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(-) Description

Title :  CRYSTAL STRUCTURE OF D235N MUTANT OF HUMAN PYRIDOXAL KINASE
 
Authors :  M. K. Safo, A. K. Gandhi, F. N. Musayev, M. Ghatge, M. L. Di Salvo, V. Schirch
Date :  10 Dec 08  (Deposition) - 23 Dec 08  (Release) - 21 Apr 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta Sheet With Alpha Helix, Atp Complex, Metal Ion, Transferase, Acetylation, Alternative Splicing, Atp-Binding, Cytoplasm, Kinase, Metal-Binding, Nucleotide-Binding, Zinc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. K. Gandhi, M. S. Ghatge, F. N. Musayev, A. Sease, S. O. Aboagye, M. L. Di Salvo, V. Schirch, M. K. Safo
Kinetic And Structural Studies Of The Role Of The Active Site Residue Asp235 Of Human Pyridoxal Kinase.
Biochem. Biophys. Res. Commun. V. 381 12 2009
PubMed-ID: 19351586  |  Reference-DOI: 10.1016/J.BBRC.2009.01.170
(for further references see the PDB file header)

(-) 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 (DE3)PLYSS COMPETENT CELLS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: C21ORF124, C21ORF97, PDXK, PKH, PNK
    Mutation: YES
    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  (5, 26)

Asymmetric/Biological Unit (5, 26)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3MPD8Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4NA2Ligand/IonSODIUM ION
5SO412Ligand/IonSULFATE ION

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:118 , SO4 A:316 , HOH A:320 , ATP A:409 , HOH A:418BINDING SITE FOR RESIDUE MG A 400
02AC2SOFTWAREASP A:113 , THR A:148 , PRO A:149 , ASN A:150 , GLU A:153 , THR A:186 , ATP A:409 , HOH A:419BINDING SITE FOR RESIDUE NA A 402
03AC3SOFTWAREASP A:113 , ASP A:118 , ASN A:150 , GLU A:153 , THR A:186 , SER A:187 , VAL A:201 , ARG A:224 , VAL A:226 , ALA A:228 , THR A:233 , GLY A:234 , LEU A:263 , LEU A:267 , SO4 A:316 , SO4 A:317 , HOH A:325 , MG A:400 , NA A:402 , HOH A:417 , HOH A:418BINDING SITE FOR RESIDUE ATP A 409
04AC4SOFTWARECYS A:5 , LEU A:31 , PHE A:33 , LYS A:247BINDING SITE FOR RESIDUE SO4 A 313
05AC5SOFTWAREGLU A:155 , LYS A:161BINDING SITE FOR RESIDUE SO4 A 314
06AC6SOFTWAREGLY A:179 , ASP A:181 , MPD A:318 , HOH A:345 , HOH A:369BINDING SITE FOR RESIDUE SO4 A 315
07AC7SOFTWAREMG A:400 , ATP A:409BINDING SITE FOR RESIDUE SO4 A 316
08AC8SOFTWAREGLY A:232 , THR A:233 , GLY A:234 , ASN A:235 , ATP A:409BINDING SITE FOR RESIDUE SO4 A 317
09AC9SOFTWAREASP A:181 , ARG A:206 , ARG A:208 , SO4 A:315BINDING SITE FOR RESIDUE MPD A 318
10BC1SOFTWAREGLN A:63 , TYR A:66 , ARG A:70 , MET A:93 , ASP A:96 , GLU A:100BINDING SITE FOR RESIDUE MPD A 319
11BC2SOFTWAREASP B:118 , SO4 B:318 , ATP B:407 , HOH B:419 , HOH B:422BINDING SITE FOR RESIDUE MG B 404
12BC3SOFTWAREASP B:113 , THR B:148 , ASN B:150 , THR B:186 , ATP B:407 , HOH B:418BINDING SITE FOR RESIDUE NA B 406
13BC4SOFTWAREASP B:113 , ASP B:118 , ASN B:150 , GLU B:153 , THR B:186 , SER B:187 , VAL B:201 , ARG B:224 , VAL B:226 , ALA B:228 , THR B:233 , GLY B:234 , LEU B:267 , SO4 B:318 , SO4 B:319 , HOH B:383 , MG B:404 , NA B:406 , HOH B:419BINDING SITE FOR RESIDUE ATP B 407
14BC5SOFTWAREARG B:160BINDING SITE FOR RESIDUE SO4 B 313
15BC6SOFTWARECYS B:5 , LEU B:31 , GLY B:32 , HIS B:246BINDING SITE FOR RESIDUE SO4 B 314
16BC7SOFTWAREVAL A:56 , GLU A:61 , VAL B:56 , GLU B:61 , HOH B:357 , HOH B:392BINDING SITE FOR RESIDUE SO4 B 315
17BC8SOFTWAREARG B:70 , GLU B:100BINDING SITE FOR RESIDUE SO4 B 316
18BC9SOFTWAREASP B:145 , GLY B:179 , ASP B:181 , HOH B:342 , HOH B:360BINDING SITE FOR RESIDUE SO4 B 317
19CC1SOFTWARELEU B:199 , MG B:404 , ATP B:407BINDING SITE FOR RESIDUE SO4 B 318
20CC2SOFTWAREVAL B:231 , GLY B:232 , THR B:233 , GLY B:234 , ASN B:235 , ATP B:407BINDING SITE FOR RESIDUE SO4 B 319
21CC3SOFTWAREASP B:181 , ARG B:207 , ARG B:208 , HOH B:326BINDING SITE FOR RESIDUE MPD B 320
22CC4SOFTWAREASP B:173 , LEU B:312BINDING SITE FOR RESIDUE MPD B 321
23CC5SOFTWAREHIS B:248 , PRO B:249 , ASN B:250 , ASN B:251BINDING SITE FOR RESIDUE MPD B 322
24CC6SOFTWAREGLY B:124 , GLU B:130BINDING SITE FOR RESIDUE MPD B 323
25CC7SOFTWAREVAL B:19 , HIS B:46 , THR B:47 , VAL B:231 , HOH B:403BINDING SITE FOR RESIDUE MPD B 324
26CC8SOFTWAREPRO B:191 , PRO B:193 , ARG B:220BINDING SITE FOR RESIDUE MPD B 325

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (11, 22)

Asymmetric/Biological Unit (11, 22)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000002915651cENSE00001861574chr21:45138993-45139262270PDXK_HUMAN1-29292A:4-29
B:4-29		26
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:171-208
B:171-208		38
38
1.17cENST0000029156517cENSE00001050587chr21:45173464-45173600137PDXK_HUMAN208-253462A:208-253 (gaps)
B:208-253		46
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:306
 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 d3fhya_ A: automated matches                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 3fhyA00 A:4-312  [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....hhhhhhhhhhhhhhhh..eeee............eeeeeeeeee...---.eeeeeeeeee.......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhh.......ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1c  PDB: A:4-29    Exon 1.6           ----------------------------------Exon 1.10b  PDB: A:83-111    ---------------Exon 1.14  PDB: A:127-155    ---------------Exon 1.16  PDB: A:171-208             ---------------------------------------------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:208-253 (gaps)             ----------------------Exon 1.19e  PDB: A:276-312            Transcript 1 (2)
                 3fhy A   4 ECRVLSIQSHVIRGYVGNRAATFPLQVLGFEIDAVNSVQFSNHTGYAHWKGQVLNSDELQELYEGLRLNNMNKYDYVLTGYTRDKSFLAMVVDIVQELKQQNPRLVYVCDPVLGDKWDGEGSMYVPEDLLPVYKEKVVPLADIITPNQFEAELLSGRKIHSQEEALRVMDMLHSMGPDTVVITSSDLPSPQGSNYLIVLGSQRRRNP---VVMERIRMDIRKVDAVFVGTGNLFAAMLLAWTHKHPNNLKVACEKTVSTLHHVLQRTIQCAKAQAGEGVRPSPMQLELRMVQSKRDIEDPEIVVQATVL 312
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203      |  -|      223       233       243       253       263       273       283       293       303         
                                                                                                                                                                                                                                        210 214                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:306
 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 d3fhyb_ B: automated matches                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 3fhyB00 B:4-312  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee....hhhhhhhhhhhhh..eeeeeeeeee..........eee.hhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhhhhhh...eeee....eee....eee..hhhhhhhhhhhhhhhh.ee..hhhhhhhhhh....hhhhhhhhhhhhhhhh..eeee............eeeeeeeeeee.....eeeeeeeeeee.......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...---..........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)
                 3fhy B   4 ECRVLSIQSHVIRGYVGNRAATFPLQVLGFEIDAVNSVQFSNHTGYAHWKGQVLNSDELQELYEGLRLNNMNKYDYVLTGYTRDKSFLAMVVDIVQELKQQNPRLVYVCDPVLGDKWDGEGSMYVPEDLLPVYKEKVVPLADIITPNQFEAELLSGRKIHSQEEALRVMDMLHSMGPDTVVITSSDLPSPQGSNYLIVLGSQRRRNPAGSVVMERIRMDIRKVDAVFVGTGNLFAAMLLAWTHKHPNNLKVACEKTVSTLHHVLQRTIQCAKAQAG---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         
                                                                                                                                                                                                                                                                                                             279 283
   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  (0, 0)

(no "Pfam Domain" information available for 3FHY)

(-) 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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        PDXK_HUMAN | O00764: 2ajp 2f7k 2yxt 2yxu 3fhx 3keu 4en4 4eoh

(-) Related Entries Specified in the PDB File

3fhx CRYSTAL STRUCTURE OF D235A MUTANT OF HUMAN PYRIDOXAL KINASE