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(-) Description

Title :  CA2+-REGULATORY REGION (CLD) FROM SOYBEAN CALCIUM-DEPENDENT PROTEIN KINASE-ALPHA (CDPK) IN THE PRESENCE OF CA2+ AND THE JUNCTION DOMAIN (JD)
 
Authors :  A. M. Weljie, H. J. Vogel
Date :  23 Jan 04  (Deposition) - 15 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (15x)
Keywords :  Ef-Hand; Helix-Loop-Helix; Calcium-Binding; Calmodulin Superfamily, Transferase, Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. Weljie, H. J. Vogel
Unexpected Structure Of The Ca2+-Regulatory Region From Soybean Calcium-Dependent Protein Kinase-Alpha
J. Biol. Chem. V. 279 35494 2004
PubMed-ID: 15155727  |  Reference-DOI: 10.1074/JBC.M311520200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CALCIUM-DEPENDENT PROTEIN KINASE SK5
    Chains: A
    EC Number: 2.7.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PT7-7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: CALMODULIN-LIKE DOMAIN (CLD) AND C-TERMINAL TAIL
    Gene: CDPK SK5
    Organism Common: SOYBEAN
    Organism Scientific: GLYCINE MAX
    Organism Taxid: 3847
    Other Details: CA2+-BINDING REGION AND C-TERMINAL TAIL, ALONG WITH HIS(6) AT C-TERMINUS
    Synonym: CDPK;
CALCIUM-DEPENDENT PROTEIN KINASE-ALPHA

 Structural Features

(-) Chains, Units

  
NMR Structure (15x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

NMR Structure (1, 4)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION

(-) Sites  (4, 4)

NMR Structure (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:20 , ASN A:23 , THR A:26 , GLU A:31BINDING SITE FOR RESIDUE CA A 189
2AC2SOFTWAREASP A:58 , SER A:60 , THR A:62 , GLU A:67BINDING SITE FOR RESIDUE CA A 190
3AC3SOFTWAREASP A:94 , SER A:96 , TYR A:98 , GLU A:103BINDING SITE FOR RESIDUE CA A 191
4AC4SOFTWAREASP A:126 , ASP A:128 , ASN A:129 , ASP A:130 , GLY A:131 , GLN A:132 , GLU A:137BINDING SITE FOR RESIDUE CA A 192

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1S6I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1S6I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S6I)

(-) PROSITE Motifs  (2, 8)

NMR Structure (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.CDPK_SOYBN335-370
371-406
407-442
445-476		  4A:7-42
A:43-78
A:79-114
A:117-150
2EF_HAND_1PS00018 EF-hand calcium-binding domain.CDPK_SOYBN348-360
384-396
420-432
454-466		  4A:20-32
A:56-68
A:92-104
A:126-138

(-) Exons   (0, 0)

(no "Exon" information available for 1S6I)

(-) Sequences/Alignments

NMR Structure
   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:182
 aligned with CDPK_SOYBN | P28583 from UniProtKB/Swiss-Prot  Length:508

    Alignment length:182
                                                                                                                                                                            473                                   
                                                                                                                                                                         472  |                                   
                                   338       348       358       368       378       388       398       408       418       428       438       448       458       468   |  |476       486       496       506  
           CDPK_SOYBN   329 AERLSEEEIGGLKELFKMIDTDNSGTITFDELKDGLKRVGSELMESEIKDLMDAADIDKSGTIDYGEFIAATVHLNKLEREENLVSAFSYFDKDGSGYITLDEIQQACKDFGLDDIHIDDMIKEIDQDNDGQIDYGEFAAMMRK--GNGGIGRRTMRKTLNLRDALGLVDNGSNQVIEGYFK 508
               SCOP domains d1s6ia_ A: Calcium-dependent protein kinase sk5 CLD                                                                                                                                    SCOP domains
               CATH domains 1s6iA01 A:1-76 EF-hand                                                      1s6iA02 A:77-182 EF-hand                                                                                   CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------efhand-1s6iA01 A:117-147       ----------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------efhand-1s6iA02 A:117-147       ----------------------------------- Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------efhand-1s6iA03 A:117-147       ----------------------------------- Pfam domains (3)
         Sec.struct. author ..........hhhhhhhh........eehhhhhhhhh......hhhhhhhhhhhh......eehhhhhhhhhh..........hhhhhhhh......eeehhhhhhh........hhhhhhhhhhh.....eee.hhhhhh......................................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------EF_HAND_2  PDB: A:7-42              EF_HAND_2  PDB: A:43-78             EF_HAND_2  PDB: A:79-114            --EF_HAND_2  PDB: A:117-150         -------------------------------- PROSITE (1)
                PROSITE (2) -------------------EF_HAND_1    -----------------------EF_HAND_1    -----------------------EF_HAND_1    ---------------------EF_HAND_1    -------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s6i A   1 AERLSEEEIGGLKELFKMIDTDNSGTITFDELKDGLKRVGSELMESEIKDLMDAADIDKSGTIDYGEFIAATVHLNKLEREENLVSAFSYFDKDGSGYITLDEIQQACKDFGLDDIHIDDMIKEIDQDNDGQIDYGEFAAMMRKRKGNGGIGRRTMRKTLNLRDALGLVDNGSNQVIEGYFK 182
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
   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  (1, 1)

NMR Structure
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 3)

NMR Structure
(-)
Clan: EF_hand (270)

(-) Gene Ontology  (20, 20)

NMR Structure(hide GO term definitions)
Chain A   (CDPK_SOYBN | P28583)
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: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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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

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        CDPK_SOYBN | P28583: 1s6j

(-) Related Entries Specified in the PDB File

1s6j N-TERMINAL REGION OF THE CA2+-SATURATED CALCIUM REGULATORY DOMAIN (CLD) FROM SOYBEAN CALCIUM-DEPENDENT PROTEIN KINASE- ALPHA (CDPK)