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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC SUBUNIT OF CAMP-DEPENDENT PROTEIN KINASE DISPLAYING COMPLETE PHOSPHORYL TRANSFER OF AMP-PNP ONTO A SUBSTRATE PEPTIDE
 
Authors :  A. C. Bastidas, J. M. Steichen, J. Wu, S. S. Taylor
Date :  24 Oct 12  (Deposition) - 20 Mar 13  (Release) - 10 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  E,I
Keywords :  Protein Kinase, Phosphotransferase, Regulatory Subunits, Pki, Magnesium, Phosphorylation, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. C. Bastidas, M. S. Deal, J. M. Steichen, Y. Guo, J. Wu, S. S. Taylor
Phosphoryl Transfer By Protein Kinase A Is Captured In A Crystal Lattice.
J. Am. Chem. Soc. V. 135 4788 2013
PubMed-ID: 23458248  |  Reference-DOI: 10.1021/JA312237Q

(-) Compounds

Molecule 1 - CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA
    Chains: E
    EC Number: 2.7.11.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PRKACA, PKACA
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: PKA C-ALPHA
 
Molecule 2 - CAMP-DEPENDENT PROTEIN KINASE INHIBITOR ALPHA
    Chains: I
    Engineered: YES
    Fragment: SP20 DERIVED FROM PKI (UNP RESIDUES 6-25)
    Mutation: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: SYNTHETIC PEPTIDE
    Synonym: PKI-ALPHA, CAMP-DEPENDENT PROTEIN KINASE INHIBITOR, MUSCLE/BRAIN ISOFORM
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : EI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG2Ligand/IonMAGNESIUM ION
3SEP2Mod. Amino AcidPHOSPHOSERINE
4TPO1Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY E:50 , GLY E:52 , VAL E:57 , ALA E:70 , LYS E:72 , VAL E:104 , MET E:120 , GLU E:121 , TYR E:122 , VAL E:123 , GLU E:127 , GLU E:170 , ASN E:171 , LEU E:173 , THR E:183 , ASP E:184 , PHE E:327 , MG E:402 , MG E:403 , HOH E:520 , HOH E:556 , HOH E:594 , HOH E:646 , ARG I:18 , SEP I:21 , HOH I:104BINDING SITE FOR RESIDUE ANP E 401
2AC2SOFTWAREASN E:171 , ASP E:184 , ANP E:401 , HOH E:520 , HOH I:104BINDING SITE FOR RESIDUE MG E 402
3AC3SOFTWAREASP E:184 , ANP E:401 , HOH E:519 , SEP I:21 , HOH I:101BINDING SITE FOR RESIDUE MG E 403
4AC4SOFTWARESER E:53 , GLN E:84 , GLU E:86 , ARG E:93 , GLU E:127 , PHE E:129 , ARG E:133 , ASP E:166 , LYS E:168 , PRO E:169 , GLU E:170 , ASP E:184 , PHE E:187 , ARG E:190 , LYS E:192 , LEU E:198 , CYS E:199 , GLY E:200 , PRO E:202 , GLU E:203 , GLU E:230 , TYR E:235 , PRO E:236 , PHE E:239 , ALA E:240 , ASP E:241 , ILE E:246 , TYR E:330 , GLU E:349 , ANP E:401 , MG E:403 , HOH E:519 , HOH E:530 , HOH E:544 , HOH E:558 , HOH E:576 , HOH E:596 , HOH E:603 , HOH E:622 , HOH I:101 , HOH I:102 , HOH I:103 , HOH I:104 , HOH I:105 , HOH I:106 , HOH I:109 , HOH I:110 , HOH I:111 , HOH I:112 , HOH I:113 , HOH I:114 , HOH I:116 , HOH I:117BINDING SITE FOR CHAIN I OF CAMP-DEPENDENT PROTEIN KINASE INHIBITOR ALPHA

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HPT)

(-) 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 E from PDB  Type:PROTEIN  Length:337
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh......hhh.eeeeeeeee...eeeeeeee.....eeeeeeeehhhhhhh.hhhhhhhhhhhhh.........eeeeee...eeeeeee.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee..........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.........hhhhhhhhhhhh..............hhhhhhhhhhh..hhhhhhh........................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hpt E  14 SVKEFLAKAKEDFLKKWETPSQNTAQLDQFDRIKTLGTGSFGRVMLVKHKESGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVAGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWtLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVsINEKCGKEFTEF 350
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193   |   203       213       223       233       243       253       263       273       283       293       303       313       323       333    |  343       
                                                                                                                                                                                                                 197-TPO                                                                                                                                      338-SEP        


Chain I from PDB  Type:PROTEIN  Length:19
                                                   
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author .hhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                 4hpt I   5 TTYADFIASGRTGRRAsIH  23
                                    14      |  
                                           21-SEP
   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  (0, 0)

(no "SCOP Domain" information available for 4HPT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (70, 72)

Asymmetric/Biological Unit(hide GO term definitions)

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  4hpt
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  IPKA_MOUSE | P63248
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  KAPCA_MOUSE | P05132
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  2.7.11.11
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 Related Entries

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

UniProtKB/Swiss-Prot
        IPKA_MOUSE | P63248: 1apm 1atp 1jbp 1jlu 1l3r 1pvk 2cpk 2gnf 2gng 2qur 3fjq 3ow3 3qal 3qam 3zo2 4dfx 4dfz 4dg0 4dg2 4dg3 4dh1 4dh3 4dh5 4dh7 4dh8 4hpu
        KAPCA_MOUSE | P05132: 1apm 1atp 1bkx 1bx6 1fmo 1j3h 1jbp 1jlu 1l3r 1pvk 1rdq 1re8 1rej 1rek 1syk 2cpk 2erz 2qcs 2qur 2qvs 3fhi 3fjq 3idb 3idc 3j4q 3j4r 3o7l 3ow3 3pvb 3qal 3qam 3tnp 3tnq 3x2u 3x2v 3x2w 4dfx 4dfy 4dfz 4dg0 4dg2 4dg3 4dh1 4dh3 4dh5 4dh7 4dh8 4din 4hpu 4iac 4iad 4iaf 4iai 4iak 4iay 4iaz 4ib0 4ib1 4ib3 4nts 4ntt 4o21 4o22 4wbb 4x6q 4x6r 4xw4 4xw5 4xw6 5jr7 5x3f

(-) Related Entries Specified in the PDB File

1atp SAME PROTEIN IN COMPLEX WITH IP20
1jbp SAME PROTEIN IN COMPLEX WITH THE SAME SUBSTRATE PEPTIDE AND ADP
1jlu SAME PROTEIN IN A COMPLEX WITH THE SAME SUBSTRATE PEPTIDE THAT WAS PHOSPHORYLATED PRIOR TO CRYSTALLIZATION
1l3r TRANSITION STATE MIMIC OF SAME PROTEIN IN COMPLEX WITH THE SAME SUBSTRATE PEPTIDE
4dfx MYRISTYLATED CATALYTIC SUBUNIT WITH A K7C MUTATION IN COMPLEX WITH AMP-PNP AND THE SAME SUBSTRATE PEPTIDE WITHOUT TRANSFER
4dg0 MYRISTYLATED CATALYTIC SUBUNIT IN COMPLEX WITH AMP-PNP AND THE SAME SUBSTRATE PEPTIDE WITHOUT TRANSFER
4dh1 STRUCTURE OF THE SAME PROTEIN WITH LOW MAGNESIUM SHOWING OCCUPANCY OF ONLY ONE MAGNESIUM SITE, MG2.
4hpu