1PYI | pdb_00001pyi

CRYSTAL STRUCTURE OF A PPR1-DNA COMPLEX: DNA RECOGNITION BY PROTEINS CONTAINING A ZN2CYS6 BINUCLEAR CLUSTER

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)
C [auth A]	d1pyia1	Small proteins	Zn2/Cys6 DNA-binding domain	Zn2/Cys6 DNA-binding domain	Zn2/Cys6 DNA-binding domain	PPR1	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C [auth A]	d1pyia2	Coiled coil proteins	Parallel coiled-coil	Leucine zipper domain	Leucine zipper domain	PPR1	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D [auth B]	d1pyib1	Small proteins	Zn2/Cys6 DNA-binding domain	Zn2/Cys6 DNA-binding domain	Zn2/Cys6 DNA-binding domain	PPR1	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D [auth B]	d1pyib2	Coiled coil proteins	Parallel coiled-coil	Leucine zipper domain	Leucine zipper domain	PPR1	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth A]	SCOP2 Family	Zn2/Cys6 DNA-binding domain	8026629	4003600	SCOP2 (2022-06-29)
C [auth A]	SCOP2 Family	Leucine zipper domain	8027081	4003836	SCOP2 (2022-06-29)
C [auth A]	SCOP2 Superfamily	Zn2/Cys6 DNA-binding domain	8039008	3001104	SCOP2 (2022-06-29)
C [auth A]	SCOP2 Superfamily	Leucine zipper-like	8039460	3001609	SCOP2 (2022-06-29)
D [auth B]	SCOP2B Superfamily	Zn2/Cys6 DNA-binding domain	8039008	3001104	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)
C [auth A]		e1pyiA1	A: Zn2/Cys6 DNA-binding domain	X: Zn2/Cys6 DNA-binding domain	H: Zn2/Cys6 DNA-binding domain	T: Zn_clus	F:	ECOD (20:10:01)
D [auth B]		e1pyiB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: EGF_CA	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth A]	4.10.240.10	Few Secondary Structures	Irregular	CD2-Gal4	Zn(2)-C6 fungal-type DNA-binding domain	CATH (4.3.0)
D [auth B]	4.10.240.10	Few Secondary Structures	Irregular	CD2-Gal4	Zn(2)-C6 fungal-type DNA-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A], D [auth B]	PF00172	Fungal Zn(2)-Cys(6) binuclear cluster domain (Zn_clus)	Fungal Zn(2)-Cys(6) binuclear cluster domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth A], D [auth B]	PROTEIN (PYRIMIDINE PATHWAY REGULATOR 1)	DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding sequence-specific DNA binding DNA binding nucleic acid binding	nucleoside phosphate metabolic process pyrimidine-containing compound metabolic process nucleotide biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process nucleotide metabolic process pyrimidine nucleotide metabolic process nucleobase-containing compound metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleobase-containing small molecule metabolic process nucleoside phosphate biosynthetic process phosphate-containing compound metabolic process nucleoside phosphate metabolic process pyrimidine-containing compound metabolic process nucleotide biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process nucleotide metabolic process pyrimidine nucleotide metabolic process nucleobase-containing compound metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleobase-containing small molecule metabolic process nucleoside phosphate biosynthetic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process pyrimidine-containing compound biosynthetic process phosphorus metabolic process pyrimidine nucleotide biosynthetic process regulation of cellular process positive regulation of nucleotide metabolic process positive regulation of biological process positive regulation of phosphate metabolic process positive regulation of nucleotide biosynthetic process regulation of nucleotide biosynthetic process regulation of primary metabolic process positive regulation of metabolic process regulation of small molecule metabolic process positive regulation of biosynthetic process regulation of nucleotide metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process positive regulation of pyrimidine nucleotide biosynthetic process regulation of biosynthetic process regulation of biological process positive regulation of phosphorus metabolic process regulation of pyrimidine nucleotide biosynthetic process biological regulation regulation of phosphorus metabolic process positive regulation of small molecule metabolic process regulation of metabolic process RNA metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process macromolecule metabolic process positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of macromolecule metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle
A [auth D], B [auth E]	DNA (5'-D(TPCPGPGPCPAPAPTPTPGPCPCPGPA)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], D [auth B]	IPR007219	Xylanolytic transcriptional activator, regulatory domain	Domain
C [auth A], D [auth B]	IPR036864	Zn(2)-C6 fungal-type DNA-binding domain superfamily	Homologous Superfamily
C [auth A], D [auth B]	IPR052202	Yeast_MetPath_Reg	Unknown
C [auth A], D [auth B]	IPR046347	Basic-leucine zipper domain superfamily	Homologous Superfamily
C [auth A], D [auth B]	IPR001138	Zn(2)Cys(6) fungal-type DNA-binding domain	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.