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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN SELENOPHOSPHATE SYNTHETASE 1 COMPLEX WITH AMPCP
 
Authors :  K. T. Wang
Date :  25 Nov 08  (Deposition) - 22 Sep 09  (Release) - 22 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Selenophosphate Synthetase, 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
1AP22Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2K2Ligand/IonPOTASSIUM ION
3MG6Ligand/IonMAGNESIUM ION
4PO42Ligand/IonPHOSPHATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:32 , LEU A:42 , GLY A:67 , MET A:68 , ASP A:69 , ASP A:87 , ASP A:110 , THR A:267 , PHE A:269 , HIS A:274 , PO4 A:394 , MG A:395 , MG A:396 , MG A:397 , K A:398 , HOH A:413 , HOH A:415 , HOH A:718 , HOH A:810 , MET B:124 , LEU B:126 , VAL B:159 , GLY B:161 , GLY B:162 , GLN B:163 , THR B:164 , HOH B:511BINDING SITE FOR RESIDUE AP2 A 393
02AC2SOFTWARELYS A:32 , ASP A:87 , THR A:267 , GLY A:268 , HIS A:274 , AP2 A:393 , MG A:396 , MG A:397 , HOH A:611 , HOH A:752 , GLN B:163BINDING SITE FOR RESIDUE PO4 A 394
03AC3SOFTWAREASP A:69 , ASP A:110 , ASP A:265 , AP2 A:393 , HOH A:399 , HOH A:718BINDING SITE FOR RESIDUE MG A 395
04AC4SOFTWAREASP A:87 , ASP A:110 , AP2 A:393 , PO4 A:394 , MG A:397 , HOH A:399 , HOH A:828BINDING SITE FOR RESIDUE MG A 396
05AC5SOFTWAREASP A:87 , AP2 A:393 , PO4 A:394 , MG A:396 , HOH A:658 , GLN B:163BINDING SITE FOR RESIDUE MG A 397
06AC6SOFTWAREASP A:69 , THR A:85 , ASP A:110 , AP2 A:393 , HOH A:658 , HOH A:659BINDING SITE FOR RESIDUE K A 398
07AC7SOFTWAREMET A:124 , LEU A:126 , VAL A:159 , GLY A:161 , GLY A:162 , GLN A:163 , THR A:164 , HOH A:460 , HOH A:661 , LYS B:32 , LEU B:38 , LEU B:42 , LEU B:45 , GLY B:67 , MET B:68 , ASP B:69 , ASP B:87 , ASP B:110 , PHE B:269 , HIS B:274 , PO4 B:394 , MG B:395 , MG B:396 , MG B:397 , K B:398 , HOH B:414 , HOH B:417 , HOH B:543 , HOH B:590BINDING SITE FOR RESIDUE AP2 B 393
08AC8SOFTWAREGLN A:163 , LYS B:32 , ASP B:87 , THR B:267 , GLY B:268 , HIS B:274 , AP2 B:393 , MG B:396 , MG B:397 , HOH B:399 , HOH B:416 , HOH B:423 , HOH B:597 , HOH B:719BINDING SITE FOR RESIDUE PO4 B 394
09AC9SOFTWAREASP B:69 , ASP B:110 , ASP B:265 , AP2 B:393 , MG B:396 , HOH B:399 , HOH B:590BINDING SITE FOR RESIDUE MG B 395
10BC1SOFTWAREASP B:87 , ASP B:110 , AP2 B:393 , PO4 B:394 , MG B:395 , MG B:397 , K B:398 , HOH B:399 , HOH B:719BINDING SITE FOR RESIDUE MG B 396
11BC2SOFTWAREASP B:69 , THR B:85 , THR B:86 , ASP B:87 , ASP B:110 , AP2 B:393 , MG B:396 , HOH B:417BINDING SITE FOR RESIDUE K B 398
12BC3SOFTWAREGLN A:163 , HOH A:661 , ASP B:87 , AP2 B:393 , PO4 B:394 , MG B:396BINDING SITE FOR RESIDUE MG B 397

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3FD5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3FD5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FD5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FD5)

(-) Exons   (0, 0)

(no "Exon" information available for 3FD5)

(-) 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:339
 aligned with SPS1_HUMAN | P49903 from UniProtKB/Swiss-Prot  Length:392

    Alignment length:369
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368         
           SPS1_HUMAN     9 PESYELDKSFRLTRFTELKGTGCKVPQDVLQKLLESLQENHFQEDEQFLGAVMPRLGIGMDTCVIPLRHGGLSLVQTTDYIYPIVDDPYMMGRIACANVLSDLYAMGVTECDNMLMLLGVSNKMTDRERDKVMPLIIQGFKDAAEEAGTSVTGGQTVLNPWIVLGGVATTVCQPNEFIMPDNAVPGDVLVLTKPLGTQVAVAVHQWLDIPEKWNKIKLVVTQEDVELAYQEAMMNMARLNRTAAGLMHTFNAHAATDITGFGILGHAQNLAKQQRNEVSFVIHNLPVLAKMAAVSKACGNMFGLMHGTCPETSGGLLICLPREQAARFCAEIKSPKYGEGHQAWIIGIVEKGNRTARIIDKPRIIEVAP 377
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.....hhhhhh.........hhhhhhhhhh..---------------..........eeee......eeeeeeeee.....hhhhhhhhhhhhhhhhhhhh......eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee...eeeeeeeeeehhhhh..........eeee....hhhhhhhhhhh------------..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhh...eeee...hhhhhhhhhhhh.....eeeeeeeeeee.hhhhhhhhh....hhhhh........eeeeehhhhhhhhhhhhhh.---.....eeeeeeee....eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fd5 A   9 PESYELDKSFRLTRFTELKGTGCKVPQDVLQKLLESL---------------MPRLGIGMDTCVIPLRHGGLSLVQTTDYIYPIVDDPYMMGRIACANVLSDLYAMGVTECDNMLMLLGVSNKMTDRERDKVMPLIIQGFKDAAEEAGTSVTGGQTVLNPWIVLGGVATTVCQPNEFIMPDNAVPGDVLVLTKPLGTQVAVAVHQW------------VVTQEDVELAYQEAMMNMARLNRTAAGLMHTFNAHAATDITGFGILGHAQNLAKQQRNEVSFVIHNLPVLAKMAAVSKACGNMFGLMHGTCPETSGGLLICLPREQAARFCAEIKSP---EGHQAWIIGIVEKGNRTARIIDKPRIIEVAP 377
                                    18        28        38      |  -         -  |     68        78        88        98       108       118       128       138       148       158       168       178       188       198       208     |   -       228       238       248       258       268       278       288       298       308       318       328       338    |  348       358       368         
                                                               45              61                                                                                                                                                      214          227                                                                                                                 343 347                              

Chain B from PDB  Type:PROTEIN  Length:355
 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.....hhhhh..........hhhhhhhhh...--------------...........eeee......eeeeeeeee.....hhhhhhhhhhhhhhhhhhh.......eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee....eeeeeeeeehhhhh..........eeee....hhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhh...eeee...hhhhhhhhhhhhh....eeeeeeeeeee.hhhhhhhhh.................eeeeehhhhhhhhhhhhhh.---.....eeeeeeee....eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3fd5 B   6 SFNPESYELDKSFRLTRFTELKGTGCKVPQDVLQKLLESL--------------VMPRLGIGMDTCVIPLRHGGLSLVQTTDYIYPIVDDPYMMGRIACANVLSDLYAMGVTECDNMLMLLGVSNKMTDRERDKVMPLIIQGFKDAAEEAGTSVTGGQTVLNPWIVLGGVATTVCQPNEFIMPDNAVPGDVLVLTKPLGTQVAVAVHQWLDIPEKWNKIKLVVTQEDVELAYQEAMMNMARLNRTAAGLMHTFNAHAATDITGFGILGHAQNLAKQQRNEVSFVIHNLPVLAKMAAVSKACGNMFGLMHGTCPETSGGLLICLPREQAARFCAEIKSP---EGHQAWIIGIVEKGNRTARIIDKPRIIEVAP 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  
                                                                  45             60                                                                                                                                                                                                                                                                                        343 347                              

   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 3FD5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3FD5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FD5)

(-) 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 | P499033fd6

(-) Related Entries Specified in the PDB File

2yye 3fd6