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(-) Description

Title :  CRYSTAL STRUCTURE OF G PROTEIN COUPLED RECEPTOR KINASE 1 BOUND TO ATP AND MAGNESIUM CHLORIDE AT 2.9A
 
Authors :  P. Singh, J. J. G. Tesmer
Date :  30 Jan 08  (Deposition) - 11 Mar 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ser/Thr Kinase, Rgs Homology Domain, G Protein Coupled Receptor Kinase, Grk, Grk1, Rhodopsin Kinase, P-Loop, Autophosphorylation, Atp-Binding, Lipoprotein, Membrane, Methylation, Nucleotide-Binding, Phosphoprotein, Prenylation, Serine/Threonine-Protein Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Singh, B. Wang, T. Maeda, K. Palczewski, J. J. Tesmer
Structures Of Rhodopsin Kinase In Different Ligand States Reveal Key Elements Involved In G Protein-Coupled Receptor Kinase Activation.
J. Biol. Chem. V. 283 14053 2008
PubMed-ID: 18339619  |  Reference-DOI: 10.1074/JBC.M708974200

(-) Compounds

Molecule 1 - RHODOPSIN KINASE
    Cell LineHIGH 5
    ChainsA, B
    EC Number2.7.11.14
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System CommonCABBAGE LOOPER
    Expression System Taxid7111
    Expression System VectorPFASTBAC DUAL
    Expression System Vector TypeBACULOVIRUS
    FragmentUNP RESIDUES 1-535
    GeneGRK1, RHOK
    Organism CommonCATTLE
    Organism ScientificBOS TAURUS
    Organism Taxid9913
    SynonymRK, G PROTEIN-COUPLED RECEPTOR KINASE 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CL2Ligand/IonCHLORIDE ION
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:332BINDING SITE FOR RESIDUE MG A 564
2AC2SOFTWARELEU A:166 , GLN B:173BINDING SITE FOR RESIDUE CL A 565
3AC3SOFTWAREGLN A:287 , ARG A:290BINDING SITE FOR RESIDUE CL A 566
4AC4SOFTWAREASN B:319 , ASP B:332BINDING SITE FOR RESIDUE MG B 563
5AC5SOFTWARELEU A:193 , GLY A:194 , ARG A:195 , GLY A:196 , GLY A:197 , LYS A:216 , THR A:265 , MET A:267 , LEU A:321 , ASP A:332 , LYS A:497 , ALA A:498 , GLU A:501BINDING SITE FOR RESIDUE ATP A 562
6AC6SOFTWARELEU B:193 , GLY B:194 , GLY B:196 , GLY B:197 , ALA B:214 , LYS B:216 , THR B:265 , MET B:267 , LEU B:321 , ASP B:332BINDING SITE FOR RESIDUE ATP B 562

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3C4X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3C4X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3C4X)

(-) PROSITE Motifs  (4, 8)

Asymmetric/Biological Unit (4, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RGSPS50132 RGS domain profile.RK_BOVIN63-172
 
  2A:63-172
B:63-172
2PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.RK_BOVIN193-216
 
  2A:193-216
B:193-216
3PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.RK_BOVIN310-322
 
  2A:310-322
B:310-322
4AGC_KINASE_CTERPS51285 AGC-kinase C-terminal domain profile.RK_BOVIN453-518
 
  2A:453-518
B:453-518

(-) Exons   (7, 14)

Asymmetric/Biological Unit (7, 14)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSBTAT000000450681ENSBTAE00000216442chr12:84918428-84919117690RK_BOVIN1-2302302A:30-230
B:31-230 (gaps)
201
200
1.2ENSBTAT000000450682ENSBTAE00000413180chr12:84920231-8492029464RK_BOVIN231-252222A:231-252
B:231-252
22
22
1.6aENSBTAT000000450686aENSBTAE00000334122chr12:84924790-84925011222RK_BOVIN252-326752A:252-326
B:252-326
75
75
1.7ENSBTAT000000450687ENSBTAE00000400759chr12:84925672-8492575584RK_BOVIN326-354292A:326-354
B:326-354
29
29
1.8ENSBTAT000000450688ENSBTAE00000334116chr12:84936606-84936730125RK_BOVIN354-395422A:354-395
B:354-395
42
42
1.9ENSBTAT000000450689ENSBTAE00000334112chr12:84938172-84938373202RK_BOVIN396-463682A:396-463
B:396-463
68
68
1.10ENSBTAT0000004506810ENSBTAE00000334107chr12:84939509-84939807299RK_BOVIN463-561992A:463-533 (gaps)
B:463-533 (gaps)
71
71

(-) 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:496
 aligned with RK_BOVIN | P28327 from UniProtKB/Swiss-Prot  Length:561

    Alignment length:504
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529    
             RK_BOVIN    30 SRDRKYLARLKLPPLSKCEALRESLDLGFEGMCLEQPIGKRLFQQFLRTHEQHGPALQLWKDIEDYDTADDALRPQKAQALRAAYLEPQAQLFCSFLDAETVARARAGAGDGLFQPLLRAVLAHLGQAPFQEFLDSLYFLRFLQWKWLEAQPMGEDWFLDFRVLGRGGFGEVFACQMKATGKLYACKKLNKKRLKKRKGYQGAMVEKKILAKVHSRFIVSLAYAFETKTDLCLVMTIMNGGDIRYHIYNVDEDNPGFQEPRAIFYTAQIVSGLEHLHQRNIIYRDLKPENVLLDDDGNVRISDLGLAVELKAGQTKTKGYAGTPGFMAPELLLGEEYDFSVDYFALGVTLYEMIAARGPFRARGEKVENKELKQRVLEQAVTYPDKFSPASKDFCEALLQKDPEKRLGFRDGSCDGLRTHPLFRDISWRQLEAGMLTPPFVPDSRTVYAKNIQDVGAFSTVKGVAFEKADTEFFQEFASGTCPIPWQEEMIETGVFGDLNVWRP 533
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------3c4xA02 A:180-270 Phosphorylase Kinase; domain 1                                           3c4xA03 A:271-472 Transferase(Phosphotransferase) domain 1                                                                                                                                                ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhh.....hhhhhhhhhhh...hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeeeeeee....eeeeeee.....eeeeeeeehhhhhhh.hhhhhhhhhhhhhhh.......eeeeee...eeeeee.....eehhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee..................hhhhhhh....hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhh........hhhhhhhhhhhhh.hhhhh.......hhhhhhhhhhh..hhhhhhhh.........--------...............hhhhhhhhhhhh.eehhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------RGS  PDB: A:63-172 UniProt: 63-172                                                                            --------------------PROTEIN_KINASE_ATP      ---------------------------------------------------------------------------------------------PROTEIN_KINAS----------------------------------------------------------------------------------------------------------------------------------AGC_KINASE_CTER  PDB: A:453-518 UniProt: 453-518                  --------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:30-230 UniProt: 1-230 [INCOMPLETE]                                                                                                                                                      Exon 1.2              -------------------------------------------------------------------------Exon 1.7  PDB: A:326-354     ------------------------------------------------------------------------------------------------------------Exon 1.10  PDB: A:463-533 (gaps) UniProt: 463-561 [INCOMPLETE]          Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.6a  PDB: A:252-326 UniProt: 252-326                                 ---------------------------Exon 1.8  PDB: A:354-395 UniProt: 354-395 Exon 1.9  PDB: A:396-463 UniProt: 396-463                           ---------------------------------------------------------------------- Transcript 1 (2)
                 3c4x A  30 SRDRKYLARLKLPPLSKCEALRESLDLGFEGMCLEQPIGKRLFQQFLRTHEQHGPALQLWKDIEDYDTADDALRPQKAQALRAAYLEPQAQLFCSFLDAETVARARAGAGDGLFQPLLRAVLAHLGQAPFQEFLDSLYFLRFLQWKWLEAQPMGEDWFLDFRVLGRGGFGEVFACQMKATGKLYACKKLNKKRLKKRKGYQGAMVEKKILAKVHSRFIVSLAYAFETKTDLCLVMTIMNGGDIRYHIYNVDEDNPGFQEPRAIFYTAQIVSGLEHLHQRNIIYRDLKPENVLLDDDGNVRISDLGLAVELKAGQTKTKGYAGTPGFMAPELLLGEEYDFSVDYFALGVTLYEMIAARGPFRARGEKVENKELKQRVLEQAVTYPDKFSPASKDFCEALLQKDPEKRLGFRDGSCDGLRTHPLFRDISWRQLEAGMLTPPFVPD--------IQDVGAFSTVKGVAFEKADTEFFQEFASGTCPIPWQEEMIETGVFGDLNVWRP 533
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469  |      - |     489       499       509       519       529    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    472      481                                                    

Chain B from PDB  Type:PROTEIN  Length:475
 aligned with RK_BOVIN | P28327 from UniProtKB/Swiss-Prot  Length:561

    Alignment length:503
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530   
             RK_BOVIN    31 RDRKYLARLKLPPLSKCEALRESLDLGFEGMCLEQPIGKRLFQQFLRTHEQHGPALQLWKDIEDYDTADDALRPQKAQALRAAYLEPQAQLFCSFLDAETVARARAGAGDGLFQPLLRAVLAHLGQAPFQEFLDSLYFLRFLQWKWLEAQPMGEDWFLDFRVLGRGGFGEVFACQMKATGKLYACKKLNKKRLKKRKGYQGAMVEKKILAKVHSRFIVSLAYAFETKTDLCLVMTIMNGGDIRYHIYNVDEDNPGFQEPRAIFYTAQIVSGLEHLHQRNIIYRDLKPENVLLDDDGNVRISDLGLAVELKAGQTKTKGYAGTPGFMAPELLLGEEYDFSVDYFALGVTLYEMIAARGPFRARGEKVENKELKQRVLEQAVTYPDKFSPASKDFCEALLQKDPEKRLGFRDGSCDGLRTHPLFRDISWRQLEAGMLTPPFVPDSRTVYAKNIQDVGAFSTVKGVAFEKADTEFFQEFASGTCPIPWQEEMIETGVFGDLNVWRP 533
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------------------------------------------3c4xB02 B:180-270 Phosphorylase Kinase; domain 1                                           3c4xB03 B:271-472 Transferase(Phosphotransferase) domain 1                                                                                                                                                ------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.....hhhhhhhhhh....hhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...........hhhhhhhh--------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeeeeeee....eeeeeee.....eeeeeeeehhhhhhh.hhhhhhhhhhhhhhh.......eeeeee...eeeeee......hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee..................hhhhhhh....hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhh........hhhhhhhhhhhh..hhhhh.......hhhhhhhhhhh..hhhhhhh.............--------------------hhhhhhhhhhhh.eehhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------RGS  PDB: B:63-172 UniProt: 63-172                                                                            --------------------PROTEIN_KINASE_ATP      ---------------------------------------------------------------------------------------------PROTEIN_KINAS----------------------------------------------------------------------------------------------------------------------------------AGC_KINASE_CTER  PDB: B:453-518 UniProt: 453-518                  --------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:31-230 (gaps) UniProt: 1-230 [INCOMPLETE]                                                                                                                                              Exon 1.2              -------------------------------------------------------------------------Exon 1.7  PDB: B:326-354     ------------------------------------------------------------------------------------------------------------Exon 1.10  PDB: B:463-533 (gaps) UniProt: 463-561 [INCOMPLETE]          Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.6a  PDB: B:252-326 UniProt: 252-326                                 ---------------------------Exon 1.8  PDB: B:354-395 UniProt: 354-395 Exon 1.9  PDB: B:396-463 UniProt: 396-463                           ---------------------------------------------------------------------- Transcript 1 (2)
                 3c4x B  31 RDRKYLARLKLPPLSKCEALRESLDLGFEGMCLEQPIGKRLFQQFLRTHEQHGPALQLWKDIEDYDTADDALRPQKAQALRAAYLEPQAQLFCSFLDAETVARA--------FQPLLRAVLAHLGQAPFQEFLDSLYFLRFLQWKWLEAQPMGEDWFLDFRVLGRGGFGEVFACQMKATGKLYACKKLNKKRLKKRKGYQGAMVEKKILAKVHSRFIVSLAYAFETKTDLCLVMTIMNGGDIRYHIYNVDEDNPGFQEPRAIFYTAQIVSGLEHLHQRNIIYRDLKPENVLLDDDGNVRISDLGLAVELKAGQTKTKGYAGTPGFMAPELLLGEEYDFSVDYFALGVTLYEMIAARGPFRARGEKVENKELKQRVLEQAVTYPDKFSPASKDFCEALLQKDPEKRLGFRDGSCDGLRTHPLFRDISWRQLEAGMLTPPFVPDSRT--------------------EKADTEFFQEFASGTCPIPWQEEMIETGVFGDLNVWRP 533
                                    40        50        60        70        80        90       100       110       120       130   |     -  |    150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470    |    -         -     | 500       510       520       530   
                                                                                                                                 134      143                                                                                                                                                                                                                                                                                                                                         475                  496                                     

   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 3C4X)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3C4X)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RK_BOVIN | P28327)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004703    G-protein coupled receptor kinase activity    Catalysis of the reaction: ATP + G-protein coupled receptor = ADP + G-protein coupled receptor phosphate.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0050254    rhodopsin kinase activity    Catalysis of the reaction: ATP + rhodopsin = ADP + phosphorhodopsin.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0022400    regulation of rhodopsin mediated signaling pathway    Any process that modulates the frequency, rate or extent of rhodopsin-mediated signaling.
    GO:0050896    response to stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
    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:0007601    visual perception    The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0097381    photoreceptor disc membrane    Ovally-shaped membranous stack located inside the photoreceptor outer segment, and containing densely packed molecules of the photoreceptor protein rhodopsin that traverse the lipid bilayer. Disc membranes are apparently derived from the plasma membrane in the region of the cilium that connects the photoreceptor outer segment to the inner segment.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RK_BOVIN | P283272i94 3c4w 3c4y 3c4z 3c50 3c51 3qc9 3t8o 4l9i 4pni 4wbo

(-) Related Entries Specified in the PDB File

3c4w 3c4y 3c4z 3c50 3c51