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(-) Description

Title :  CRYSTAL STRUCTURE OF CHOLINE KINASE
 
Authors :  D. Peisach, P. Gee, C. Kent, Z. Xu
Date :  05 Feb 03  (Deposition) - 10 Jun 03  (Release) - 30 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.02
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Choline Kinase, Phospholipid Synthesis, Protein Kinase Fold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Peisach, P. Gee, C. Kent, Z. Xu
The Crystal Structure Of Choline Kinase Reveals A Eukaryoti Protein Kinase Fold
Structure V. 11 703 2003
PubMed-ID: 12791258  |  Reference-DOI: 10.1016/S0969-2126(03)00094-7

(-) Compounds

Molecule 1 - CHOLINE KINASE (49.2 KD)
    Chains: A, B
    EC Number: 2.7.1.32
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET43A
    Expression System Strain: BL21(DE3) CELLS
    Expression System Taxid: 562
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239

 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
1CA2Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:258 , GLU A:320 , ILE A:323 , TYR A:325BINDING SITE FOR RESIDUE CA A 430
2AC2SOFTWAREGLU B:258 , GLU B:320 , ILE B:323 , TYR B:325BINDING SITE FOR RESIDUE CA B 430

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NW1)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:330 -Pro A:331
2Ala B:330 -Pro B:331

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NW1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1NW1)

(-) Exons   (0, 0)

(no "Exon" information available for 1NW1)

(-) 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:365
 aligned with CKA2_CAEEL | Q22942 from UniProtKB/Swiss-Prot  Length:429

    Alignment length:395
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421     
           CKA2_CAEEL    32 GMKELLSTMDLDTDANTIPELKERAHMLCARFLGGAWKTVPLEHLRISRIKGGMSNMLFLCRLSEVYPPIRNEPNKVLLRVYFNPETESHLVAESVIFTLLSERHLGPKLYGIFSGGRLEEYIPSRPLSCHEISLAHMSTKIAKRVAKVHQLEVPIWKEPDYLCEALQRWLKQLTGTVDAEHRFDLPEECGVSSVNCLDLARELEFLRAHISLSKSPVTFCHNDLQEGNILLPKASSGNIRMPSLSDETQALGNSLSAFNPADPRLVLIDFEYASYNYRAFDFANHFIEWTIDYDIDEAPFYKIQTENFPENDQMLEFFLNYLREQGNTRENELYKKSEDLVQETLPFVPVSHFFWGVWGLLQVELSPVGFGFADYGRDRLSLYFKHKQLLKNLA 426
               SCOP domains d1nw1a_ A: Choline kinase                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1nw1A01 A:32-113,A:140-153 Choline kinase; domain 1                               1nw1A02                   1nw1A01       1nw1A02 A:114-139,A:154-425  [code=3.90.1200.10, no name defined]                                                                                                                                                                                                               - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.....eeeeeeee............eeeeeee....hhhhhhhhhhhhhhhhhh.....eeeee..eeee....eee...hhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.....ee.hhhhh..eehhhhhhhhhhhhhhhhh.....eeee....hhh.eeee.------------------------------..ee......eeeehhhhhhhhhhhh.ee.........ee.hhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nw1 A  32 GMKELLSTMDLDTDANTIPELKERAHMLCARFLGGAWKTVPLEHLRISRIKGGMSNMLFLCRLSEVYPPIRNEPNKVLLRVYFNPETESHLVAESVIFTLLSERHLGPKLYGIFSGGRLEEYIPSRPLSCHEISLAHMSTKIAKRVAKVHQLEVPIWKEPDYLCEALQRWLKQLTGTVDAEHRFDLPEECGVSSVNCLDLARELEFLRAHISLSKSPVTFCHNDLQEGNILLPK------------------------------RLVLIDFEYASYNYRAFDFANHFIEWTIDYDIDEAPFYKIQTENFPENDQMLEFFLNYLREQGNTRENELYKKSEDLVQETLPFVPVSHFFWGVWGLLQVELSPVGFGFADYGRDRLSLYFKHKQLLKNLA 426
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261   |     -         -         -    |  301       311       321       331       341       351       361       371       381       391       401       411       421     
                                                                                                                                                                                                                                                                   265                            296                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:357
 aligned with CKA2_CAEEL | Q22942 from UniProtKB/Swiss-Prot  Length:429

    Alignment length:387
                                    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       
           CKA2_CAEEL    40 MDLDTDANTIPELKERAHMLCARFLGGAWKTVPLEHLRISRIKGGMSNMLFLCRLSEVYPPIRNEPNKVLLRVYFNPETESHLVAESVIFTLLSERHLGPKLYGIFSGGRLEEYIPSRPLSCHEISLAHMSTKIAKRVAKVHQLEVPIWKEPDYLCEALQRWLKQLTGTVDAEHRFDLPEECGVSSVNCLDLARELEFLRAHISLSKSPVTFCHNDLQEGNILLPKASSGNIRMPSLSDETQALGNSLSAFNPADPRLVLIDFEYASYNYRAFDFANHFIEWTIDYDIDEAPFYKIQTENFPENDQMLEFFLNYLREQGNTRENELYKKSEDLVQETLPFVPVSHFFWGVWGLLQVELSPVGFGFADYGRDRLSLYFKHKQLLKNLA 426
               SCOP domains d1nw1b_ B: Choline kinase                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1nw1B01 B:40-113,B:140-153 Choline kinase; domain 1                       1nw1B02                   1nw1B01       1nw1B02 B:114-139,B:154-425  [code=3.90.1200.10, no name defined]                                                                                                                                                                                                               - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.....eeeeeeee............eeeeeee....hhhhhhhhhhhhhhhhhh.....eeeee..eeee....eee...hhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh.......ee.hhhhh..eehhhhhhhhhhhhhhhhh.....eeee....hhh.eeee.------------------------------..ee......eeeehhhhhhhhhhhh.ee.........ee.hhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nw1 B  40 MDLDTDANTIPELKERAHMLCARFLGGAWKTVPLEHLRISRIKGGMSNMLFLCRLSEVYPPIRNEPNKVLLRVYFNPETESHLVAESVIFTLLSERHLGPKLYGIFSGGRLEEYIPSRPLSCHEISLAHMSTKIAKRVAKVHQLEVPIWKEPDYLCEALQRWLKQLTGTVDAEHRFDLPEECGVSSVNCLDLARELEFLRAHISLSKSPVTFCHNDLQEGNILLPK------------------------------RLVLIDFEYASYNYRAFDFANHFIEWTIDYDIDEAPFYKIQTENFPENDQMLEFFLNYLREQGNTRENELYKKSEDLVQETLPFVPVSHFFWGVWGLLQVELSPVGFGFADYGRDRLSLYFKHKQLLKNLA 426
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259     |   -         -         -      |299       309       319       329       339       349       359       369       379       389       399       409       419       
                                                                                                                                                                                                                                                           265                            296
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1NW1)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CKA2_CAEEL | Q22942)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004103    choline kinase activity    Catalysis of the reaction: ATP + choline = ADP + choline phosphate + 2 H(+).
    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: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: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: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: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.

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