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(-) Description

Title :  CRYSTAL STRUCTURE OF A CBS DOMAIN PAIR FROM THE REGULATORY GAMMA1 SUBUNIT OF HUMAN AMPK IN COMPLEX WITH AMP
 
Authors :  P. Day, A. Sharff, L. Parra, A. Cleasby, M. Williams, S. Horer, H. Nar, N. Redemann, I. Tickle, J. Yon
Date :  09 Mar 07  (Deposition) - 08 May 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase, Cbs Domain, Lipid Synthesis, Fatty Acid Biosynthesis, Ampk Gamma1 Subunit Cbs 3 Plus 4 Amp Regulatory Subunit. R Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Day, A. Sharff, L. Parra, A. Cleasby, M. Williams, S. Horer, H. Nar, N. Redemann, I. Tickle, J. Yon
Structure Of A Cbs-Domain Pair From The Regulatory Gamma1 Subunit Of Human Ampk In Complex With Amp And Zmp.
Acta Crystallogr. , Sect. D V. 63 587 2007
PubMed-ID: 17452784  |  Reference-DOI: 10.1107/S0907444907009110

(-) Compounds

Molecule 1 - 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT GAMMA-1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentCBS 3 AND 4 FRAGMENT, RESIDUES 182-325
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAMPK GAMMA-1 CHAIN, AMPKG, AMPK GAMMA1 CHAIN CBS DOMAINS 3 AND 4

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:200 , ASN A:203 , ILE A:204 , ALA A:205 , VAL A:225 , SER A:226 , ALA A:227 , ILE A:312 , SER A:314 , SER A:316 , ASP A:317 , HOH A:2072 , HOH A:2195 , HOH A:2196 , HOH A:2197 , HOH A:2198BINDING SITE FOR RESIDUE AMP A1324

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2UV7)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Phe A:183 -Pro A:184

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2UV7)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CBSPS51371 CBS domain profile.AAKG1_HUMAN43-103
125-187
198-260
272-329
  2-
-
A:198-260
A:272-324
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CBSPS51371 CBS domain profile.AAKG1_HUMAN43-103
125-187
198-260
272-329
  4-
-
A:198-260
A:272-324

(-) Exons   (0, 0)

(no "Exon" information available for 2UV7)

(-) 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:144
 aligned with AAKG1_HUMAN | P54619 from UniProtKB/Swiss-Prot  Length:331

    Alignment length:144
                                   190       200       210       220       230       240       250       260       270       280       290       300       310       320    
          AAKG1_HUMAN   181 TEFPKPEFMSKSLEELQIGTYANIAMVRTTTPVYVALGIFVQHRVSALPVVDEKGRVVDIYSKFDVINLAAEKTYNNLDVSVTKALQHRSHYFEGVLKCYLHETLETIINRLVEAEVHRLVVVDENDVVKGIVSLSDILQALVL 324
               SCOP domains d2uv7a_ A: automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------CBS-2uv7A01 A:263-324                                          Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------CBS-2uv7A02 A:263-324                                          Pfam domains (2)
         Sec.struct. author ....hhhhhh.hhhhhh.........ee...hhhhhhhhhhhh...eeeee.....eeeeeehhhhhhhhhh.........hhhhhhh.........ee....hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE CBS    ----------CBS  PDB: A:198-260 UniProt: 198-260                           -----------CBS  PDB: A:272-324 UniProt: 272-329                  PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2uv7 A  -1 HEFPKPEFMSKSLEELQIGTYANIAMVRTTTPVYVALGIFVQHRVSALPVVDEKGRVVDIYSKFDVINLAAEKTYNNLDVSVTKALQHRSHYFEGVLKCYLHETLETIINRLVEAEVHGLVVVDENDVVKGIVSLSDILQALVL 324
                            ||     190       200       210       220       230       240       250       260       270       280       290       300       310       320    
                            ||                                                                                                                                              
                           -1|                                                                                                                                              
                           182                                                                                                                                              

   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 2UV7)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Family: CBS (51)
1aCBS-2uv7A01A:263-324
1bCBS-2uv7A02A:263-324

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)
Chain A   (AAKG1_HUMAN | P54619)
molecular function
    GO:0043531    ADP binding    Interacting selectively and non-covalently with ADP, adenosine 5'-diphosphate.
    GO:0016208    AMP binding    Interacting selectively and non-covalently with AMP, adenosine monophosphate.
    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:0004691    cAMP-dependent protein kinase activity    Catalysis of the reaction: ATP + a protein = ADP + a phosphoprotein. This reaction requires the presence of cAMP.
    GO:0008603    cAMP-dependent protein kinase regulator activity    Modulation of the activity of the enzyme cAMP-dependent protein kinase.
    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:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
biological process
    GO:0007050    cell cycle arrest    A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
    GO:0006633    fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
    GO:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0016236    macroautophagy    The major inducible pathway for the general turnover of cytoplasmic constituents in eukaryotic cells, it is also responsible for the degradation of active cytoplasmic enzymes and organelles during nutrient starvation. Macroautophagy involves the formation of double-membrane-bounded autophagosomes which enclose the cytoplasmic constituent targeted for degradation in a membrane-bounded structure. Autophagosomes then fuse with a lysosome (or vacuole) releasing single-membrane-bounded autophagic bodies that are then degraded within the lysosome (or vacuole). Though once thought to be a purely non-selective process, it appears that some types of macroautophagy, e.g. macropexophagy, macromitophagy, may involve selective targeting of the targets to be degraded.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0045860    positive regulation of protein kinase activity    Any process that activates or increases the frequency, rate or extent of protein kinase activity.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0006110    regulation of glycolytic process    Any process that modulates the frequency, rate or extent of glycolysis.
    GO:1901796    regulation of signal transduction by p53 class mediator    Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AAKG1_HUMAN | P546192uv4 2uv5 2uv6 4cfe 4cff 4rer 4rew 4zhx 5ezv 5iso

(-) Related Entries Specified in the PDB File

2uv4 CRYSTAL STRUCTURE OF A CBS DOMAIN PAIR FROM THE REGULATORY GAMMA1 SUBUNIT OF HUMAN AMPK IN COMPLEX WITH AMP
2uv5 CRYSTAL STRUCTURE OF A CBS DOMAIN PAIR FROM THE REGULATORY GAMMA1 SUBUNIT OF HUMAN AMPK IN COMPLEX WITH AMP
2uv6 CRYSTAL STRUCTURE OF A CBS DOMAIN PAIR FROM THE REGULATORY GAMMA1 SUBUNIT OF HUMAN AMPK IN COMPLEX WITH AMP