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Asym./Biol. Unit (Jmol Viewer)

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

Authors :   R. Marmorstein, S. C. Harrison

Date :   04 Jan 95 (Deposition) - 27 Feb 95 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.20

Chains :   Asym./Biol. Unit : A,B,D,E

Keywords :   Protein-Dna Complex, Transcription/Dna Complex, Gal4, Zinc Finger, Zn2Cys6, Binuclear Cluster, Transcription Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Marmorstein, S. C. Harrison
Crystal Structure Of A Ppr1-Dna Complex: Dna Recognition By Proteins Containing A Zn2Cys6 Binuclear Cluster.
Genes Dev. V. 8 2504 1994
PubMed-ID: 7958913
(for further references see the PDB file header)

*Molecule 1 - DNA (5'- D(TPCPGPGPCPAPAPTPTPGPCPCPGPA)-3')*
	Chains	:	D, E
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - PROTEIN (PYRIMIDINE PATHWAY REGULATOR 1)
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cell	:	BL21 (PLYSS)
	Expression System Gene	:	YSCPPR1 (ACCESSION X01739)
	Expression System Plasmid	:	PRSETA
	Expression System Taxid	:	562
	Gene	:	YSCPPR1 (ACCESSION X01739)
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	D	E

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 4)

No.	Name	Count	Type	Full Name
1	ZN	4	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ZN A:22 , CYS A:34 , CYS A:51 , CYS A:54 , CYS A:61	BINDING SITE FOR RESIDUE ZN A 21
2	AC2	SOFTWARE	ZN A:21 , CYS A:34 , CYS A:37 , CYS A:44 , CYS A:51	BINDING SITE FOR RESIDUE ZN A 22
3	AC3	SOFTWARE	CYS B:34 , CYS B:51 , CYS B:54 , CYS B:61 , ZN B:322	BINDING SITE FOR RESIDUE ZN B 321
4	AC4	SOFTWARE	CYS B:34 , CYS B:37 , CYS B:44 , CYS B:51 , ZN B:321	BINDING SITE FOR RESIDUE ZN B 322

(no "SS Bond" information available for 1PYI)

Asymmetric/Biological Unit

No.	Residues
1	Phe A:48	-	Pro A:49
2	Phe B:48	-	Pro B:49

(no "SAP(SNP)/Variant" information available for 1PYI)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZN2_CY6_FUNGAL_1	PS00463	Zn(2)-C6 fungal-type DNA-binding domain signature.	PPR1_YEAST	33-61	2	A:33-61 B:33-61
2	ZN2_CY6_FUNGAL_2	PS50048	Zn(2)-C6 fungal-type DNA-binding domain profile.	PPR1_YEAST	33-63	2	A:33-63 B:33-63

Asymmetric/Biological Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YLR014C	1	YLR014C.1	XII:174981-172267	2715	PPR1_YEAST	1-904	904	2	A:30-117 B:30-99	88 70

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

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	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:88
 aligned with PPR1_YEAST | P07272 from UniProtKB/Swiss-Prot  Length:904

    Alignment length:88
                                    39        49        59        69        79        89        99       109        
           PPR1_YEAST    30 SRTACKRCRLKKIKCDQEFPSCKRCAKLEVPCVSLDPATGKDVPRSYVFFLEDRLAVMMRVLKEYGVDPTKIRGNIPATSDDEPFDLK 117
               SCOP domains d1pyia1 A:30-71 PPR1                      d1pyia2 A:72-117 PPR1                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh...........hhhhh.....eee......eeehhhhhhhhhhhhhhhhhhhh........................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---ZN2_CY6_FUNGAL_2  PDB: A:33-63 ------------------------------------------------------ PROSITE (1)
                PROSITE (2) ---ZN2_CY6_FUNGAL_1  PDB: A:33-6-------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:30-117 UniProt: 1-904 [INCOMPLETE]                                      Transcript 1
                 1pyi A  30 SRTACKRCRLKKIKCDQEFPSCKRCAKLEVPCVSLDPATGKDVPRSYVFFLEDRLAVMMRVLKEYGVDPTKIRGNIPATSDDEPFDLK 117
                                    39        49        59        69        79        89        99       109

Chain B from PDB  Type:PROTEIN  Length:70
 aligned with PPR1_YEAST | P07272 from UniProtKB/Swiss-Prot  Length:904

    Alignment length:70
                                    39        49        59        69        79        89        99
           PPR1_YEAST    30 SRTACKRCRLKKIKCDQEFPSCKRCAKLEVPCVSLDPATGKDVPRSYVFFLEDRLAVMMRVLKEYGVDPT  99
               SCOP domains d1pyib1 B:30-71 PPR1                      d1pyib2 B:72-99 PPR1         SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh...........hhhhhh..................hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---ZN2_CY6_FUNGAL_2  PDB: B:33-63 ------------------------------------ PROSITE (1)
                PROSITE (2) ---ZN2_CY6_FUNGAL_1  PDB: B:33-6-------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: B:30-99 UniProt: 1-904 [INCOMPLETE]                     Transcript 1
                 1pyi B  30 SRTACKRCRLKKIKCDQEFPSCKRCAKLEVPCVSLDPATGKDVPRSYVFFLEDRLAVMMRVLKEYGVDPT  99
                                    39        49        59        69        79        89        99

Chain D from PDB  Type:DNA  Length:14
                                              
                 1pyi D   1 TCGGCAATTGCCGA  14
                                    10

Chain E from PDB  Type:DNA  Length:14
                                              
                 1pyi E  15 TCGGCAATTGCCGA  28
                                    24

Legend:		→ Mismatch	(orange background)
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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Coiled coil proteins (689)

Fold: Parallel coiled-coil (407)

Superfamily: Leucine zipper domain (105)

Family: Leucine zipper domain (105)

Protein domain: PPR1 (1)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (1)

1a	d1pyia2	A:72-117
1b	d1pyib2	B:72-99

Class: Small proteins (3458)

Fold: Zn2/Cys6 DNA-binding domain (15)

Superfamily: Zn2/Cys6 DNA-binding domain (15)

Family: Zn2/Cys6 DNA-binding domain (15)

Protein domain: PPR1 (1)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (1)

2a	d1pyia1	A:30-71
2b	d1pyib1	B:30-71

(no "CATH Domain" information available for 1PYI)

(no "Pfam Domain" information available for 1PYI)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PPR1_YEAST | P07272)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000981	RNA polymerase II transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:1900399	positive regulation of pyrimidine nucleotide biosynthetic process	Any process that activates or increases the frequency, rate or extent of pyrimidine nucleotide biosynthetic process.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0006221	pyrimidine nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric/Biological Unit
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