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(-) Description

Title :  CRYSTAL STRUCTURE OF SELENOPHOSPHATE SYNTHETASE FROM AQUIFEX AEOLICUS
 
Authors :  S. I. Sekine, E. Matsumoto, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  09 May 08  (Deposition) - 27 May 08  (Release) - 09 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Full-Length Selenophosphate Synthetase, Transferase, Atp-Binding, Kinase, Magnesium, Nucleotide-Binding, Selenium, Selenocysteine, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Itoh, S. Sekine, E. Matsumoto, R. Akasaka, C. Takemoto, M. Shirouzu S. Yokoyama
Structure Of Selenophosphate Synthetase Essential For Selenium Incorporation Into Proteins And Rnas.
J. Mol. Biol. V. 385 1456 2009
PubMed-ID: 18773910  |  Reference-DOI: 10.1016/J.JMB.2008.08.042

(-) Compounds

Molecule 1 - SELENIDE, WATER DIKINASE
    Chains: A, B
    EC Number: 2.7.9.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCOLD TF
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SELD, AQ_1030
    Mutation: YES
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Strain: VF5
    Synonym: SELENOPHOSPHATE SYNTHETASE, SELENIUM DONOR PROTEIN

 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
1SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:179 , PRO A:263 , LYS A:264BINDING SITE FOR RESIDUE SO4 A 701
2AC2SOFTWARESER B:10 , LYS B:179 , PRO B:263 , LYS B:264BINDING SITE FOR RESIDUE SO4 B 702

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZOD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZOD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZOD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZOD)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZOD)

(-) 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:315
 aligned with SELD_AQUAE | O67139 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:334
                                    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       322       332    
           SELD_AQUAE     3 ELLKLVRSSGUAAKVGPGDLQEILKGFNIYTDESTLVSIGDDAGVYEHNGIIWVYTVDIITPVVNDPYLWGAISTANALSDVYAMGGIPVNALAISCFNNCELDIEIFREVIRGALDKLREAKTVLLGGHTIDDKEPKFGLSVAGICPEGKYITQSGAQVGQLLILTKPIGTGILIKGLKEGILKEEDINEAIENMLALNDKARNLMLSLDATACTDVTGFGLLGHAWNICKNSNIGARIFFEKVPYYQLSENLVKKKIYPKGAIENLNFVKNYLKSNLDNWKLILLSDPVTSGGLLFTINKEKLEKIDETAKELEVNYWIIGETIAENVLEVL 336
               SCOP domains d2zoda1           A:3-154 Seleni         de, water dikinase SelD                                                                                        d2zoda2 A:155-336 Selenide, water dikinase SelD                                                                                                                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.----------...hhhhhhh.....---------...eeee..eeeeeeeeee.....hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeeeeee....eeeeeeeee.hhhh...........eeee....hhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhh.eeeee.hhh..hhhhhhhhhh...hhhhhhhhhhhh..ee...hhhhhhhhhh......eeeeehhhhhhhhhhhhhhhh...eeeeeee....eeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zod A   3 ELLKLVR----------GDLQEILKGFNIYTD---------DAGVYEHNGIIWVYTVDIITPVVNDPYLWGAISTANALSDVYAMGGIPVNALAISCFNNCELDIEIFREVIRGALDKLREAKTVLLGGHTIDDKEPKFGLSVAGICPEGKYITQSGAQVGQLLILTKPIGTGILIKGLKEGILKEEDINEAIENMLALNDKARNLMLSLDATACTDVTGFGLLGHAWNICKNSNIGARIFFEKVPYYQLSENLVKKKIYPKGAIENLNFVKNYLKSNLDNWKLILLSDPVTSGGLLFTINKEKLEKIDETAKELEVNYWIIGETIAENVLEVL 336
                                  |  -       |22        32 |       - |      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       322       332    
                                  9         20            34        44                                                                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:321
 aligned with SELD_AQUAE | O67139 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:334
                                    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       322       332    
           SELD_AQUAE     3 ELLKLVRSSGUAAKVGPGDLQEILKGFNIYTDESTLVSIGDDAGVYEHNGIIWVYTVDIITPVVNDPYLWGAISTANALSDVYAMGGIPVNALAISCFNNCELDIEIFREVIRGALDKLREAKTVLLGGHTIDDKEPKFGLSVAGICPEGKYITQSGAQVGQLLILTKPIGTGILIKGLKEGILKEEDINEAIENMLALNDKARNLMLSLDATACTDVTGFGLLGHAWNICKNSNIGARIFFEKVPYYQLSENLVKKKIYPKGAIENLNFVKNYLKSNLDNWKLILLSDPVTSGGLLFTINKEKLEKIDETAKELEVNYWIIGETIAENVLEVL 336
               SCOP domains d2zodb1 B          :3-154 Selenide, wat   er dikinase SelD                                                                                              d2zodb2 B:155-336 Selenide, water dikinase SelD                                                                                                                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------AIRS-2zodB01 B:45-133                                                                    ---------------------------AIRS_C-2zodB03 B:161-336                                                                                                                                                         Pfam domains (1)
           Pfam domains (2) ------------------------------------------AIRS-2zodB02 B:45-133                                                                    ---------------------------AIRS_C-2zodB04 B:161-336                                                                                                                                                         Pfam domains (2)
         Sec.struct. author .hhhhh...----------hhhhhhh.............---.eeeee..eeeeeeeeee.....hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee.......hhhhhhhhhhhhhhhhh..eeeeeeeee....eeeeeeeee.hhhh...........eeee....hhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhh.eeeee.hhh..hhhhhhhhhh...hhhhhhhhhhh...eee..hhhhhhhhhh......eeeeehhhhhhhhhhhhhhhh...eeeeeee....eeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zod B   3 ELLKLVRSS----------LQEILKGFNIYTDESTLVSI---AGVYEHNGIIWVYTVDIITPVVNDPYLWGAISTANALSDVYAMGGIPVNALAISCFNNCELDIEIFREVIRGALDKLREAKTVLLGGHTIDDKEPKFGLSVAGICPEGKYITQSGAQVGQLLILTKPIGTGILIKGLKEGILKEEDINEAIENMLALNDKARNLMLSLDATACTDVTGFGLLGHAWNICKNSNIGARIFFEKVPYYQLSENLVKKKIYPKGAIENLNFVKNYLKSNLDNWKLILLSDPVTSGGLLFTINKEKLEKIDETAKELEVNYWIIGETIAENVLEVL 336
                                    |-        22        32        |-  |     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       322       332    
                                   11         22                 41  45
   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  (2, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ZOD)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: AIRS] (11)
(-)
Family: AIRS (11)
(-)
Aquifex aeolicus (2)
1aAIRS-2zodB01B:45-133
1bAIRS-2zodB02B:45-133
(-)
Clan: no clan defined [family: AIRS_C] (13)
(-)
Family: AIRS_C (13)
(-)
Aquifex aeolicus (2)
2aAIRS_C-2zodB03B:161-336
2bAIRS_C-2zodB04B:161-336

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SELD_AQUAE | O67139)
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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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: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: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:0016260    selenocysteine biosynthetic process    The chemical reactions and pathways resulting in the formation of selenocysteine, an essential component of glutathione peroxidase and some other proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SELD_AQUAE | O67139: 2yye 2zau

(-) Related Entries Specified in the PDB File

2yye THE SAME PROTEIN COMPLEXED WITH ALPHA, BETA-METHYLENE ATP (AMPCPP).
2zau AN N-TERMINALLY TRUNCATED FRAGMENT, CORRESPONDING TO RESIDUES 26-336 OF THE FULL-LENGTH SPS. RELATED ID: AAE001001030.2 RELATED DB: TARGETDB