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(-) Description

Title :  CRYSTAL SCTUCTURE OF TRANSCRIPTIONAL REGULATOR GAL80P FROM KLUYVEROMYMES LACTIS
 
Authors :  J. B. Thoden, C. A. Sellick, R. J. Reece, H. M. Holden
Date :  13 Nov 06  (Deposition) - 21 Nov 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Biol. Unit 3:  A,B  (2x)
Keywords :  Transcription, Galactose Metabolism, Repressor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. B. Thoden, C. A. Sellick, R. J. Reece, H. M. Holden
Understanding A Transcriptional Paradigm At The Molecular Level. The Structure Of Yeast Gal80P.
J. Biol. Chem. V. 282 1534 2007
PubMed-ID: 17121853  |  Reference-DOI: 10.1074/JBC.C600285200
(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: PET28
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GAL80
    Organism Scientific: KLUYVEROMYCES LACTIS
    Organism Taxid: 28985

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB
Biological Unit 3 (2x): AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2NVW)

(-) Sites  (0, 0)

(no "Site" information available for 2NVW)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2NVW)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Trp A:123 -Ala A:124
2Thr A:284 -Pro A:285
3Trp B:123 -Ala B:124
4Thr B:284 -Pro B:285

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2NVW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2NVW)

(-) Exons   (0, 0)

(no "Exon" information available for 2NVW)

(-) 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:413
 aligned with GAL80_KLULA | Q06433 from UniProtKB/Swiss-Prot  Length:457

    Alignment length:472
                                           1                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
                                     -     |   5        15        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       445       455  
          GAL80_KLULA     - ---------------MNNNKRSKLSTVPSSRPIRVGFVGLTSGKSWVAKTHFLAIQQLSSQFQIVALYNPTLKSSLQTIEQLQLKHATGFDSLESFAQYKDIDMIVVSVKVPEHYEVVKNILEHSSQNLNLRYLYVEWALAASVQQAEELYSISQQRANLQTIICLQGRKSPYIVRAKELISEGCIGDINSIEISGNGGWYGYERPMRSPEYLYDIESGVNLISNSFGHTIDVLQYITGSYFQKINAMISNNIPTQFLLDENGKRTKETISKTCPDHLLFQGILENGKVPVSCSFKGGTPVKKLTKNLVIDIHGTKGDLKIEGDAGFVEISNLVLYFYGIKNGNGSSNGTDNNGAAAIKDKEKVTKSPSPSTGTSEEEQTMEVFHLRNYNSVVGNILRIYESIADYHFLGKPESKSSRGPDDLFASTKFDKQGFRFEGFPTFKDAIILHRLIDAVFRSDKEEKTLDVSKIMI 457
               SCOP domains ----------------d2nvwa1 A:2-154,A:374-457 Galactose/lactose metabolism regulatory protein GAL80                                                                          d2nvwa2 A:155-373 Galactose/lactose metabolism regulatory protein GAL80                                                                                                                                                    d2nvwa1 A:2-154,A:374                  -457 Galactose/lactose metabolism regulatory  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh.........hhhhhhhhhh.eeeeee......hhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhh.....eee.hhhhhhhh....eeee..hhhhhhhhhhhhhhhh.......eeeee.....hhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhh.....eeeeeeeee......eee...hhhhhhhhhh.....hhhhhhhhhhhhhhh..eeeeeeeee....eeeee.--......eee.....eeeeeeee.hhh.eeeeeee...........eeeeeee...eeeeee.------..eeeeeeee...---------------------------------..eeeeee.....hhhhhhhhhhhhhhhhhhhh------------------.............hhhhhhhhhhhhhhhhhhhhhh..ee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nvw A -14 HHHSSENLYFQGHMLANNNKRSKLSTVPSSRPIRVGFVGLTSGKSWVAKTHFLAIQQLSSQFQIVALYNPTLKSSLQTIEQLQLKHATGFDSLESFAQYKDIDMIVVSVKVPEHYEVVKNILEHSSQNLNLRYLYVEWALAASVQQAEELYSISQQRANLQTIICLQGRKSPYIVRAKELISEGCIGDINSIEISGNGGWYGYERPMRSPEYLYDIESGVNLISNSFGHTIDVLQYITGSYFQKINAMISNNIPTQFLLD--GKRTKETISKTCPDHLLFQGILENGKVPVSCSFKGGTPVKKLTKNLVIDIHGTKGDLKIEGD------SNLVLYFYGIKNG---------------------------------EEQTMEVFHLRNYNSVVGNILRIYESIADYHFL------------------KFDKQGFRFEGFPTFKDAIILHRLIDAVFRSDKEEKTLDVSKIMI 457
                                    -5         5        15        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   |     -|      325  |      -         -         -      |365       375       385        |-         -       415       425       435       445       455  
                                                                                                                                                                                                                                                                                             245  |                                                          309    316         328                               362                             394                413                                            
                                                                                                                                                                                                                                                                                                248                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:405
 aligned with GAL80_KLULA | Q06433 from UniProtKB/Swiss-Prot  Length:457

    Alignment length:460
                               1                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457
          GAL80_KLULA     - ---MNNNKRSKLSTVPSSRPIRVGFVGLTSGKSWVAKTHFLAIQQLSSQFQIVALYNPTLKSSLQTIEQLQLKHATGFDSLESFAQYKDIDMIVVSVKVPEHYEVVKNILEHSSQNLNLRYLYVEWALAASVQQAEELYSISQQRANLQTIICLQGRKSPYIVRAKELISEGCIGDINSIEISGNGGWYGYERPMRSPEYLYDIESGVNLISNSFGHTIDVLQYITGSYFQKINAMISNNIPTQFLLDENGKRTKETISKTCPDHLLFQGILENGKVPVSCSFKGGTPVKKLTKNLVIDIHGTKGDLKIEGDAGFVEISNLVLYFYGIKNGNGSSNGTDNNGAAAIKDKEKVTKSPSPSTGTSEEEQTMEVFHLRNYNSVVGNILRIYESIADYHFLGKPESKSSRGPDDLFASTKFDKQGFRFEGFPTFKDAIILHRLIDAVFRSDKEEKTLDVSKIMI 457
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------GFO_IDH_MocA-2nvwB01 B:18-149                                                                                                       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------GFO_IDH_MocA-2nvwB02 B:18-149                                                                                                       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhh............eeeeee......hhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhh.....eee.hhhhhhhh....eeee..hhhhhhhhhhhhhhh........eeeee.....hhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhh.....eeeeeeeee......ee....hhhhhhhhhh.....hhhhhhhhhhhhhhh..eeeeeeeee....eeee....--....eee.....eeeeeeee....eeeeeeee...........eeeeeee...eeeeee...----...eeeeee....--------------------------------....eeeee.....hhhhhhhhhhhhhhhhhhhh.-----------------.............hhhhhhhhhhhhhhhhhhhhhh..ee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nvw B -14 HHHSSENLYFQGHMLASSRPIRVGFVGLTSGKSWVAKTHFLAIQQLSSQFQIVALYNPTLKSSLQTIEQLQLKHATGFDSLESFAQYKDIDMIVVSVKVPEHYEVVKNILEHSSQNLNLRYLYVEWALAASVQQAEELYSISQQRANLQTIICLQGRKSPYIVRAKELISEGCIGDINSIEISGNGGWYGYERPMRSPEYLYDIESGVNLISNSFGHTIDVLQYITGSYFQKINAMISNNIPTQFLLDEN--RTKETISKTCPDHLLFQGILENGKVPVSCSFKGGTPVKKLTKNLVIDIHGTKGDLKIEGDAG----SNLVLYFYGIKNG--------------------------------EEEQTMEVFHLRNYNSVVGNILRIYESIADYHFLG-----------------KFDKQGFRFEGFPTFKDAIILHRLIDAVFRSDKEEKTLDVSKIMI 457
                                    -5     || 17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247  |    257       267       277       287       297       307   |   317       327|        -         -         -   |   367       377       387       | -         -     | 417       427       437       447       457
                                           1|                                                                                                                                                                                                                                      247  |                                                          311  316         328                              361                               395               413                                            
                                           14                                                                                                                                                                                                                                         250
   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  (2, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2NVW)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GAL80_KLULA | Q06433)
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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 Related Entries

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        GAL80_KLULA | Q06433: 3e1k

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