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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BATEMAN2 DOMAIN OF YEAST SNF4
 
Authors :  M. J. Rudolph, G. A. Amodeo, S. Iram, S. Hong, G. Pirino, M. Carlson, L. To
Date :  20 Nov 06  (Deposition) - 12 Dec 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Bateman2 Domain, Snf4, Amp Kinase, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. J. Rudolph, G. A. Amodeo, S. Iram, S. P. Hong, G. Pirino, M. Carlson, L. Tong
Structure Of The Bateman2 Domain Of Yeast Snf4: Dimeric Association And Relevance For Amp Binding.
Structure V. 15 65 2007
PubMed-ID: 17223533  |  Reference-DOI: 10.1016/J.STR.2006.11.014

(-) Compounds

Molecule 1 - NUCLEAR PROTEIN SNF4
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET26B
    Expression System StrainBL21 DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentBATEMAN2 DOMAIN
    GeneSNF4, CAT3
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymREGULATORY PROTEIN CAT3

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2NYC)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2NYC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CBSPS51371 CBS domain profile.AAKG_YEAST37-97
118-181
194-253
262-322
  2-
-
A:194-253
A:262-320
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CBSPS51371 CBS domain profile.AAKG_YEAST37-97
118-181
194-253
262-322
  4-
-
A:194-253
A:262-320

(-) Exons   (1, 1)

Asymmetric Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YGL115W1YGL115W.1VII:292036-293004969AAKG_YEAST1-3223221A:181-320 (gaps)140

(-) 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:130
 aligned with AAKG_YEAST | P12904 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:140
                                   190       200       210       220       230       240       250       260       270       280       290       300       310       320
           AAKG_YEAST   181 THFLKIPIGDLNIITQDNMKSCQMTTPVIDVIQMLTQGRVSSVPIIDENGYLINVYEAYDVLGLIKGGIYNDLSLSVGEALMRRSDDFEGVYTCTKNDKLSTIMDNIRKARVHRFFVVDDVGRLVGVLTLSDILKYILLG 320
               SCOP domains d2nyca1 A:181-320 Nuclear protein SNF4                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh...............hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhhhh.----...hhhhhhhhh.------.ee....hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE C------------CBS  PDB: A:194-253 UniProt: 194-253                        --------CBS  PDB: A:262-320 UniProt: 262-322                        PROSITE
               Transcript 1 Exon 1.1  PDB: A:181-320 (gaps) UniProt: 1-322 [INCOMPLETE]                                                                                  Transcript 1
                 2nyc A 181 THFLKIPIGDLNIITQDNMKSCQMTTPVIDVIQMLTQGRVSSVPIIDENGYLINVYEAYDVLGLIKGG----LSLSVGEALMRRS------YTCTKNDKLSTIMDNIRKARVHRFFVVDDVGRLVGVLTLSDILKYILLG 320
                                   190       200       210       220       230       240       | -  |    260    |    - |     280       290       300       310       320
                                                                                             248  253         265    272                                                

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2NYC)

(-) Gene Ontology  (20, 20)

Asymmetric Unit(hide GO term definitions)
Chain A   (AAKG_YEAST | P12904)
molecular function
    GO:0004679    AMP-activated protein kinase activity    Catalysis of the reaction: ATP + a protein = ADP + a phosphoprotein. This reaction requires the presence of AMP.
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0043539    protein serine/threonine kinase activator activity    Binds to and increases the activity of a protein serine/threonine kinase.
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:0007031    peroxisome organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a peroxisome. A peroxisome is a small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules.
    GO:0045722    positive regulation of gluconeogenesis    Any process that activates or increases the frequency, rate or extent of gluconeogenesis.
    GO:0071902    positive regulation of protein serine/threonine kinase activity    Any process that increases the rate, frequency, or extent of protein serine/threonine kinase activity.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent 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:0001302    replicative cell aging    The process associated with progression of the cell from its inception to the end of its lifespan that occurs as the cell continues cycles of growth and division.
    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:0005641    nuclear envelope lumen    The region between the two lipid bilayers of the nuclear envelope; 20-40 nm wide.
    GO:0031588    nucleotide-activated protein kinase complex    A protein complex that possesses nucleotide-dependent protein kinase activity. The nucleotide can be AMP (in S. pombe and human) or ADP (in S. cerevisiae).
    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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AAKG_YEAST | P129042nye 2qlv 3t4n 3tdh 3te5

(-) Related Entries Specified in the PDB File

2nye