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(-) Description

Title :  CO-CRYSTAL STRUCTURE OF AN CHIMERIC AMPK CORE WITH ATP
 
Authors :  L. Chen, J. Wang, Y. -Y. Zhang, S. F. Yan, D. Neumann, U. Schlattner, Z. -X W. Wu
Date :  22 Mar 12  (Deposition) - 06 Jun 12  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Ampk, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Chen, J. Wang, Y. -Y. Zhang, S. F. Yan, D. Neumann, U. Schlattner, Z. -X. Wang, J. -W. Wu
Amp-Activated Protein Kinase Undergoes Nucleotide-Dependent Conformational Changes
Nat. Struct. Mol. Biol. V. 19 716 2012
PubMed-ID: 22659875  |  Reference-DOI: 10.1038/NSMB.2319

(-) Compounds

Molecule 1 - EG:132E8.2 PROTEIN
    Chains: A
    EC Number: 2.7.11.-, 2.7.11.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 458-582
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Synonym: FI03728P, SNF1A/AMP-ACTIVATED PROTEIN KINASE, SNF1A/AMP- ACTIVATED PROTEIN KINASE, ISOFORM A, SNF1A/AMP-ACTIVATED PROTEIN KINASE, ISOFORM B, SNF1A/AMP-ACTIVATED PROTEIN KINASE, ISOFORM C
 
Molecule 2 - 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT BETA-1
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 187-270
    Gene: PRKAB1
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: AMPK SUBUNIT BETA-1, AMPKB, 5'-AMP-ACTIVATED PROTEIN KINASE 40 KDA SUBUNIT
 
Molecule 3 - 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT GAMMA-1
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PRKAG1
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: AMPK GAMMA1, AMPK SUBUNIT GAMMA-1, AMPKG

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2TAM1Ligand/IonTRIS(HYDROXYETHYL)AMINOMETHANE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET C:84 , THR C:86 , ILE C:87 , THR C:88 , ASP C:89 , GLN C:122 , PRO C:127 , LEU C:128 , VAL C:129 , ILE C:149 , HIS C:150 , ARG C:151 , PRO C:153 , SER C:225 , PHE C:243 , HOH C:509 , HOH C:539BINDING SITE FOR RESIDUE ATP C 401
2AC2SOFTWAREHIS C:150 , THR C:199 , ALA C:204 , VAL C:224 , SER C:225 , ALA C:226 , PRO C:228 , HIS C:297 , ARG C:298 , SER C:313 , LEU C:314 , SER C:315 , ASP C:316 , HOH C:515 , HOH C:538BINDING SITE FOR RESIDUE ATP C 402
3AC3SOFTWAREVAL C:68 , ARG C:69 , ARG C:151 , THR C:167 , LYS C:169 , ARG C:170 , HIS C:297 , HOH C:503 , HOH C:521 , HOH C:527 , HOH C:536BINDING SITE FOR RESIDUE TAM C 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EAG)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4EAG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EAG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EAG)

(-) Exons   (0, 0)

(no "Exon" information available for 4EAG)

(-) Sequences/Alignments

Asymmetric/Biological 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:98
                                                                                                                                  
               SCOP domains d4eaga_ A: automated matches                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee......hhhhhhhhhhhhhhhh..eeeeee..eeeeeee......eeeeeeeeee.....eeeeeee.......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4eag A 458 AKWHLGIRSQSKPNDIMLEVYRAMKALSYEWKIINPYHVRVRRQNVKTGKFSKMSLQLYQVDAKSYLLDFKSLTLQPTGHHTMEFFEMCAALIIQLAR 582
                                   467       477       487       497       507       517       527   ||  564       574        
                                                                                                   531|                       
                                                                                                    559                       


Chain B from PDB  Type:PROTEIN  Length:58
                                                                                          
               SCOP domains ---------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author ..............ee..ee.ee....eee.....eeeeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                 4eag B 186 MYHQEPAPPILPLQVILGISHVMLNHLYALSIKDGVMVLSATHRYKKKYVTTLLYKPI 270
                                 ||205 ||   |222|      242       252       262        
                               191|  207| 215| ||                                     
                                202   211  220 ||                                     
                                             222|                                     
                                              233                                     


Chain C from PDB  Type:PROTEIN  Length:289
                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4eagc1 C:26-181 5'-AMP-activated protein kinase subunit gamma-1, AMPKg                                                                                     d4eagc2 C:182-324 5'-AMP-activated protein kinase subunit gamma-1, AMPKg                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh..hhhhhh..eeeeeeee...hhhhhhhhhhhh....eeeee....eeeeeehhhhhhhhhhhhhhh.hhhhhh....hhhhhhhhhhhhhhh.........hhhhhhhhhhhh....eeee......eeeeehhhhhhhhhhhhhhh....hhhhhhhhhhh.........ee...hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhh.....hhhhhh......ee....hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eag C  26 SVYTTFMKSHRCYDLIPTSSKLVVFDTSLQVKKAFFALVTNGVRAAPLWDSKKQSFVGMLTITDFINILHRYYKSALVQIYELEEHKIETWREVYLQDSFKPLVCISPNASLFDAVSSLIRNKIHRLPVIDPESGNTLYILTHKRILKFLKLFITEFPKPEFMSKSLEELQIGTYANIAMVRTTTPVYVALGIFVQHRVSALPVVDEKGRVVDIYSKFDVINLAANLDVSVTKALQHRGVLKCYLHETLEAIINRLVEAEVHRLVVVDEHDVVKGIVSLSDILQALVLT 324
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245    || 260       275       285       295       305       315         
                                                                                                                                                                                                                                                          250|         268|                                                  
                                                                                                                                                                                                                                                           256          274
   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, 3)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EAG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EAG)

(-) Gene Ontology  (45, 65)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        AAKB1_RAT | P80386: 1z0m 1z0n 4eak 4eal 4qfg 4qfr 4qfs 4yef 5kq5 5t5t 5ufu
        AAKG1_RAT | P80385: 2v8q 2v92 2v9j 2y8l 2y8q 2ya3 4cfh 4eai 4eaj 4eak 4eal 4qfg 4qfr 4qfs 5kq5 5t5t 5ufu

(-) Related Entries Specified in the PDB File

4eai 4eaj 4eak 4eal