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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SUPER-REPRESSOR MUTANT OF GAL80P FROM SACCHAROMYCES CEREVISIAE; GAL80(S0)-[G301R]
 
Authors :  P. R. Kumar, L. Joshua-Tor
Date :  31 Dec 07  (Deposition) - 04 Mar 08  (Release) - 26 May 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Keywords :  Eukaryotic Transcription Repressor, Acetylation, Carbohydrate Metabolism, Dna-Binding, Galactose Metabolism, Transcription Regulation (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)

(-) Compounds

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

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3BTV)

(-) Sites  (0, 0)

(no "Site" information available for 3BTV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Trp A:123 -Ala A:124
2Arg A:356 -Asn A:357
3Ser A:434 -Leu A:435
4Trp B:123 -Ala B:124
5Gly B:281 -Gly B:282
6Pro B:383 -Glu B:384

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YML051W1YML051W.1XIII:171594-1729011308GAL80_YEAST1-4354352A:16-435 (gaps)
B:16-433 (gaps)		420
418

(-) Sequences/Alignments

Asymmetric 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:390
 aligned with GAL80_YEAST | P04387 from UniProtKB/Swiss-Prot  Length:435

    Alignment length:420
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435
          GAL80_YEAST    16 APIRVGFVGLNAAKGWAIKTHYPAILQLSSQFQITALYSPKIETSIATIQRLKLSNATAFPTLESFASSSTIDMIVIAIQVASHYEVVMPLLEFSKNNPNLKYLFVEWALACSLDQAESIYKAAAERGVQTIISLQGRKSPYILRAKELISQGYIGDINSIEIAGNGGWYGYERPVKSPKYIYEIGNGVDLVTTTFGHTIDILQYMTSSYFSRINAMVFNNIPEQELIDERGNRLGQRVPKTVPDHLLFQGTLLNGNVPVSCSFKGGKPTKKFTKNLVIDIHGTKGDLKLEGDAGFAEISNLVLYYSGTRANDFPLANGQQAPLDPGYDAGKEIMEVYHLRNYNAIVGNIHRLYQSISDFHFNTKKIPELPSQFVMQGFDFEGFPTLMDALILHRLIESVYKSNMMGSTLNVSNISHYSL 435
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee...........hhhhhhhhh...eeeeeee..hhhhhhhhhhhh.....ee..hhhhhhhh....eeee..hhhhhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhh.....eeeeeeeee......eee...hhhhhh.........hhhhhhhhhhhhhhh..eeeeeeeee....eeeee.....eeeeeee.....eeeeeeee....eeeeeeee.....---...eeeeeee...eeeee..-----..eeeeeee.----------------------..eeeeee.....hhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhh..ee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:16-435 (gaps) UniProt: 1-435 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                           Transcript 1
                 3btv A  16 APIRVGFVGLNAAKGWAIKTHYPAILQLSSQFQITALYSPKIETSIATIQRLKLSNATAFPTLESFASSSTIDMIVIAIQVASHYEVVMPLLEFSKNNPNLKYLFVEWALACSLDQAESIYKAAAERGVQTIISLQGRKSPYILRAKELISQGYIGDINSIEIAGNGGWYGYERPVKSPKYIYEIGNGVDLVTTTFGHTIDILQYMTSSYFSRINAMVFNNIPEQELIDERGNRLGQRVPKTVPDHLLFQGTLLNGNVPVSCSFKGGKPT---TKNLVIDIHGTKRDLKLEGD-----ISNLVLYYSG----------------------GKEIMEVYHLRNYNAIVGNIHRLYQSISDFHFNTKKIPELPSQFVMQGFDFEGFPTLMDALILHRLIESVYKSNMMGSTLNVSNISHYSL 435
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285   |   295       305  |    315       | -         -         -|      355       365       375       385       395       405       415       425       435
                                                                                                                                                                                                                                                                                                       285 289                308   314      323                    346                                                                                         


Chain B from PDB  Type:PROTEIN  Length:392
 aligned with GAL80_YEAST | P04387 from UniProtKB/Swiss-Prot  Length:435

    Alignment length:418
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425        
          GAL80_YEAST    16 APIRVGFVGLNAAKGWAIKTHYPAILQLSSQFQITALYSPKIETSIATIQRLKLSNATAFPTLESFASSSTIDMIVIAIQVASHYEVVMPLLEFSKNNPNLKYLFVEWALACSLDQAESIYKAAAERGVQTIISLQGRKSPYILRAKELISQGYIGDINSIEIAGNGGWYGYERPVKSPKYIYEIGNGVDLVTTTFGHTIDILQYMTSSYFSRINAMVFNNIPEQELIDERGNRLGQRVPKTVPDHLLFQGTLLNGNVPVSCSFKGGKPTKKFTKNLVIDIHGTKGDLKLEGDAGFAEISNLVLYYSGTRANDFPLANGQQAPLDPGYDAGKEIMEVYHLRNYNAIVGNIHRLYQSISDFHFNTKKIPELPSQFVMQGFDFEGFPTLMDALILHRLIESVYKSNMMGSTLNVSNISHY 433
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...........hhhhhhhhh...eeeeeee..hhhhhhhhhhhh.....ee..hhhhhhhh....eeee..hhhhhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhh.....eeeeeeeee......eee...hhhhhh.........hhhhhhhhhhhhhhh..eeeeeeeee....eeeee.....eeeeeee.....eeeeeeee....eeeeeeee..---......eeeeeee...eeeeee.----...eeeeee.-------------------.......eeeee.....hhhhhhhhhhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhhhhhh..ee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:16-433 (gaps) UniProt: 1-435 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                         Transcript 1
                 3btv B  16 APIRVGFVGLNAAKGWAIKTHYPAILQLSSQFQITALYSPKIETSIATIQRLKLSNATAFPTLESFASSSTIDMIVIAIQVASHYEVVMPLLEFSKNNPNLKYLFVEWALACSLDQAESIYKAAAERGVQTIISLQGRKSPYILRAKELISQGYIGDINSIEIAGNGGWYGYERPVKSPKYIYEIGNGVDLVTTTFGHTIDILQYMTSSYFSRINAMVFNNIPEQELIDERGNRLGQRVPKTVPDHLLFQGTLLNGNVPVSCSFKGG---KKFTKNLVIDIHGTKRDLKLEGD----EISNLVLYYS-------------------GYDAGKEIMEVYHLRNYNAIVGNIHRLYQSISDFHFNTKKIPELPSQFVMQGFDFEGFPTLMDALILHRLIESVYKSNMMGSTLNVSNISHY 433
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275      |  -|      295       305  |    315      |  -         -      |345       355       365       375       385       395       405       415       425        
                                                                                                                                                                                                                                                                                                    282 286                   308  313      322                 342
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric 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.

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  Cis Peptide Bonds
    Arg A:356 - Asn A:357   [ RasMol ]  
    Gly B:281 - Gly B:282   [ RasMol ]  
    Pro B:383 - Glu B:384   [ RasMol ]  
    Ser A:434 - Leu A:435   [ RasMol ]  
    Trp A:123 - Ala A:124   [ RasMol ]  
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        GAL80_YEAST | P04387: 3bts 3btu 3v2u

(-) Related Entries Specified in the PDB File

3bts S.CEREVISIAE COMPLEX WITH NAD
3btu S.CEREVISIAE WITH E351K MUTATION