1ZME | pdb_00001zme

CRYSTAL STRUCTURE OF PUT3/DNA 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)
C	d1zmec1	Small proteins	Zn2/Cys6 DNA-binding domain	Zn2/Cys6 DNA-binding domain	Zn2/Cys6 DNA-binding domain	PUT3	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d1zmec2	Coiled coil proteins	Parallel coiled-coil	Leucine zipper domain	Leucine zipper domain	PUT3	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D	d1zmed1	Small proteins	Zn2/Cys6 DNA-binding domain	Zn2/Cys6 DNA-binding domain	Zn2/Cys6 DNA-binding domain	PUT3	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D	d1zmed2	Coiled coil proteins	Parallel coiled-coil	Leucine zipper domain	Leucine zipper domain	PUT3	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	SCOP2 Family	Zn2/Cys6 DNA-binding domain	8026632	4003600	SCOP2 (2022-06-29)
C	SCOP2 Family	Leucine zipper domain	8027082	4003836	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Zn2/Cys6 DNA-binding domain	8039011	3001104	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Leucine zipper-like	8039461	3001609	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Zn2/Cys6 DNA-binding domain	8039011	3001104	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Leucine zipper-like	8039461	3001609	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	Zn_clus	e1zmeC1	A: few secondary structure elements	X: Zn2/Cys6 DNA-binding domain	H: Zn2/Cys6 DNA-binding domain	T: Zn2/Cys6 DNA-binding domain	F: Zn_clus	ECOD (v294.1)
D	V_ATPase_I	e1zmeD1	A: a/b three-layered sandwiches	X: Alpha-beta plaits	H: Pseudouridine synthase	T: Pseudouridine synthase	F: V_ATPase_I	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	4.10.240.10	Few Secondary Structures	Irregular	CD2-Gal4	Zn(2)-C6 fungal-type DNA-binding domain	CATH (4.3.0)
C	1.20.5.460	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Single helix bin	CATH (4.3.0)
D	4.10.240.10	Few Secondary Structures	Irregular	CD2-Gal4	Zn(2)-C6 fungal-type DNA-binding domain	CATH (4.3.0)
D	1.20.5.460	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Single helix bin	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D	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, D	PROLINE UTILIZATION TRANSCRIPTION ACTIVATOR	DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding cation binding transition metal ion binding zinc ion binding DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity	oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process alpha-amino acid metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process L-proline metabolic process metabolic process cellular process small molecule metabolic process cellular component organization organelle organization oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process alpha-amino acid metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process L-proline metabolic process metabolic process cellular process small molecule metabolic process cellular component organization organelle organization chromosome organization cellular component organization or biogenesis transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery regulation of cellular process catabolic process L-proline catabolic process positive regulation of biological process organic acid catabolic process regulation of primary metabolic process positive regulation of metabolic process regulation of small molecule metabolic process carboxylic acid catabolic process regulation of amino acid metabolic process amino acid catabolic process positive regulation of cellular process regulation of L-proline catabolic process regulation of biological process biological regulation L-amino acid catabolic process regulation of catabolic process positive regulation of amino acid metabolic process positive regulation of catabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process positive regulation of L-proline catabolic process positive regulation of small molecule metabolic process small molecule catabolic process regulation of metabolic process RNA metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process 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 biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of 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
B	DNA (5'-D(APCPGPGPAPGP(5IU)PTPGPGPCPTP(5IU)PCPCPCP*G)-3')	-	-	-
A	DNA (5'-D(APCPGPGPGPAPAPGPCPCPAPAPCPTPCPCP*G)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR007219	Xylanolytic transcriptional activator, regulatory domain	Domain
C, D	IPR036864	Zn(2)-C6 fungal-type DNA-binding domain superfamily	Homologous Superfamily
C, D	IPR046347	Basic-leucine zipper domain superfamily	Homologous Superfamily
C, D	IPR001138	Zn(2)Cys(6) fungal-type DNA-binding domain	Domain
C, D	IPR051127	Fungal secondary metabolite regulators	Family

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.