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(-) Description

Title :  CRYSTAL STRUCTURE OF CAMP BOUND CGMP-DEPENDENT PROTEIN KINASE(92-227)
 
Authors :  J. J. Kim, G. Huang, T. K. Kwon, P. Zwart, J. Headd, C. Kim
Date :  10 Aug 10  (Deposition) - 11 May 11  (Release) - 18 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Serine/Threonine Kinase, Tf2I And Irag, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. J. Kim, D. E. Casteel, G. Huang, T. H. Kwon, R. K. Ren, P. Zwart, J. J. Headd, N. G. Brown, D. C. Chow, T. Palzkill, C. Kim
Co-Crystal Structures Of Pkg Ibeta (92-227) With Cgmp And Camp Reveal The Molecular Details Of Cyclic-Nucleotide Binding
Plos One V. 6 E1841 2011
PubMed-ID: 21526164  |  Reference-DOI: 10.1371/JOURNAL.PONE.0018413

(-) Compounds

Molecule 1 - PRKG1 PROTEIN
    ChainsA, B
    EC Number2.7.11.12
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQTEV
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentCYCLIC NUCLEOTIE BINDING DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CMP2Ligand/IonADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:172 , CYS A:173 , PHE A:181 , GLY A:182 , GLU A:183 , LEU A:184 , ALA A:185 , ARG A:192 , THR A:193 , ALA A:194 , HOH A:239BINDING SITE FOR RESIDUE CMP A 250
2AC2SOFTWARETYR A:188 , VAL B:165 , LEU B:172 , CYS B:173 , MET B:175 , PHE B:181 , GLY B:182 , GLU B:183 , LEU B:184 , ALA B:185 , ARG B:192 , THR B:193 , ALA B:194 , HOH B:232BINDING SITE FOR RESIDUE CMP B 250

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_070434R177QKGP1_HUMANDisease (AAT8)397515330A/BR192Q

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CNMP_BINDING_3PS50042 cAMP/cGMP binding motif profile.KGP1_HUMAN103-218
 
221-342
  2A:118-218
B:118-219
-
2CNMP_BINDING_1PS00888 Cyclic nucleotide-binding domain signature 1.KGP1_HUMAN130-146
 
248-264
  2A:145-161
B:145-161
-
3CNMP_BINDING_2PS00889 Cyclic nucleotide-binding domain signature 2.KGP1_HUMAN166-183
 
290-307
  2A:181-198
B:181-198
-

(-) Exons   (4, 8)

Asymmetric/Biological Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003739851aENSE00001462090chr10:52751118-52751404287KGP1_HUMAN1-77772A:92-98
B:92-98
7
7
1.3aENST000003739853aENSE00001290472chr10:52912924-52913090167KGP1_HUMAN77-133572A:99-148
B:99-148
50
50
1.4ENST000003739854ENSE00001311075chr10:53227483-53227596114KGP1_HUMAN133-171392A:148-186
B:148-186
39
39
1.5ENST000003739855ENSE00001319764chr10:53564345-53564450106KGP1_HUMAN171-206362A:186-218
B:186-219
33
34
1.6ENST000003739856ENSE00001295696chr10:53667267-5366733064KGP1_HUMAN206-227220--
1.9ENST000003739859ENSE00001660611chr10:53814244-5381432178KGP1_HUMAN228-253260--
1.10ENST0000037398510ENSE00001716439chr10:53822297-5382239195KGP1_HUMAN254-285320--
1.13ENST0000037398513ENSE00001660103chr10:53893600-5389366566KGP1_HUMAN285-307230--
1.14ENST0000037398514ENSE00001757920chr10:53921649-5392172375KGP1_HUMAN307-332260--
1.15ENST0000037398515ENSE00001724869chr10:54011330-5401142697KGP1_HUMAN332-364330--
1.16ENST0000037398516ENSE00001705894chr10:54031110-54031249140KGP1_HUMAN365-411470--
1.17ENST0000037398517ENSE00001313981chr10:54032152-5403224190KGP1_HUMAN411-441310--
1.18ENST0000037398518ENSE00001317306chr10:54040549-54040690142KGP1_HUMAN441-488480--
1.19ENST0000037398519ENSE00001323221chr10:54041913-54042076164KGP1_HUMAN489-543550--
1.20ENST0000037398520ENSE00001300564chr10:54048486-54048608123KGP1_HUMAN543-584420--
1.21ENST0000037398521ENSE00001321548chr10:54048691-5404875363KGP1_HUMAN584-605220--
1.22ENST0000037398522ENSE00001303642chr10:54049984-5405005067KGP1_HUMAN605-627230--
1.23cENST0000037398523cENSE00001462071chr10:54053562-540581104549KGP1_HUMAN628-659320--

(-) 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:127
 aligned with KGP1_HUMAN | Q13976 from UniProtKB/Swiss-Prot  Length:671

    Alignment length:161
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202 
           KGP1_HUMAN    43 CQSVLPVPSTHIGPRTTRAQGISAEPQTYRSFHDLRQAFRKFTKSERSKDLIKEAILDNDFMKNLELSQIQEIVDCMYPVEYGKDSCIIKEGDVGSLVYVMEDGKVEVTKEGVKLCTMGPGKVFGELAILYNCTRTATVKTLVNVKLWAIDRQCFQTIMMR 203
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......----------------------------------...hhhhhhhhhhhhhhh......hhhhhhhhhhhheeeee....eee.......eeeeeee..eeeee..eeeeee....ee.hhhhhhh.....eeee...eeeeeeehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------Q-------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------------CNMP_BINDING_3  PDB: A:118-218 UniProt: 103-218                                                       PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------CNMP_BINDING_1   -------------------CNMP_BINDING_2    -------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1a  PDB: A:92-98            -------------------------------------------------------Exon 1.4  PDB: A:148-186               -------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.3a  PDB: A:99-148 UniProt: 77-133 [INCOMPLETE]    -------------------------------------Exon 1.5  PDB: A:186-218          Transcript 1 (2)
                 3ocp A  92 SHVTLPF----------------------------------YPKSPQSKDLIKEAILDNDFMKNLELSQIQEIVDCMYPVEYGKDSCIIKEGDVGSLVYVMEDGKVEVTKEGVKLCTMGPGKVFGELAILYNCTRTATVKTLVNVKLWAIDRQCFQTIMMR 218
                                  |  -         -         -         - |     107       117       127       137       147       157       167       177       187       197       207       217 
                                 98                                 99                                                                                                                       

Chain B from PDB  Type:PROTEIN  Length:128
 aligned with KGP1_HUMAN | Q13976 from UniProtKB/Swiss-Prot  Length:671

    Alignment length:162
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202  
           KGP1_HUMAN    43 CQSVLPVPSTHIGPRTTRAQGISAEPQTYRSFHDLRQAFRKFTKSERSKDLIKEAILDNDFMKNLELSQIQEIVDCMYPVEYGKDSCIIKEGDVGSLVYVMEDGKVEVTKEGVKLCTMGPGKVFGELAILYNCTRTATVKTLVNVKLWAIDRQCFQTIMMRT 204
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------cNMP_binding-3ocpB01 B:136-219                                                       Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------cNMP_binding-3ocpB02 B:136-219                                                       Pfam domains (2)
         Sec.struct. author .......----------------------------------...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhheeeee....eee.......eeeeeee..eeeee..eeeeee....ee.hhhhhh......eeee...eeeeeeehhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------Q--------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------------CNMP_BINDING_3  PDB: B:118-219 UniProt: 103-218                                                        PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------CNMP_BINDING_1   -------------------CNMP_BINDING_2    --------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1a  PDB: B:92-98            -------------------------------------------------------Exon 1.4  PDB: B:148-186               --------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.3a  PDB: B:99-148 UniProt: 77-133 [INCOMPLETE]    -------------------------------------Exon 1.5  PDB: B:186-219           Transcript 1 (2)
                 3ocp B  92 SHVTLPF----------------------------------YPKSPQSKDLIKEAILDNDFMKNLELSQIQEIVDCMYPVEYGKDSCIIKEGDVGSLVYVMEDGKVEVTKEGVKLCTMGPGKVFGELAILYNCTRTATVKTLVNVKLWAIDRQCFQTIMMRT 219
                                  |  -         -         -         - |     107       117       127       137       147       157       167       177       187       197       207       217  
                                 98                                 99                                                                                                                        

   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 3OCP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OCP)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (KGP1_HUMAN | Q13976)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0030553    cGMP binding    Interacting selectively and non-covalently with cGMP, the nucleotide cyclic GMP (guanosine 3',5'-cyclophosphate).
    GO:0004692    cGMP-dependent protein kinase activity    Catalysis of the reaction: ATP + a protein = ADP + a phosphoprotein. This reaction requires the presence of cGMP.
    GO:0005246    calcium channel regulator activity    Modulates the activity of a calcium channel.
    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: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: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:0030036    actin cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0019934    cGMP-mediated signaling    Any intracellular signal transduction in which the signal is passed on within the cell via cyclic GMP (cGMP). Includes production of cGMP, and downstream effectors that further transmit the signal within the cell.
    GO:0016358    dendrite development    The process whose specific outcome is the progression of the dendrite over time, from its formation to the mature structure. A dendrite is a freely branching protoplasmic process of a nerve cell.
    GO:0030900    forebrain development    The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions).
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0090331    negative regulation of platelet aggregation    Any process that decreases the rate, frequency or extent of platelet aggregation. Platelet aggregation is the adhesion of one platelet to one or more other platelets via adhesion molecules.
    GO:0045986    negative regulation of smooth muscle contraction    Any process that stops, prevents, or reduces the frequency, rate or extent of smooth muscle contraction.
    GO:0001764    neuron migration    The characteristic movement of an immature neuron from germinal zones to specific positions where they will reside as they mature.
    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:0098779    positive regulation of macromitophagy in response to mitochondrial depolarization    The macromitophagy process that is triggered by a detection of the loss of mitochondrial membrane potential.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0043087    regulation of GTPase activity    Any process that modulates the rate of GTP hydrolysis by a GTPase.
    GO:0060087    relaxation of vascular smooth muscle    A negative regulation of smooth muscle contraction resulting in relaxation of vascular smooth muscle. The relaxation is mediated by a decrease in the phosphorylation state of myosin light chain. This can be achieved by removal of calcium from the cytoplasm to the sarcoplasmic reticulum lumen through the action of Ca2+ ATPases leading to a decrease myosin light chain kinase activity, and through calcium-independent pathways leading to a increase in myosin light chain phosphatase activity.
    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.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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
        KGP1_HUMAN | Q139761zxa 3nmd 3od0 3ogj 4ku7 4ku8 4qx5 4qxk 4r4l 4r4m 4z07 5j48 5jax

(-) Related Entries Specified in the PDB File

3od0 CRYSTAL STRUCTURE OF CGMP BOUND PKG(92-227)
3ogj CRYSTAL STRUCTURE OF PARTIAL APO (92-227) OF CGMP-DEPENDENT PROTEIN KINASE