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(-) Description

Title :  CRYSTAL STRUCTURE OF AN N-TERMINALLY TRUNCATED SELENOPHOSPHATE SYNTHETASE FROM AQUIFEX AEOLICUS
 
Authors :  S. Sekine, E. Matsumoto, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  10 Oct 07  (Deposition) - 17 Jun 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Intramolecular S-S Bond, Trimer Of Dimers, Atp-Binding, Kinase, Magnesium, Nucleotide-Binding, Selenium, Selenocysteine, Transferase, 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 :  E. Matsumoto, S. Sekine, R. Akasaka, Y. Otta, K. Katsura, M. Inoue, T. Kaminishi, T. Terada, M. Shirouzu, S. Yokoyama
Structure Of An N-Terminally Truncated Selenophosphate Synthetase From Aquifex Aeolicus
Acta Crystallogr. , Sect. F V. 64 453 2008
PubMed-ID: 18540050  |  Reference-DOI: 10.1107/S1744309108012074
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SELENIDE, WATER DIKINASE
    Chains: A, B, C
    EC Number: 2.7.9.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET25B
    Expression System Strain: BL21(DE3) CODONPLUS-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINALLY TRUNCATED FORM, RESIDUES 2-311 (27- 336)
    Gene: SELD
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Strain: VF5
    Synonym: SELENOPHOSPHATE SYNTHETASE, SELENIUM DONOR PROTEIN

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1PO43Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1PO46Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:179 , LYS C:179 , LYS C:182 , PRO C:263 , LYS C:264BINDING SITE FOR RESIDUE PO4 C 901
2AC2SOFTWARELYS A:179 , LYS A:182 , PRO A:263 , LYS A:264 , HOH A:1222 , LYS C:179BINDING SITE FOR RESIDUE PO4 A 902
3AC3SOFTWARELYS B:179 , LYS B:182 , LYS B:264 , HOH B:1244BINDING SITE FOR RESIDUE PO4 B 903

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:99 -A:103
2B:99 -B:103
3C:99 -C:103

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ZAU)

(-) Sequences/Alignments

Asymmetric 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:307
 aligned with SELD_AQUAE | O67139 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:309
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327         
           SELD_AQUAE    28 GFNIYTDESTLVSIGDDAGVYEHNGIIWVYTVDIITPVVNDPYLWGAISTANALSDVYAMGGIPVNALAISCFNNCELDIEIFREVIRGALDKLREAKTVLLGGHTIDDKEPKFGLSVAGICPEGKYITQSGAQVGQLLILTKPIGTGILIKGLKEGILKEEDINEAIENMLALNDKARNLMLSLDATACTDVTGFGLLGHAWNICKNSNIGARIFFEKVPYYQLSENLVKKKIYPKGAIENLNFVKNYLKSNLDNWKLILLSDPVTSGGLLFTINKEKLEKIDETAKELEVNYWIIGETIAENVLEVL 336
               SCOP domains d2zaua1 A:28-154 Selenide, water dikinase SelD                                                                                 d2zaua2 A:155-336 Selenide, water dikinase SelD                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee.....eeeee..eeeeeeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeeeeee......--.hhhhhhhhhhhhhhhhh..eeeeeee.......eeeeeeee.hhhh...........eeee....hhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhh.eeeee.hhh..hhhhhhhhhh...hhhhhhhhhhhh..eee..hhhhhhhhhh......eeeeehhhhhhhhhhhhhhhh...eeeeeee....eeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zau A  28 GFNIYTDESTLVSIGDDAGVYEHNGIIWVYTVDIITPVVNDPYLWGAISTANALSDVYAMGGIPVNALAISCFNNCE--IEIFREVIRGALDKLREAKTVLLGGHTIDDKEPKFGLSVAGICPEGKYITQSGAQVGQLLILTKPIGTGILIKGLKEGILKEEDINEAIENMLALNDKARNLMLSLDATACTDVTGFGLLGHAWNICKNSNIGARIFFEKVPYYQLSENLVKKKIYPKGAIENLNFVKNYLKSNLDNWKLILLSDPVTSGGLLFTINKEKLEKIDETAKELEVNYWIIGETIAENVLEVL 336
                                    37        47        57        67        77        87        97      |107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327         
                                                                                                      104  |                                                                                                                                                                                                                                     
                                                                                                         107                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:303
 aligned with SELD_AQUAE | O67139 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:309
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327         
           SELD_AQUAE    28 GFNIYTDESTLVSIGDDAGVYEHNGIIWVYTVDIITPVVNDPYLWGAISTANALSDVYAMGGIPVNALAISCFNNCELDIEIFREVIRGALDKLREAKTVLLGGHTIDDKEPKFGLSVAGICPEGKYITQSGAQVGQLLILTKPIGTGILIKGLKEGILKEEDINEAIENMLALNDKARNLMLSLDATACTDVTGFGLLGHAWNICKNSNIGARIFFEKVPYYQLSENLVKKKIYPKGAIENLNFVKNYLKSNLDNWKLILLSDPVTSGGLLFTINKEKLEKIDETAKELEVNYWIIGETIAENVLEVL 336
               SCOP domains d2zaub1 B:28-1  54 Selenide, water dikinase SelD                                                                               d2zaub2 B:155-336 Selenide, water dikinase SelD                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee.--..eeeee..eeeeeeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeeeeee.....----hhhhhhhhhhhhhhhhh..eeeeeee.......eeeeeeee.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
                 2zau B  28 GFNIYTDESTLVSI--DAGVYEHNGIIWVYTVDIITPVVNDPYLWGAISTANALSDVYAMGGIPVNALAISCFNNC----EIFREVIRGALDKLREAKTVLLGGHTIDDKEPKFGLSVAGICPEGKYITQSGAQVGQLLILTKPIGTGILIKGLKEGILKEEDINEAIENMLALNDKARNLMLSLDATACTDVTGFGLLGHAWNICKNSNIGARIFFEKVPYYQLSENLVKKKIYPKGAIENLNFVKNYLKSNLDNWKLILLSDPVTSGGLLFTINKEKLEKIDETAKELEVNYWIIGETIAENVLEVL 336
                                    37   |  | 47        57        67        77        87        97     |   -|      117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327         
                                        41 44                                                        103  108                                                                                                                                                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:304
 aligned with SELD_AQUAE | O67139 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:309
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327         
           SELD_AQUAE    28 GFNIYTDESTLVSIGDDAGVYEHNGIIWVYTVDIITPVVNDPYLWGAISTANALSDVYAMGGIPVNALAISCFNNCELDIEIFREVIRGALDKLREAKTVLLGGHTIDDKEPKFGLSVAGICPEGKYITQSGAQVGQLLILTKPIGTGILIKGLKEGILKEEDINEAIENMLALNDKARNLMLSLDATACTDVTGFGLLGHAWNICKNSNIGARIFFEKVPYYQLSENLVKKKIYPKGAIENLNFVKNYLKSNLDNWKLILLSDPVTSGGLLFTINKEKLEKIDETAKELEVNYWIIGETIAENVLEVL 336
               SCOP domains d2zauc1 C:28-15  4 Selenide, water dikinase SelD                                                                               d2zauc2 C:155-336 Selenide, water dikinase SelD                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee..--.eeeee..eeeeeeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeeeeee.....---..hhhhhhhhhhhhhhhh..eeeeeee.......eeeeeeee.hhhh...........eeee....hhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhh.eeeee.hhh..hhhhhhhhh....hhhhhhhhhhhh..eee..hhhhhhhhhh......eeeeehhhhhhhhhhhhhhhh...eeeeeee....eeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zau C  28 GFNIYTDESTLVSIG--AGVYEHNGIIWVYTVDIITPVVNDPYLWGAISTANALSDVYAMGGIPVNALAISCFNNC---IEIFREVIRGALDKLREAKTVLLGGHTIDDKEPKFGLSVAGICPEGKYITQSGAQVGQLLILTKPIGTGILIKGLKEGILKEEDINEAIENMLALNDKARNLMLSLDATACTDVTGFGLLGHAWNICKNSNIGARIFFEKVPYYQLSENLVKKKIYPKGAIENLNFVKNYLKSNLDNWKLILLSDPVTSGGLLFTINKEKLEKIDETAKELEVNYWIIGETIAENVLEVL 336
                                    37    |  |47        57        67        77        87        97     | 107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327         
                                         42 45                                                       103 107
   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, 6)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2ZAU)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (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 2zod

(-) Related Entries Specified in the PDB File

2yye FULL-LENGTH SELENOPHOSPHATE SYNTHETASE FROM AQUIFEX AEOLICUS COMPLEXED WITH AMPCPP RELATED ID: AAE001001030.1 RELATED DB: TARGETDB
2zod FULL-LENGTH SELENOPHOSPHATE SYNTHETASE FROM AQUIFEX AEOLICUS