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(-) Description

Title :  REGULATORY APPARATUS OF CALCIUM DEPENDENT PROTEIN KINASE FROM ARABIDOPSIS THALIANA
 
Authors :  V. Chandran, E. J. Stollar, K. Lindorff-Larsen, J. F. Harper, W. J. Chaz C. M. Dobson, B. F. Luisi, J. Christodoulou
Date :  13 Jul 05  (Deposition) - 27 Dec 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Calcium Dependent Protein Kinase, Calmodulin-Like Domain, Ef Hand, Calcium Binding Protein, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. Chandran, E. J. Stollar, K. Lindorff-Larsen, J. F. Harper, W. J. Chazin, C. M. Dobson, B. F. Luisi, J. Christodoulou
Structure Of The Regulatory Apparatus Of A Calcium-Dependen Protein Kinase (Cdpk): A Novel Mode Of Calmodulin-Target Recognition.
J. Mol. Biol. V. 357 400 2006
PubMed-ID: 16430916  |  Reference-DOI: 10.1016/J.JMB.2005.11.093

(-) Compounds

Molecule 1 - CALCIUM-DEPENDENT PROTEIN KINASE, ISOFORM AK1
    ChainsA, B
    EC Number2.7.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneAK1
    Organism CommonTHALE CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    SynonymCDPK

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (1x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 25)

Asymmetric Unit (2, 25)
No.NameCountTypeFull Name
1CA9Ligand/IonCALCIUM ION
2MSE16Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 8)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 16)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE16Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:37 , ASP A:39 , SER A:41 , GLN A:43 , GLU A:48 , HOH A:298BINDING SITE FOR RESIDUE CA A 293
2AC2SOFTWAREASP A:73 , ASP A:75 , SER A:77 , THR A:79 , GLU A:84 , HOH A:305BINDING SITE FOR RESIDUE CA A 294
3AC3SOFTWAREASP A:109 , ASP A:111 , SER A:113 , TYR A:115 , GLU A:120 , HOH A:309BINDING SITE FOR RESIDUE CA A 295
4AC4SOFTWAREASP A:143 , ASP A:145 , ASP A:147 , ARG A:149 , GLU A:154 , HOH A:310BINDING SITE FOR RESIDUE CA A 296
5AC5SOFTWAREASP B:37 , ASP B:39 , SER B:41 , GLN B:43 , GLU B:48 , HOH B:305BINDING SITE FOR RESIDUE CA B 297
6AC6SOFTWAREASP B:73 , ASP B:75 , SER B:77 , THR B:79 , GLU B:84 , HOH B:312BINDING SITE FOR RESIDUE CA B 298
7AC7SOFTWAREASP B:109 , ASP B:111 , SER B:113 , TYR B:115 , GLU B:120BINDING SITE FOR RESIDUE CA B 299
8AC8SOFTWAREASP B:143 , ASP B:145 , ASP B:147 , ARG B:149 , GLU B:154 , HOH B:316BINDING SITE FOR RESIDUE CA B 300
9AC9SOFTWAREHOH A:359 , ASN B:76 , HOH B:311BINDING SITE FOR RESIDUE CA B 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2AAO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 16)

Asymmetric Unit (2, 16)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.CDPK1_ARATH451-486
 
487-522
 
523-558
 
561-592
 
  8A:24-59
B:24-59
A:60-95
B:60-95
A:96-127
B:96-123
A:136-160
B:139-160
2EF_HAND_1PS00018 EF-hand calcium-binding domain.CDPK1_ARATH464-476
 
500-512
 
536-548
 
570-582
 
  8A:37-49
B:37-49
A:73-85
B:73-85
A:109-121
B:109-121
A:143-155
B:143-155
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.CDPK1_ARATH451-486
 
487-522
 
523-558
 
561-592
 
  4A:24-59
-
A:60-95
-
A:96-127
-
A:136-160
-
2EF_HAND_1PS00018 EF-hand calcium-binding domain.CDPK1_ARATH464-476
 
500-512
 
536-548
 
570-582
 
  4A:37-49
-
A:73-85
-
A:109-121
-
A:143-155
-
Biological Unit 2 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.CDPK1_ARATH451-486
 
487-522
 
523-558
 
561-592
 
  4-
B:24-59
-
B:60-95
-
B:96-123
-
B:139-160
2EF_HAND_1PS00018 EF-hand calcium-binding domain.CDPK1_ARATH464-476
 
500-512
 
536-548
 
570-582
 
  4-
B:37-49
-
B:73-85
-
B:109-121
-
B:143-155
Biological Unit 3 (2, 16)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.CDPK1_ARATH451-486
 
487-522
 
523-558
 
561-592
 
  8A:24-59
B:24-59
A:60-95
B:60-95
A:96-127
B:96-123
A:136-160
B:139-160
2EF_HAND_1PS00018 EF-hand calcium-binding domain.CDPK1_ARATH464-476
 
500-512
 
536-548
 
570-582
 
  8A:37-49
B:37-49
A:73-85
B:73-85
A:109-121
B:109-121
A:143-155
B:143-155

(-) Exons   (0, 0)

(no "Exon" information available for 2AAO)

(-) 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:147
 aligned with CDPK1_ARATH | Q06850 from UniProtKB/Swiss-Prot  Length:610

    Alignment length:155
                                   442       452       462       472       482       492       502       512       522       532       542       552       562       572       582     
          CDPK1_ARATH   433 MNKFKKMALRVIAESLSEEEIAGLKEMFNMIDADKSGQITFEELKAGLKRVGANLKESEILDLMQAADVDNSGTIDYKEFIAATLHLNKIEREDHLFAAFTYFDKDGSGYITPDELQQACEEFGVEDVRIEELMRDVDQDNDGRIDYNEFVAMMQ 587
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhhhhhhhhh.hhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.--------.hhhhhhh.......hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------EF_HAND_2  PDB: A:24-59             EF_HAND_2  PDB: A:60-95             EF_HAND_2  PDB: A:96-127            --EF_HAND_2  PDB: A:136-160   PROSITE (1)
                PROSITE (2) -------------------------------EF_HAND_1    -----------------------EF_HAND_1    -----------------------EF_HAND_1    ---------------------EF_HAND_1    ----- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aao A   6 mNKFKKmALRVIAESLSEEEIAGLKEmFNmIDADKSGQITFEELKAGLKRVGANLKESEILDLmQAADVDNSGTIDYKEFIAATLHLNKIEREDHLFAAFTYFDKDGSGYITPDELQQACEE--------EELmRDVDQDNDGRIDYNEFVAmmQ 160
                            |     | 15        25      | 35        45        55        65   |    75        85        95       105       115       125 |       -|  |   145       155  || 
                            |     |                  32-MSE                               69-MSE                                                   127      136  |                158-MSE
                            6-MSE |                     35-MSE                                                                                                 139-MSE             159-MSE
                                 12-MSE                                                                                                                                                

Chain B from PDB  Type:PROTEIN  Length:140
 aligned with CDPK1_ARATH | Q06850 from UniProtKB/Swiss-Prot  Length:610

    Alignment length:155
                                   442       452       462       472       482       492       502       512       522       532       542       552       562       572       582     
          CDPK1_ARATH   433 MNKFKKMALRVIAESLSEEEIAGLKEMFNMIDADKSGQITFEELKAGLKRVGANLKESEILDLMQAADVDNSGTIDYKEFIAATLHLNKIEREDHLFAAFTYFDKDGSGYITPDELQQACEEFGVEDVRIEELMRDVDQDNDGRIDYNEFVAMMQ 587
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.....eeehhhhhhhhhhhh...hhhhhhhhhhhhh.....eeehhhhhhhhh.......hhhhhhhhhhhh.........hhhhh---------------............hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------EF_HAND_2  PDB: B:24-59             EF_HAND_2  PDB: B:60-95             EF_HAND_2  PDB: B:96-123            --EF_HAND_2  PDB: B:139-160   PROSITE (1)
                PROSITE (2) -------------------------------EF_HAND_1    -----------------------EF_HAND_1    -----------------------EF_HAND_1    ---------------------EF_HAND_1    ----- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aao B   6 mNKFKKmALRVIAESLSEEEIAGLKEmFNmIDADKSGQITFEELKAGLKRVGANLKESEILDLmQAADVDNSGTIDYKEFIAATLHLNKIEREDHLFAAFTYFDKDGSGYITPDELQQ---------------mRDVDQDNDGRIDYNEFVAmmQ 160
                            |     | 15        25      | 35        45        55        65   |    75        85        95       105       115       | -         -   |   145       155  || 
                            |     |                  32-MSE                               69-MSE                                               123             139-MSE            158-MSE
                            6-MSE |                     35-MSE                                                                                                                     159-MSE
                                 12-MSE                                                                                                                                                

   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 2AAO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2AAO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2AAO)

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CDPK1_ARATH | Q06850)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0009931    calcium-dependent protein serine/threonine kinase activity    Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; and ATP + a protein threonine = ADP + protein threonine phosphate. These reactions are dependent on the presence of calcium ions.
    GO:0005516    calmodulin binding    Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
    GO:0004683    calmodulin-dependent protein kinase activity    Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; and ATP + a protein threonine = ADP + protein threonine phosphate. These reactions require the presence of calcium-bound calmodulin.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0009738    abscisic acid-activated signaling pathway    A series of molecular signals generated by the binding of the plant hormone abscisic acid (ABA) to a receptor, and ending with modulation of a cellular process, e.g. transcription.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0018105    peptidyl-serine phosphorylation    The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
    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.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.
    GO:0005778    peroxisomal membrane    The lipid bilayer surrounding a peroxisome.
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.
    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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