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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CHOLINE KINASE ALPHA 2
 
Authors :  E. Malito, A. Lavie
Date :  20 Apr 06  (Deposition) - 04 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Kinase, Transferase, Choline Kinase, Phosphatydilcholine, Alternative Splicing (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Malito, N. Sekulic, W. C. Too, M. Konrad, A. Lavie
Elucidation Of Human Choline Kinase Crystal Structures In Complex With The Products Adp Or Phosphocholine.
J. Mol. Biol. V. 364 136 2006
PubMed-ID: 17007874  |  Reference-DOI: 10.1016/J.JMB.2006.08.084

(-) Compounds

Molecule 1 - CHOLINE KINASE ALPHA
    ChainsA, B
    EC Number2.7.1.32
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPGEX-RB
    FragmentSPLICE ISOFORM 2, RESIDUES 50-439
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCK, CHETK-ALPHA

 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
1DTT2Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN B:308 , HOH B:2191 , TYR A:440BINDING SITE FOR RESIDUE DTT A1458
2AC2SOFTWAREGLN B:308 , HOH B:2191BINDING SITE FOR RESIDUE DTT B1458

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:359 -Pro A:360
2Tyr B:359 -Pro B:360

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric/Biological Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_054863S220GCHKA_HUMANPolymorphism17853641A/BS220G
2UniProtVAR_054864L422QCHKA_HUMANPolymorphism17853642A/BL422Q

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2CKO)

(-) Exons   (11, 22)

Asymmetric/Biological Unit (11, 22)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002656891bENSE00002184538chr11:67888671-67888295377CHKA_HUMAN1-1171172A:88-117
B:87-117
30
31
1.2ENST000002656892ENSE00001201105chr11:67864597-67864486112CHKA_HUMAN117-154382A:117-151 (gaps)
B:117-149
35
33
1.5cENST000002656895cENSE00001166770chr11:67848924-6784887154CHKA_HUMAN155-172180--
1.6ENST000002656896ENSE00001267789chr11:67842297-67842184114CHKA_HUMAN173-210382A:177-210
B:175-210
34
36
1.7bENST000002656897bENSE00000736988chr11:67838324-67838191134CHKA_HUMAN211-255452A:211-255
B:211-255
45
45
1.8bENST000002656898bENSE00000736987chr11:67837760-67837656105CHKA_HUMAN255-290362A:255-290
B:255-290
36
36
1.9ENST000002656899ENSE00000736986chr11:67836404-6783634659CHKA_HUMAN290-310212A:290-310
B:290-310
21
21
1.10cENST0000026568910cENSE00000736983chr11:67833983-6783389688CHKA_HUMAN310-339302A:310-339
B:310-339
30
30
1.11ENST0000026568911ENSE00000736982chr11:67833361-67833253109CHKA_HUMAN339-375372A:339-375
B:339-375
37
37
1.12ENST0000026568912ENSE00000736981chr11:67832098-67831992107CHKA_HUMAN376-411362A:376-411
B:376-411
36
36
1.13ENST0000026568913ENSE00001117236chr11:67829501-6782942082CHKA_HUMAN411-438282A:411-438
B:411-438
28
28
1.15dENST0000026568915dENSE00001166765chr11:67821514-678203261189CHKA_HUMAN439-457192A:439-457
B:439-457
19
19

(-) 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:344
 aligned with CHKA_HUMAN | P35790 from UniProtKB/Swiss-Prot  Length:457

    Alignment length:370
                                    97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457
           CHKA_HUMAN    88 RRRAYLWCKEFLPGAWRGLREDEFHISVIRGGLSNMLFQCSLPDTTATLGDEPRKVLLRLYGAILQMRSCNKEGSEQAQKENEFQGAEAMVLESVMFAILAERSLGPKLYGIFPQGRLEQFIPSRRLDTEELSLPDISAEIAEKMATFHGMKMPFNKEPKWLFGTMEKYLKEVLRIKFTEESRIKKLHKLLSYNLPLELENLRSLLESTPSPVVFCHNDCQEGNILLLEGRENSEKQKLMLIDFEYSSYNYRGFDIGNHFCEWMYDYSYEKYPFFRANIRKYPTKKQQLHFISSYLPAFQNDFENLSTEEKSIIKEEMLLEVNRFALASHFLWGLWSIVQAKISSIEFGYMDYAQARFDAYFHQKRKLGV 457
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------- ------------------------------2                         ckoA02 A:151-194,A--------------2ckoA02 A:151-194,A:209-457  [code=3.90.1200.10, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh..hhhhheeeeee..-..eeeeee.............eeeeee....-------------------------hhhhhhhhhhhhhh.....eeeee..eeeee...eee.hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhhh....eeee....hhh.eeee..........eee......eeeehhhhhhhhhhhh.ee.........ee.hhhh.hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------G---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Q----------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1b  PDB: A:88-117      -------------------------------------Exon 1.5c  PDB: - Exon 1.6  PDB: A:177-210 [INCOMPLETE] Exon 1.7b  PDB: A:211-255 UniProt: 211-255   ------------------------------------------------------Exon 1.10c  PDB: A:310-339    ------------------------------------Exon 1.12  PDB: A:376-411           ---------------------------Exon 1.15d          Transcript 1 (1)
           Transcript 1 (2) -----------------------------Exon 1.2  PDB: A:117-151 (gaps)       ----------------------------------------------------------------------------------------------------Exon 1.8b  PDB: A:255-290           ------------------------------------------------Exon 1.11  PDB: A:339-375            -----------------------------------Exon 1.13  PDB: A:411-438   ------------------- Transcript 1 (2)
           Transcript 1 (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9             --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (3)
                 2cko A  88 RRRAYLWCKEFLPGAWRGLREDEFHISVIRGG-SNMLFQCSLPDTTATLGDEPRKVLLRLYGAI-------------------------MVLESVMFAILAERSLGPKLYGIFPQGRLEQFIPSRRLDTEELSLPDISAEIAEKMATFHGMKMPFNKEPKWLFGTMEKYLKEVLRIKFTEESRIKKLHKLLSYNLPLELENLRSLLESTPSPVVFCHNDCQEGNILLLEGRENSEKQKLMLIDFEYSSYNYRGFDIGNHFCEWMYDYSYEKYPFFRANIRKYPTKKQQLHFISSYLPAFQNDFENLSTEEKSIIKEEMLLEVNRFALASHFLWGLWSIVQAKISSIEFGYMDYAQARFDAYFHQKRKLGV 457
                                    97       107       117 | |   127       137       147   |     -         -       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457
                                                         119 |                           151                       177                                                                                                                                                                                                                                                                                        
                                                           121                                                                                                                                                                                                                                                                                                                                                

Chain B from PDB  Type:PROTEIN  Length:346
 aligned with CHKA_HUMAN | P35790 from UniProtKB/Swiss-Prot  Length:457

    Alignment length:371
                                    96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456 
           CHKA_HUMAN    87 TRRRAYLWCKEFLPGAWRGLREDEFHISVIRGGLSNMLFQCSLPDTTATLGDEPRKVLLRLYGAILQMRSCNKEGSEQAQKENEFQGAEAMVLESVMFAILAERSLGPKLYGIFPQGRLEQFIPSRRLDTEELSLPDISAEIAEKMATFHGMKMPFNKEPKWLFGTMEKYLKEVLRIKFTEESRIKKLHKLLSYNLPLELENLRSLLESTPSPVVFCHNDCQEGNILLLEGRENSEKQKLMLIDFEYSSYNYRGFDIGNHFCEWMYDYSYEKYPFFRANIRKYPTKKQQLHFISSYLPAFQNDFENLSTEEKSIIKEEMLLEVNRFALASHFLWGLWSIVQAKISSIEFGYMDYAQARFDAYFHQKRKLGV 457
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------2ckoB02           --------------2ckoB02 B:177-194,B:209-457  [code=3.90.1200.10, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhheeeeee.....eeeeee.............eeeeee..-------------------------hhhhhhhhhhhhhhhh.....eeeee..eeeee...eee.hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhh....eeee....hhh.eeee..........eee......eeeehhhhhhhhhhh..ee.........ee.hhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------G---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Q----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1b  PDB: B:87-117       -------------------------------------Exon 1.5c  PDB: - Exon 1.6  PDB: B:175-210 [INCOMPLETE] Exon 1.7b  PDB: B:211-255 UniProt: 211-255   ------------------------------------------------------Exon 1.10c  PDB: B:310-339    ------------------------------------Exon 1.12  PDB: B:376-411           ---------------------------Exon 1.15d          Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.2  PDB: B:117-149 [INCOMPLETE] ----------------------------------------------------------------------------------------------------Exon 1.8b  PDB: B:255-290           ------------------------------------------------Exon 1.11  PDB: B:339-375            -----------------------------------Exon 1.13  PDB: B:411-438   ------------------- Transcript 1 (2)
           Transcript 1 (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9             --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (3)
                 2cko B  87 TRRRAYLWCKEFLPGAWRGLREDEFHISVIRGGLSNMLFQCSLPDTTATLGDEPRKVLLRLYG-------------------------EAMVLESVMFAILAERSLGPKLYGIFPQGRLEQFIPSRRLDTEELSLPDISAEIAEKMATFHGMKMPFNKEPKWLFGTMEKYLKEVLRIKFTEESRIKKLHKLLSYNLPLELENLRSLLESTPSPVVFCHNDCQEGNILLLEGRENSEKQKLMLIDFEYSSYNYRGFDIGNHFCEWMYDYSYEKYPFFRANIRKYPTKKQQLHFISSYLPAFQNDFENLSTEEKSIIKEEMLLEVNRFALASHFLWGLWSIVQAKISSIEFGYMDYAQARFDAYFHQKRKLGV 457
                                    96       106       116       126       136       146  |      -         -       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456 
                                                                                        149                       175                                                                                                                                                                                                                                                                                          

   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 2CKO)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CHKA_HUMAN | P35790)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0033265    choline binding    Interacting selectively and non-covalently with choline, the amine 2-hydroxy-N,N,N-trimethylethanaminium.
    GO:0004103    choline kinase activity    Catalysis of the reaction: ATP + choline = ADP + choline phosphate + 2 H(+).
    GO:0004104    cholinesterase activity    Catalysis of the reaction: an acylcholine + H2O = choline + a carboxylic acid anion.
    GO:0008144    drug binding    Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
    GO:0004305    ethanolamine kinase activity    Catalysis of the reaction: ATP + ethanolamine = ADP + 2 H(+) + phosphoethanolamine.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
    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:0006657    CDP-choline pathway    The phosphatidylcholine biosynthetic process that begins with the phosphorylation of choline and ends with the combination of CDP-choline with diacylglycerol to form phosphatidylcholine.
    GO:0019695    choline metabolic process    The chemical reactions and pathways involving choline (2-hydroxyethyltrimethylammonium), an amino alcohol that occurs widely in living organisms as a constituent of certain types of phospholipids and in the neurotransmitter acetylcholine.
    GO:0006580    ethanolamine metabolic process    The chemical reactions and pathways involving ethanolamine (2-aminoethanol), an important water-soluble base of phospholipid (phosphatidylethanolamine).
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0006869    lipid transport    The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0006656    phosphatidylcholine biosynthetic process    The chemical reactions and pathways resulting in the formation of phosphatidylcholines, any of a class of glycerophospholipids in which the phosphatidyl group is esterified to the hydroxyl group of choline.
    GO:0006646    phosphatidylethanolamine biosynthetic process    The chemical reactions and pathways resulting in the formation of phosphatidylethanolamine, any of a class of glycerophospholipids in which a phosphatidyl group is esterified to the hydroxyl group of ethanolamine.
    GO:0008654    phospholipid biosynthetic process    The chemical reactions and pathways resulting in the formation of phospholipids, any lipid containing phosphoric acid as a mono- or diester.
    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:1904681    response to 3-methylcholanthrene    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 3-methylcholanthrene stimulus.
    GO:0009636    response to toxic substance    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 toxic stimulus.
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CHKA_HUMAN | P357902ckp 2ckq 2i7q 3f2r 3g15 3zm9 4br3 4cg8 4cg9 4cga 4da5 5afv 5eqe 5eqp 5eqy 5ftg 5fut

(-) Related Entries Specified in the PDB File

2ckp CRYSTAL STRUCTURE OF HUMAN CHOLINE KINASE ALPHA-2 IN COMPLEX WITH ADP
2ckq CRYSTAL STRUCTURE OF HUMAN CHOLINE KINASE ALPHA 2 IN COMPLEX WITH PHOSPHOCHOLINE