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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. Tong
Date :  20 Nov 06  (Deposition) - 12 Dec 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (24x)
Biol. Unit 3:  A,B  (4x)
Biol. Unit 4:  A,B  (2x)
Keywords :  Bateman2 Domain, Amp Kinase, Snf4, 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
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NUCLEAR PROTEIN SNF4
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET26B
    Expression System StrainBL21 DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentBATEMAN 2 DOMAIN
    GeneSNF4, CAT3
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymREGULATORY PROTEIN CAT3

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)AB
Biological Unit 2 (24x)AB
Biological Unit 3 (4x)AB
Biological Unit 4 (2x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric Unit (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 240)
No.NameCountTypeFull Name
1MSE240Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 40)
No.NameCountTypeFull Name
1MSE40Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (1, 20)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2NYE)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CBSPS51371 CBS domain profile.AAKG_YEAST37-97
118-181
194-253
 
262-322
 
  4-
-
A:194-253
B:194-253
A:262-322
B:262-322
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
B:194-253
A:262-322
B:262-322
Biological Unit 2 (1, 96)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CBSPS51371 CBS domain profile.AAKG_YEAST37-97
118-181
194-253
 
262-322
 
  96-
-
A:194-253
B:194-253
A:262-322
B:262-322
Biological Unit 3 (1, 16)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CBSPS51371 CBS domain profile.AAKG_YEAST37-97
118-181
194-253
 
262-322
 
  16-
-
A:194-253
B:194-253
A:262-322
B:262-322
Biological Unit 4 (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CBSPS51371 CBS domain profile.AAKG_YEAST37-97
118-181
194-253
 
262-322
 
  8-
-
A:194-253
B:194-253
A:262-322
B:262-322

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YGL115W1YGL115W.1VII:292036-293004969AAKG_YEAST1-3223222A:181-322 (gaps)
B:181-322 (gaps)
142
142

(-) 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:132
 aligned with AAKG_YEAST | P12904 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:142
                                   190       200       210       220       230       240       250       260       270       280       290       300       310       320  
           AAKG_YEAST   181 THFLKIPIGDLNIITQDNMKSCQMTTPVIDVIQMLTQGRVSSVPIIDENGYLINVYEAYDVLGLIKGGIYNDLSLSVGEALMRRSDDFEGVYTCTKNDKLSTIMDNIRKARVHRFFVVDDVGRLVGVLTLSDILKYILLGSN 322
               SCOP domains d2nyea1 A:181-320 Nuclear protein SNF4                                                                                                      -- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh...............hhhhhhhhhhhh...eeeee.....eeeeeehhhhhhhh.----.....hhhhhhh...------.ee....hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE C------------CBS  PDB: A:194-253 UniProt: 194-253                        --------CBS  PDB: A:262-322 UniProt: 262-322                          PROSITE
               Transcript 1 Exon 1.1  PDB: A:181-322 (gaps) UniProt: 1-322 [INCOMPLETE]                                                                                    Transcript 1
                 2nye A 181 THFLKIPIGDLNIITQDNmKSCQmTTPVIDVIQmLTQGRVSSVPIIDENGYLINVYEAYDVLGLIK----NDLSLSVGEALmRRS------YTCTKNDKLSTImDNIRKARVHRFFVVDDVGRLVGVLTLSDILKYILLGSN 322
                                   190       200   |   210   |   220       230       240     |   -|      260 |  |    - |     280   |   290       300       310       320  
                                            199-MSE|       214-MSE                         246  251        262-MSE   272         284-MSE                                  
                                                 204-MSE                                                      265                                                         

Chain B from PDB  Type:PROTEIN  Length:130
 aligned with AAKG_YEAST | P12904 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:142
                                   190       200       210       220       230       240       250       260       270       280       290       300       310       320  
           AAKG_YEAST   181 THFLKIPIGDLNIITQDNMKSCQMTTPVIDVIQMLTQGRVSSVPIIDENGYLINVYEAYDVLGLIKGGIYNDLSLSVGEALMRRSDDFEGVYTCTKNDKLSTIMDNIRKARVHRFFVVDDVGRLVGVLTLSDILKYILLGSN 322
               SCOP domains d2nyeb1 B:181-320 Nuclear protein SNF4                                                                                                      -- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh...............hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhh.------...hhhhhhh...------.ee....hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE C------------CBS  PDB: B:194-253 UniProt: 194-253                        --------CBS  PDB: B:262-322 UniProt: 262-322                          PROSITE
               Transcript 1 Exon 1.1  PDB: B:181-322 (gaps) UniProt: 1-322 [INCOMPLETE]                                                                                    Transcript 1
                 2nye B 181 THFLKIPIGDLNIITQDNmKSCQmTTPVIDVIQmLTQGRVSSVPIIDENGYLINVYEAYDVLGLIK------LSLSVGEALmRRS------YTCTKNDKLSTImDNIRKARVHRFFVVDDVGRLVGVLTLSDILKYILLGSN 322
                                   190       200   |   210   |   220       230       240     |   -  |    260 |  |    - |     280   |   290       300       310       320  
                                            199-MSE|       214-MSE                         246    253      262-MSE   272         284-MSE                                  
                                                 204-MSE                                                      265                                                         

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 20)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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 | P129042nyc 2qlv 3t4n 3tdh 3te5

(-) Related Entries Specified in the PDB File

2nyc