	Pyocin S killer protein	Family
A, C, E, G	IPR044925	His-Me finger superfamily	Homologous Superfamily
A, C, E, G	IPR003615	HNH nuclease	Domain

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.