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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PL KINASE WITH BOUND PLP AND ATP
 
Authors :  M. K. Safo, A. K. Gandhi, F. N. Musayev
Date :  26 Oct 09  (Deposition) - 03 Nov 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pyridoxal 5'-Phosphate, Pyridoxal Kinase, Vitamin B6, Plp, Atp- Binding, Kinase, Metal-Binding, Nucleotide-Binding, Phosphoprotein, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. K. Gandhi, F. N. Musayev, M. K. Safo
Crystal Structure Of Pl Kinase In Complex With Mgatp And Plp: Structural Basis Of Severe Induced Mgatp Substrate Inhibition Of The Enzyme
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PYRIDOXAL KINASE
    Chains: A, B
    EC Number: 2.7.1.35
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: ROSETTA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: C21ORF124, C21ORF97, PDXK, PKH, PNK
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PYRIDOXINE KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 27)

Asymmetric/Biological Unit (6, 27)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG4Ligand/IonMAGNESIUM ION
3MPD9Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4NA2Ligand/IonSODIUM ION
5PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
6SO48Ligand/IonSULFATE ION

(-) Sites  (27, 27)

Asymmetric Unit (27, 27)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:118 , ATP A:407 , MPD A:512 , HOH A:792 , HOH A:806BINDING SITE FOR RESIDUE MG A 400
02AC2SOFTWAREASP A:235 , ATP A:407 , PLP A:500BINDING SITE FOR RESIDUE MG A 401
03AC3SOFTWAREASP A:113 , THR A:148 , THR A:186 , ATP A:407 , HOH A:656BINDING SITE FOR RESIDUE NA A 402
04AC4SOFTWAREASP A:113 , ASP A:118 , ASN A:150 , GLU A:153 , THR A:186 , SER A:187 , VAL A:201 , ARG A:224 , LYS A:225 , VAL A:226 , ALA A:228 , THR A:233 , GLY A:234 , LEU A:267 , MG A:400 , MG A:401 , NA A:402 , PLP A:500 , MPD A:512 , HOH A:792 , HOH A:805 , HOH A:806 , HOH A:824 , HOH A:849BINDING SITE FOR RESIDUE ATP A 407
05AC5SOFTWARESER A:12 , VAL A:19 , GLY A:20 , THR A:47 , VAL A:231 , GLY A:232 , THR A:233 , GLY A:234 , ASP A:235 , MG A:401 , ATP A:407BINDING SITE FOR RESIDUE PLP A 500
06AC6SOFTWARESER A:12 , THR A:47 , TYR A:84BINDING SITE FOR RESIDUE MPD A 508
07AC7SOFTWAREASP A:118 , LEU A:199 , MG A:400 , ATP A:407 , HOH A:822BINDING SITE FOR RESIDUE MPD A 512
08AC8SOFTWARELYS A:76 , ASP A:78 , ASN A:105 , HOH A:907BINDING SITE FOR RESIDUE MPD A 516
09AC9SOFTWAREGLU A:155BINDING SITE FOR RESIDUE SO4 A 524
10BC1SOFTWAREGLN A:63 , ARG A:70 , MET A:93 , GLU A:100BINDING SITE FOR RESIDUE SO4 A 528
11BC2SOFTWARECYS A:5 , LEU A:31 , GLY A:32 , LYS A:247BINDING SITE FOR RESIDUE SO4 A 538
12BC3SOFTWAREASP B:118 , ATP B:409 , MPD B:514 , HOH B:797 , HOH B:798BINDING SITE FOR RESIDUE MG B 404
13BC4SOFTWAREVAL B:115 , ASP B:235 , ATP B:409 , PLP B:500BINDING SITE FOR RESIDUE MG B 405
14BC5SOFTWAREASP B:113 , THR B:148 , PRO B:149 , ASN B:150 , THR B:186 , ATP B:409 , HOH B:796BINDING SITE FOR RESIDUE NA B 406
15BC6SOFTWAREASP B:113 , ASP B:118 , TYR B:127 , ASN B:150 , GLU B:153 , THR B:186 , SER B:187 , VAL B:201 , ARG B:224 , LYS B:225 , VAL B:226 , ALA B:228 , THR B:233 , GLY B:234 , LEU B:263 , LEU B:267 , MG B:404 , MG B:405 , NA B:406 , PLP B:500 , MPD B:514 , HOH B:766 , HOH B:797 , HOH B:846BINDING SITE FOR RESIDUE ATP B 409
16BC7SOFTWARESER B:12 , VAL B:19 , HIS B:46 , THR B:47 , VAL B:231BINDING SITE FOR RESIDUE MPD B 508
17BC8SOFTWARESER B:12 , VAL B:19 , GLY B:20 , THR B:47 , PHE B:230 , VAL B:231 , GLY B:232 , THR B:233 , GLY B:234 , ASP B:235 , MG B:405 , ATP B:409BINDING SITE FOR RESIDUE PLP B 500
18BC9SOFTWAREASP B:181 , ARG B:206 , ARG B:207 , ARG B:208 , HOH B:842BINDING SITE FOR RESIDUE MPD B 510
19CC1SOFTWAREASP B:118 , LYS B:225 , MG B:404 , ATP B:409 , HOH B:798 , HOH B:884BINDING SITE FOR RESIDUE MPD B 514
20CC2SOFTWARESER B:177 , LEU B:312 , MPD B:520 , HOH B:785BINDING SITE FOR RESIDUE MPD B 518
21CC3SOFTWAREASP B:173 , SER B:177 , ARG B:206 , LEU B:312 , MPD B:518 , HOH B:785BINDING SITE FOR RESIDUE MPD B 520
22CC4SOFTWAREGLN B:165BINDING SITE FOR RESIDUE MPD B 522
23CC5SOFTWAREGLN B:63 , GLU B:100BINDING SITE FOR RESIDUE SO4 B 526
24CC6SOFTWAREGLU B:4 , CYS B:5 , ASP B:78 , HIS B:246 , HOH B:869BINDING SITE FOR RESIDUE SO4 B 530
25CC7SOFTWAREGLU B:155 , ARG B:160BINDING SITE FOR RESIDUE SO4 B 532
26CC8SOFTWARELEU B:31 , GLY B:32 , HIS B:246BINDING SITE FOR RESIDUE SO4 B 534
27CC9SOFTWARETYR B:84 , HOH B:896BINDING SITE FOR RESIDUE SO4 B 536

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KEU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KEU)

(-) Exons   (11, 22)

Asymmetric/Biological Unit (11, 22)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000002915651cENSE00001861574chr21:45138993-45139262270PDXK_HUMAN1-29292A:3-29
B:4-29		27
26
1.6ENST000002915656ENSE00001050589chr21:45153950-4515400455PDXK_HUMAN30-48192A:30-48
B:30-48		19
19
1.9eENST000002915659eENSE00001050594chr21:45161548-45161652105PDXK_HUMAN48-83362A:48-83
B:48-83		36
36
1.10bENST0000029156510bENSE00001050590chr21:45163605-4516368884PDXK_HUMAN83-111292A:83-111
B:83-111		29
29
1.12bENST0000029156512bENSE00001050584chr21:45165960-4516600647PDXK_HUMAN111-126162A:111-126
B:111-126		16
16
1.14ENST0000029156514ENSE00001050578chr21:45168876-4516896186PDXK_HUMAN127-155292A:127-155
B:127-155		29
29
1.15ENST0000029156515ENSE00001050582chr21:45170381-4517042646PDXK_HUMAN155-170162A:155-170
B:155-170		16
16
1.16ENST0000029156516ENSE00001050593chr21:45172399-45172510112PDXK_HUMAN171-208382A:171-207
B:171-208		37
38
1.17cENST0000029156517cENSE00001050587chr21:45173464-45173600137PDXK_HUMAN208-253462A:213-253
B:208-253		41
46
1.18bENST0000029156518bENSE00001050583chr21:45175579-4517564567PDXK_HUMAN254-276232A:254-276
B:254-276		23
23
1.19eENST0000029156519eENSE00001431057chr21:45175832-451821886357PDXK_HUMAN276-312372A:276-312
B:276-312 (gaps)		37
37

(-) 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:305
 aligned with PDXK_HUMAN | O00764 from UniProtKB/Swiss-Prot  Length:312

    Alignment length:310
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312
           PDXK_HUMAN     3 EECRVLSIQSHVIRGYVGNRAATFPLQVLGFEIDAVNSVQFSNHTGYAHWKGQVLNSDELQELYEGLRLNNMNKYDYVLTGYTRDKSFLAMVVDIVQELKQQNPRLVYVCDPVLGDKWDGEGSMYVPEDLLPVYKEKVVPLADIITPNQFEAELLSGRKIHSQEEALRVMDMLHSMGPDTVVITSSDLPSPQGSNYLIVLGSQRRRNPAGSVVMERIRMDIRKVDAVFVGTGDLFAAMLLAWTHKHPNNLKVACEKTVSTLHHVLQRTIQCAKAQAGEGVRPSPMQLELRMVQSKRDIEDPEIVVQATVL 312
               SCOP domains d3keua_ A: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 3keuA00 A:3-312  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.....hhhhhhhhhhhh..eeeeeeeeee..........eee.hhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhhhhhh...eeee....eee....eee....hhhhhhhhhhhhhh.ee..hhhhhhhhhh....hhhhhhhhhhhhhhh...eeee............eeeeeeeee.-----...eeeeeeeee.......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhh.......eee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1c  PDB: A:3-29     Exon 1.6           ----------------------------------Exon 1.10b  PDB: A:83-111    ---------------Exon 1.14  PDB: A:127-155    ---------------Exon 1.16  PDB: A:171-207 [INCOMPLETE]---------------------------------------------Exon 1.18b             ------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------Exon 1.9e  PDB: A:48-83             ---------------------------Exon 1.12b      ----------------------------Exon 1.15       -------------------------------------Exon 1.17c  PDB: A:213-253 UniProt: 208-253   ----------------------Exon 1.19e  PDB: A:276-312            Transcript 1 (2)
                 3keu A   3 EECRVLSIQSHVIRGYVGNRAATFPLQVLGFEIDAVNSVQFSNHTGYAHWKGQVLNSDELQELYEGLRLNNMNKYDYVLTGYTRDKSFLAMVVDIVQELKQQNPRLVYVCDPVLGDKWDGEGSMYVPEDLLPVYKEKVVPLADIITPNQFEAELLSGRKIHSQEEALRVMDMLHSMGPDTVVITSSDLPSPQGSNYLIVLGSQRR-----SVVMERIRMDIRKVDAVFVGTGDLFAAMLLAWTHKHPNNLKVACEKTVSTLHHVLQRTIQCAKAQAGEGVRPSPMQLELRMVQSKRDIEDPEIVVQATVL 312
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202    |    -|      222       232       242       252       262       272       282       292       302       312
                                                                                                                                                                                                                                      207   213                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:305
 aligned with PDXK_HUMAN | O00764 from UniProtKB/Swiss-Prot  Length:312

    Alignment length:309
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303         
           PDXK_HUMAN     4 ECRVLSIQSHVIRGYVGNRAATFPLQVLGFEIDAVNSVQFSNHTGYAHWKGQVLNSDELQELYEGLRLNNMNKYDYVLTGYTRDKSFLAMVVDIVQELKQQNPRLVYVCDPVLGDKWDGEGSMYVPEDLLPVYKEKVVPLADIITPNQFEAELLSGRKIHSQEEALRVMDMLHSMGPDTVVITSSDLPSPQGSNYLIVLGSQRRRNPAGSVVMERIRMDIRKVDAVFVGTGDLFAAMLLAWTHKHPNNLKVACEKTVSTLHHVLQRTIQCAKAQAGEGVRPSPMQLELRMVQSKRDIEDPEIVVQATVL 312
               SCOP domains d3keub_ B: automated matches                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 3keuB00 B:4-312  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                                                                 CATH domains
           Pfam domains (1) PfkB-3keuB01 B:4-283                                                                                                                                                                                                                                                                    ----------------------------- Pfam domains (1)
           Pfam domains (2) PfkB-3keuB02 B:4-283                                                                                                                                                                                                                                                                    ----------------------------- Pfam domains (2)
         Sec.struct. author ..eeeeeeeee.....hhhhhhhhhhhh..eeeeeeeeee..........eee.hhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhhhhhh...eeee....eeee..eeee..hhhhhhhhhhhhhhhh.ee..hhhhhhhhhh....hhhhhhhhhhhhhhhh..eeee............eeeeeeeeeee.....eeeeeeeeeee.......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..----..hhhhhh..hhhhhhhhhh.......eee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1c  PDB: B:4-29    Exon 1.6           ----------------------------------Exon 1.10b  PDB: B:83-111    ---------------Exon 1.14  PDB: B:127-155    ---------------Exon 1.16  PDB: B:171-208             ---------------------------------------------Exon 1.18b             ------------------------------------ Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.9e  PDB: B:48-83             ---------------------------Exon 1.12b      ----------------------------Exon 1.15       -------------------------------------Exon 1.17c  PDB: B:208-253 UniProt: 208-253   ----------------------Exon 1.19e  PDB: B:276-312 (gaps)     Transcript 1 (2)
                 3keu B   4 ECRVLSIQSHVIRGYVGNRAATFPLQVLGFEIDAVNSVQFSNHTGYAHWKGQVLNSDELQELYEGLRLNNMNKYDYVLTGYTRDKSFLAMVVDIVQELKQQNPRLVYVCDPVLGDKWDGEGSMYVPEDLLPVYKEKVVPLADIITPNQFEAELLSGRKIHSQEEALRVMDMLHSMGPDTVVITSSDLPSPQGSNYLIVLGSQRRRNPAGSVVMERIRMDIRKVDAVFVGTGDLFAAMLLAWTHKHPNNLKVACEKTVSTLHHVLQRTIQCAKAQA----RPSPMQLELRMVQSKRDIEDPEIVVQATVL 312
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273    |  283       293       303         
                                                                                                                                                                                                                                                                                                            278  283
   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) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Ribokinase (55)

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PDXK_HUMAN | O00764)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0031403    lithium ion binding    Interacting selectively and non-covalently with lithium ions (Li+).
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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:0030955    potassium ion binding    Interacting selectively and non-covalently with potassium (K+) ions.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0008478    pyridoxal kinase activity    Catalysis of the reaction: ATP + pyridoxal = ADP + pyridoxal 5'-phosphate.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
    GO:0031402    sodium ion binding    Interacting selectively and non-covalently with sodium ions (Na+).
    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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    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:0009443    pyridoxal 5'-phosphate salvage    Any process that generates pyridoxal 5'-phosphate, the active form of vitamin B6, from derivatives of it without de novo synthesis.
    GO:0042823    pyridoxal phosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of pyridoxal phosphate, pyridoxal phosphorylated at the hydroxymethyl group of C-5, the active form of vitamin B6.
    GO:0042816    vitamin B6 metabolic process    The chemical reactions and pathways involving any of the vitamin B6 compounds: pyridoxal, pyridoxamine and pyridoxine and the active form, pyridoxal phosphate.
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.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.

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  PDXK_HUMAN | O00764
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  2.7.1.35
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 Related Entries

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        PDXK_HUMAN | O00764: 2ajp 2f7k 2yxt 2yxu 3fhx 3fhy 4en4 4eoh

(-) Related Entries Specified in the PDB File

2yxt CRYSTAL STRUCTURE OF HUMAN PYRIDOXAL KINASE