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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN SELENOPHOSPHATE SYNTHETASE 1 COMPLEX WITH ADP AND PHOSPHATE
 
Authors :  K. T. Wang
Date :  25 Nov 08  (Deposition) - 22 Sep 09  (Release) - 22 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Selenophosphate Synthetase 1, Seld, Atp-Binding, Kinase, Nucleotide-Binding, Selenium, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. T. Wang, J. Wang, L. F. Li, X. D. Su
Crystal Structures Of Catalytic Intermediates Of Human Selenophosphate Synthetase 1.
J. Mol. Biol. V. 390 747 2009
PubMed-ID: 19477186  |  Reference-DOI: 10.1016/J.JMB.2009.05.032
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SELENIDE, WATER DIKINASE 1
    ChainsA, B
    EC Number2.7.9.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneSEPHS1, SELD, SPS, SPS1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSELENOPHOSPHATE SYNTHETASE 1, SELENIUM DONOR PROTEIN 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG6Ligand/IonMAGNESIUM ION
3NA2Ligand/IonSODIUM ION
4PO42Ligand/IonPHOSPHATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:32 , LEU A:38 , LEU A:42 , ILE A:66 , GLY A:67 , MET A:68 , ASP A:69 , ASP A:110 , THR A:267 , PHE A:269 , PO4 A:394 , MG A:395 , MG A:396 , MG A:397 , NA A:398 , HOH A:445 , HOH A:447 , HOH A:476 , HOH A:480 , MET B:124 , VAL B:159 , GLY B:161 , GLY B:162 , GLN B:163 , THR B:164 , HOH B:618BINDING SITE FOR RESIDUE ADP A 393
02AC2SOFTWARELYS A:32 , ASP A:87 , ASN A:106 , THR A:267 , GLY A:268 , ADP A:393 , MG A:396 , MG A:397 , HOH A:426 , HOH A:427 , GLN B:163BINDING SITE FOR RESIDUE PO4 A 394
03AC3SOFTWAREASP A:69 , ASP A:110 , ASP A:265 , ADP A:393 , HOH A:399 , HOH A:425BINDING SITE FOR RESIDUE MG A 395
04AC4SOFTWAREASP A:110 , ADP A:393 , PO4 A:394 , MG A:397 , HOH A:399 , HOH A:426 , HOH A:427BINDING SITE FOR RESIDUE MG A 396
05AC5SOFTWAREASP A:69 , THR A:85 , ADP A:393 , HOH B:429BINDING SITE FOR RESIDUE NA A 398
06AC6SOFTWAREGLN A:163 , HOH A:421 , ASP B:87 , ADP B:393 , PO4 B:394 , MG B:396 , HOH B:430BINDING SITE FOR RESIDUE MG B 397
07AC7SOFTWAREADP A:393 , PO4 A:394 , MG A:396 , HOH A:427 , HOH A:447 , GLN B:163BINDING SITE FOR RESIDUE MG A 397
08AC8SOFTWAREMET A:124 , LEU A:126 , GLY A:161 , GLY A:162 , GLN A:163 , THR A:164 , HOH A:421 , LYS B:32 , LEU B:42 , GLY B:67 , MET B:68 , ASP B:69 , ASP B:110 , PHE B:269 , PO4 B:394 , MG B:395 , MG B:396 , MG B:397 , NA B:398 , HOH B:430 , HOH B:451 , HOH B:453 , HOH B:456 , HOH B:560 , HOH B:822BINDING SITE FOR RESIDUE ADP B 393
09AC9SOFTWAREGLN A:163 , LYS B:32 , ASP B:87 , ASN B:106 , THR B:267 , GLY B:268 , ADP B:393 , MG B:396 , MG B:397 , HOH B:399 , HOH B:423 , HOH B:660BINDING SITE FOR RESIDUE PO4 B 394
10BC1SOFTWAREASP B:69 , ASP B:110 , ASP B:265 , ADP B:393 , HOH B:399 , HOH B:424BINDING SITE FOR RESIDUE MG B 395
11BC2SOFTWAREASP B:110 , ADP B:393 , PO4 B:394 , MG B:397 , HOH B:399 , HOH B:423 , HOH B:430BINDING SITE FOR RESIDUE MG B 396
12BC3SOFTWAREASP B:69 , THR B:85 , ASP B:110 , ADP B:393 , HOH B:422BINDING SITE FOR RESIDUE NA B 398

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3FD6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3FD6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FD6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FD6)

(-) Exons   (0, 0)

(no "Exon" information available for 3FD6)

(-) 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:342
 aligned with SPS1_HUMAN | P49903 from UniProtKB/Swiss-Prot  Length:392

    Alignment length:371
                                    16        26        36        46        56        66        76        86        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 
           SPS1_HUMAN     7 FNPESYELDKSFRLTRFTELKGTGCKVPQDVLQKLLESLQENHFQEDEQFLGAVMPRLGIGMDTCVIPLRHGGLSLVQTTDYIYPIVDDPYMMGRIACANVLSDLYAMGVTECDNMLMLLGVSNKMTDRERDKVMPLIIQGFKDAAEEAGTSVTGGQTVLNPWIVLGGVATTVCQPNEFIMPDNAVPGDVLVLTKPLGTQVAVAVHQWLDIPEKWNKIKLVVTQEDVELAYQEAMMNMARLNRTAAGLMHTFNAHAATDITGFGILGHAQNLAKQQRNEVSFVIHNLPVLAKMAAVSKACGNMFGLMHGTCPETSGGLLICLPREQAARFCAEIKSPKYGEGHQAWIIGIVEKGNRTARIIDKPRIIEVAP 377
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.....hhhhh..........hhhhhhhhh...---------------..........eeee......eeeeeeeee.....hhhhhhhhhhhhhhhhhhh.......eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee...eeeeeeeeeehhhhh..........eeee....hhhhhhhhhhhh-----------..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhh...eeee...hhhhhhhhhhhhh....eeeeeeeeeee.hhhhhhhhh.................eeeeehhhhhhhhhhhhhh.---.....eeeeeeee....eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fd6 A   7 FNPESYELDKSFRLTRFTELKGTGCKVPQDVLQKLLESL---------------MPRLGIGMDTCVIPLRHGGLSLVQTTDYIYPIVDDPYMMGRIACANVLSDLYAMGVTECDNMLMLLGVSNKMTDRERDKVMPLIIQGFKDAAEEAGTSVTGGQTVLNPWIVLGGVATTVCQPNEFIMPDNAVPGDVLVLTKPLGTQVAVAVHQWL-----------VVTQEDVELAYQEAMMNMARLNRTAAGLMHTFNAHAATDITGFGILGHAQNLAKQQRNEVSFVIHNLPVLAKMAAVSKACGNMFGLMHGTCPETSGGLLICLPREQAARFCAEIKSP---EGHQAWIIGIVEKGNRTARIIDKPRIIEVAP 377
                                    16        26        36        |-         -    |   66        76        86        96       106       116       126       136       146       156       166       176       186       196       206        |-         -|      236       246       256       266       276       286       296       306       316       326       336      |  -|      356       366       376 
                                                                 45              61                                                                                                                                                       215         227                                                                                                                 343 347                              

Chain B from PDB  Type:PROTEIN  Length:353
 aligned with SPS1_HUMAN | P49903 from UniProtKB/Swiss-Prot  Length:392

    Alignment length:372
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375  
           SPS1_HUMAN     6 SFNPESYELDKSFRLTRFTELKGTGCKVPQDVLQKLLESLQENHFQEDEQFLGAVMPRLGIGMDTCVIPLRHGGLSLVQTTDYIYPIVDDPYMMGRIACANVLSDLYAMGVTECDNMLMLLGVSNKMTDRERDKVMPLIIQGFKDAAEEAGTSVTGGQTVLNPWIVLGGVATTVCQPNEFIMPDNAVPGDVLVLTKPLGTQVAVAVHQWLDIPEKWNKIKLVVTQEDVELAYQEAMMNMARLNRTAAGLMHTFNAHAATDITGFGILGHAQNLAKQQRNEVSFVIHNLPVLAKMAAVSKACGNMFGLMHGTCPETSGGLLICLPREQAARFCAEIKSPKYGEGHQAWIIGIVEKGNRTARIIDKPRIIEVAP 377
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......-......hhhhh.........hhhhhhhhhh..--------------...........eeee......eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhh.....eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee...eeeeeeeeeehhhhh..........eeee....hhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhh...eeee...hhhhhhhhhhhhhh...eeeeeeeeeee.hhhhhhhhhhhhh.............eeeee...hhhhhhhhhhh.----....eeeeeeee....eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3fd6 B   6 SFNPESY-LDKSFRLTRFTELKGTGCKVPQDVLQKLLESL--------------VMPRLGIGMDTCVIPLRHGGLSLVQTTDYIYPIVDDPYMMGRIACANVLSDLYAMGVTECDNMLMLLGVSNKMTDRERDKVMPLIIQGFKDAAEEAGTSVTGGQTVLNPWIVLGGVATTVCQPNEFIMPDNAVPGDVLVLTKPLGTQVAVAVHQWLDIPEKWNKIKLVVTQEDVELAYQEAMMNMARLNRTAAGLMHTFNAHAATDITGFGILGHAQNLAKQQRNEVSFVIHNLPVLAKMAAVSKACGNMFGLMHGTCPETSGGLLICLPREQAARFCAEIKSP----GHQAWIIGIVEKGNRTARIIDKPRIIEVAP 377
                                  | 15        25        35        45         -    |   65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       | -  |    355       365       375  
                                 12 |                             45             60                                                                                                                                                                                                                                                                                        343  348                             
                                   14                                                                                                                                                                                                                                                                                                                                                                           

   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 3FD6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3FD6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FD6)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SPS1_HUMAN | P49903)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0004756    selenide, water dikinase activity    Catalysis of the reaction: ATP + H(2)O + hydrogen selenide = AMP + 3 H(+) + phosphate + selenophosphorate.
    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:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    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

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

UniProtKB/Swiss-Prot
        SPS1_HUMAN | P499033fd5

(-) Related Entries Specified in the PDB File

2yye 3fd5