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Title :   STRUCTURAL BASIS FOR DIMERIZATION IN DNA RECOGNITION BY GAL4

Authors :   M. Hong, M. X. Fitzgerald, S. Harper, C. Luo, D. W. Speicher

Date :   29 Mar 08 (Deposition) - 01 Jul 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Helix Bundle, Protein-Dna Complex, Zinc Binuclear Cluster, Activator, Carbohydrate Metabolism, Dna-Binding, Galactose Metabolism, Metal- Binding, Nucleus, Phosphoprotein, Transcription, Transcription Regulation, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Hong, M. X. Fitzgerald, S. Harper, C. Luo, D. W. Speicher, R. Marmorstein
Structural Basis For Dimerization In Dna Recognition By Gal4.
Structure V. 16 1019 2008
PubMed-ID: 18611375 | Reference-DOI: 10.1016/J.STR.2008.03.015

Molecule 1 - REGULATORY PROTEIN GAL4
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Vector Type	:	PLASMID
	Fragment	:	DNA BINDING DOMAIN WITH COMPLETE DIMERIZATION DOMAIN
	Gene	:	GAL4
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE

*Molecule 2 - DNA (5'- D(DAPDCPDCPDGPDGPDAPDGPDGPDAPDCPDAPDGPDTPDCPDCPDTPDC PDCPDGPDG)-3')*
	Chains	:	D
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 3 - DNA (5'- D(DTPDCPDCPDGPDGPDAPDGPDGPDAPDCPDTPDGPDTPDCPDCPDTPDC PDCPDGPDG)-3')*
	Chains	:	E
	Engineered	:	YES
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 5)

No.	Name	Count	Type	Full Name
1	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
2	ZN	4	Ligand/Ion	ZINC ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:11 , CYS A:14 , CYS A:21 , CYS A:28	BINDING SITE FOR RESIDUE ZN A 1001
2	AC2	SOFTWARE	CYS A:11 , CYS A:28 , CYS A:31 , CYS A:38	BINDING SITE FOR RESIDUE ZN A 1002
3	AC3	SOFTWARE	CYS B:11 , CYS B:14 , CYS B:21 , CYS B:28	BINDING SITE FOR RESIDUE ZN B 1
4	AC4	SOFTWARE	CYS B:11 , CYS B:28 , CYS B:31 , CYS B:38	BINDING SITE FOR RESIDUE ZN B 2
5	AC5	SOFTWARE	LEU A:49 , DA D:11 , DG D:12 , DT D:13 , DT E:31 , DG E:32 , DT E:33	BINDING SITE FOR RESIDUE MPD D 100

(no "SS Bond" information available for 3COQ)

Asymmetric/Biological Unit

No.	Residues
1	Lys A:25	-	Pro A:26
2	Lys B:25	-	Pro B:26

(no "SAP(SNP)/Variant" information available for 3COQ)

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.	GAL4_YEAST	10-38	2	A:10-38 B:10-38
2	ZN2_CY6_FUNGAL_2	PS50048	Zn(2)-C6 fungal-type DNA-binding domain profile.	GAL4_YEAST	10-40	2	A:10-40 B:10-40

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	YPL248C	1	YPL248C.1	XVI:82356-79711	2646	GAL4_YEAST	1-881	881	2	A:8-96 B:8-96	89 89

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

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:89
 aligned with GAL4_YEAST | P04386 from UniProtKB/Swiss-Prot  Length:881

    Alignment length:89
                                    17        27        37        47        57        67        77        87         
            GAL4_YEAST    8 EQACDICRLKKLKCSKEKPKCAKCLKNNWECRYSPKTKRSPLTRAHLTEVESRLERLEQLFLLIFPREDLDMILKMDSLQDIKALLTGL 96
               SCOP domains d3coqa1 A:8-48 Gal4                      -d3coqa2 A:50-96 CD2-Gal4                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh.........hhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh.hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --ZN2_CY6_FUNGAL_1  PDB: A:10-3---------------------------------------------------------- PROSITE (1)
                PROSITE (2) --ZN2_CY6_FUNGAL_2  PDB: A:10-40 -------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:8-96 UniProt: 1-881 [INCOMPLETE]                                         Transcript 1
                  3coq A  8 EQACDICRLKKLKCSKEKPKCAKCLKNNWECRYSPKTKRSPLTRAHLTEVESRLERLEQLFLLIFPREDLDMILKMDSLQDIKALLTGL 96
                                    17        27        37        47        57        67        77        87

Chain B from PDB  Type:PROTEIN  Length:89
 aligned with GAL4_YEAST | P04386 from UniProtKB/Swiss-Prot  Length:881

    Alignment length:89
                                    17        27        37        47        57        67        77        87         
            GAL4_YEAST    8 EQACDICRLKKLKCSKEKPKCAKCLKNNWECRYSPKTKRSPLTRAHLTEVESRLERLEQLFLLIFPREDLDMILKMDSLQDIKALLTGL 96
               SCOP domains d3coqb1 B:8-48 Gal4                      -d3coqb2 B:50-96 CD2-Gal4                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh.........hhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --ZN2_CY6_FUNGAL_1  PDB: B:10-3---------------------------------------------------------- PROSITE (1)
                PROSITE (2) --ZN2_CY6_FUNGAL_2  PDB: B:10-40 -------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: B:8-96 UniProt: 1-881 [INCOMPLETE]                                         Transcript 1
                  3coq B  8 EQACDICRLKKLKCSKEKPKCAKCLKNNWECRYSPKTKRSPLTRAHLTEVESRLERLEQLFLLIFPREDLDMILKMDSLQDIKALLTGL 96
                                    17        27        37        47        57        67        77        87

Chain D from PDB  Type:DNA  Length:20
                                                   
                  3coq D  1 ACCGGAGGACAGTCCTCCGG 20
                                    10        20

Chain E from PDB  Type:DNA  Length:20
                                                   
                  3coq E 21 TCCGGAGGACTGTCCTCCGG 40
                                    30        40

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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: CD2-Gal4 (3)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (3)

1a	d3coqa2	A:50-96
1b	d3coqb2	B:50-96

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: Gal4 (3)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (3)

2a	d3coqa1	A:8-48
2b	d3coqb1	B:8-48

(no "CATH Domain" information available for 3COQ)

(no "Pfam Domain" information available for 3COQ)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (GAL4_YEAST | P04386)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000978	RNA polymerase II core promoter proximal region sequence-specific DNA binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
	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:0001133	RNA polymerase II transcription factor activity, sequence-specific transcription regulatory region DNA binding	Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA by RNA polymerase II and recruiting another transcription factor to the DNA in order to modulate transcription by RNAP II.
	GO:0001085	RNA polymerase II transcription factor binding	Interacting selectively and non-covalently with an RNA polymerase II transcription factor, any protein required to initiate or regulate transcription by RNA polymerase II.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0001077	transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0006012	galactose metabolic process	The chemical reactions and pathways involving galactose, the aldohexose galacto-hexose. D-galactose is widely distributed in combined form in plants, animals and microorganisms as a constituent of oligo- and polysaccharides; it also occurs in galactolipids and as its glucoside in lactose and melibiose.
	GO:0000435	positive regulation of transcription from RNA polymerase II promoter by galactose	Any process involving galactose that activates or increases the rate of transcription from an RNA polymerase II promoter.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006366	transcription from RNA polymerase II promoter	The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
	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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Description

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Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

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