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Title :   CRYSTAL STRUCTURE OF A TERNARY COMPLEX OF THE TRANSCRIPTIONAL REPRESSOR GAL80P (GAL80S0 [G301R]) AND THE ACIDIC ACTIVATION DOMAIN OF GAL4P (AA 854-874) FROM SACCHAROMYCES CEREVISIAE WITH NAD

Authors :   P. R. Kumar, L. Joshua-Tor

Date :   30 Dec 07 (Deposition) - 04 Mar 08 (Release) - 26 May 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Eukaryotic Transcription Complex, Nad, Rossmann Fold, Acetylation, Carbohydrate Metabolism, Dna-Binding, Galactose Metabolism, Repressor, Transcription Regulation, Activator, Metal-Binding, Nucleus, Phosphoprotein, Zinc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. R. Kumar, Y. Yu, R. Sternglanz, S. A. Johnston, L. Joshua-Tor
Nadp Regulates The Yeast Gal Induction System.
Science V. 319 1090 2008
PubMed-ID: 18292341 | Reference-DOI: 10.1126/SCIENCE.1151903
(for further references see the PDB file header)

Molecule 1 - GALACTOSE/LACTOSE METABOLISM REGULATORY PROTEIN GAL80
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)-RIPL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GAL80
	Mutation	:	YES
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

Molecule 2 - REGULATORY PROTEIN GAL4
	Chains	:	E, F
	Engineered	:	YES
	Fragment	:	S. CEREVISIAE GAL4P PEPTIDE
	Other Details	:	S.CEREVISIAE GAL4(854-874) WAS MADE SYNTHETICALLY
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:24 , ASN A:26 , GLY A:30 , TRP A:31 , PRO A:55 , ALA A:93 , ILE A:94 , GLN A:95 , HIS A:99 , GLU A:122 , TRP A:123 , GLN A:151 , HIS A:213 , ASP E:509	BINDING SITE FOR RESIDUE NAD A 436
2	AC2	SOFTWARE	GLY B:24 , ASN B:26 , LYS B:29 , GLY B:30 , TRP B:31 , PRO B:55 , ALA B:93 , ILE B:94 , GLN B:95 , SER B:98 , HIS B:99 , GLU B:122 , TRP B:123 , GLN B:151 , HIS B:213	BINDING SITE FOR RESIDUE NAD B 436

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

Asymmetric/Biological Unit

No.	Residues
1	Trp A:123	-	Ala A:124
2	Trp B:123	-	Ala B:124
3	Glu B:313	-	Ile B:314
4	Asp B:344	-	Ala B:345

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

(no "PROSITE Motif" information available for 3BTS)

Asymmetric/Biological Unit (2, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YML051W	1	YML051W.1	XIII:171594-172901	1308	GAL80_YEAST	1-435	435	2	A:14-435 (gaps) B:15-434 (gaps)	422 420

2.1	YPL248C	1	YPL248C.1	XVI:82356-79711	2646	GAL4_YEAST	1-881	881	2	E:501-509 F:505-509	9 5

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
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:384
 aligned with GAL80_YEAST | P04387 from UniProtKB/Swiss-Prot  Length:435

    Alignment length:422
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433  
          GAL80_YEAST    14 NAAPIRVGFVGLNAAKGWAIKTHYPAILQLSSQFQITALYSPKIETSIATIQRLKLSNATAFPTLESFASSSTIDMIVIAIQVASHYEVVMPLLEFSKNNPNLKYLFVEWALACSLDQAESIYKAAAERGVQTIISLQGRKSPYILRAKELISQGYIGDINSIEIAGNGGWYGYERPVKSPKYIYEIGNGVDLVTTTFGHTIDILQYMTSSYFSRINAMVFNNIPEQELIDERGNRLGQRVPKTVPDHLLFQGTLLNGNVPVSCSFKGGKPTKKFTKNLVIDIHGTKGDLKLEGDAGFAEISNLVLYYSGTRANDFPLANGQQAPLDPGYDAGKEIMEVYHLRNYNAIVGNIHRLYQSISDFHFNTKKIPELPSQFVMQGFDFEGFPTLMDALILHRLIESVYKSNMMGSTLNVSNISHYSL 435
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee......hhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhh.....ee..hhhhhhhh....eeee..hhhhhhhhhhhhhhhhhhh....eeee......hhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhhhh.....eeeeeeeee......eee....hhhhh.........hhhhhhhhhhhhhh...eeeeeeeee....eeeee.....eeeeeee.....eeeeeeee.hhh.eeeeeee...------..eeeeeee...eeeeee.---..eeeeeeee.-----------------------...eeeee.....hhhhhhhhhhhhhhhhhhhhh------...............hhhhhhhhhhhhhhhhhhhhhh..ee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:14-435 (gaps) UniProt: 1-435 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                             Transcript 1
                 3bts A  14 NAAPIRVGFVGLNAAKGWAIKTHYPAILQLSSQFQITALYSPKIETSIATIQRLKLSNATAFPTLESFASSSTIDMIVIAIQVASHYEVVMPLLEFSKNNPNLKYLFVEWALACSLDQAESIYKAAAERGVQTIISLQGRKSPYILRAKELISQGYIGDINSIEIAGNGGWYGYERPVKSPKYIYEIGNGVDLVTTTFGHTIDILQYMTSSYFSRINAMVFNNIPEQELIDERGNRLGQRVPKTVPDHLLFQGTLLNGNVPVSCSFKGGK------KNLVIDIHGTKRDLKLEGD---AEISNLVLYYS-----------------------GKEIMEVYHLRNYNAIVGNIHRLYQSISDFHFNT------PSQFVMQGFDFEGFPTLMDALILHRLIESVYKSNMMGSTLNVSNISHYSL 435
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283      |293       303    |  313        |-         -         -  |    353       363       373     |   -  |    393       403       413       423       433  
                                                                                                                                                                                                                                                                                                       283    290               308 312       322                     346                              379    386

Chain B from PDB  Type:PROTEIN  Length:390
 aligned with GAL80_YEAST | P04387 from UniProtKB/Swiss-Prot  Length:435

    Alignment length:420
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434
          GAL80_YEAST    15 AAPIRVGFVGLNAAKGWAIKTHYPAILQLSSQFQITALYSPKIETSIATIQRLKLSNATAFPTLESFASSSTIDMIVIAIQVASHYEVVMPLLEFSKNNPNLKYLFVEWALACSLDQAESIYKAAAERGVQTIISLQGRKSPYILRAKELISQGYIGDINSIEIAGNGGWYGYERPVKSPKYIYEIGNGVDLVTTTFGHTIDILQYMTSSYFSRINAMVFNNIPEQELIDERGNRLGQRVPKTVPDHLLFQGTLLNGNVPVSCSFKGGKPTKKFTKNLVIDIHGTKGDLKLEGDAGFAEISNLVLYYSGTRANDFPLANGQQAPLDPGYDAGKEIMEVYHLRNYNAIVGNIHRLYQSISDFHFNTKKIPELPSQFVMQGFDFEGFPTLMDALILHRLIESVYKSNMMGSTLNVSNISHYS 434
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee......hhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhh.....eee.hhhhhhhh....eeee..hhhhhhhhhhhhhhhhhhh....eeee......hhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhhhh.....eeeeeeeee......eee....hhhhh.........hhhhhhhhhhhhhh...eeeeeeeee....eeeee.....eeeeeee.....eeeeeeee.hhh.eeeeeee..-------..eeeeeee...eeeeee..--....eeeeee.---------------------.....eeeee.....hhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhh..ee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: B:15-434 (gaps) UniProt: 1-435 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                           Transcript 1
                 3bts B  15 AAPIRVGFVGLNAAKGWAIKTHYPAILQLSSQFQITALYSPKIETSIATIQRLKLSNATAFPTLESFASSSTIDMIVIAIQVASHYEVVMPLLEFSKNNPNLKYLFVEWALACSLDQAESIYKAAAERGVQTIISLQGRKSPYILRAKELISQGYIGDINSIEIAGNGGWYGYERPVKSPKYIYEIGNGVDLVTTTFGHTIDILQYMTSSYFSRINAMVFNNIPEQELIDERGNRLGQRVPKTVPDHLLFQGTLLNGNVPVSCSFKGG-------KNLVIDIHGTKRDLKLEGDA--AEISNLVLYYS---------------------DAGKEIMEVYHLRNYNAIVGNIHRLYQSISDFHFNTKKIPELPSQFVMQGFDFEGFPTLMDALILHRLIESVYKSNMMGSTLNVSNISHYS 434
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       | -     | 294       304    |  314       | -         -       344       354       364       374       384       394       404       414       424       434
                                                                                                                                                                                                                                                                                                     282     290                309  |       322                   344                                                                                          
                                                                                                                                                                                                                                                                                                                                   312

Chain E from PDB  Type:PROTEIN  Length:9
 aligned with GAL4_YEAST | P04386 from UniProtKB/Swiss-Prot  Length:881

    Alignment length:9
           GAL4_YEAST   855 MFNTTTMDD 863
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
               Transcript 2 Exon 2.1  Transcript 2
                 3bts E 501 MFNTTTMDD 509

Chain F from PDB  Type:PROTEIN  Length:5
 aligned with GAL4_YEAST | P04386 from UniProtKB/Swiss-Prot  Length:881

    Alignment length:5
           GAL4_YEAST   859 TTMDD 863
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
               Transcript 2 2.1   Transcript 2
                 3bts F 505 TTMDD 509

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 '\|'

(no "SCOP Domain" information available for 3BTS)

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (GAL80_YEAST | P04387)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0001102	RNA polymerase II activating transcription factor binding	Interacting selectively and non-covalently with an RNA polymerase II transcription activating factor, a protein involved in positive regulation of transcription.
	GO:0019210	kinase inhibitor activity	Stops, prevents or reduces the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
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:0033673	negative regulation of kinase activity	Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0043433	negative regulation of sequence-specific DNA binding transcription factor activity	Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.

Chain E,F (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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	Cis Peptide Bonds
		Asp B:344 - Ala B:345	[ RasMol ]
		Glu B:313 - Ile B:314	[ RasMol ]
		Trp A:123 - Ala A:124	[ RasMol ]
		Trp B:123 - Ala B:124	[ RasMol ]

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	GAL80_YEAST \| P04387
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UniProtKB/Swiss-Prot
	GAL4_YEAST \| P04386	:	1aw6 1d66 1hbw 3coq
	GAL80_YEAST \| P04387	:	3btu 3btv 3v2u

3btu	THE SAME PROTEIN WITH E351K MUTATION
3btv	CRYSTAL STRUCTURE OF THE SUPER-REPRESSOR MUTANT OF GAL80P FROM SACCHAROMYCES CEREVISIAE; GAL80(S0)-[G301R]

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

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Exons (2, 4)

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Gene Ontology (23, 29)

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