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(-) Description

Title :  CRYSTAL STRUCTURE OF SELENOPHOSPHATE SYNTHETASE FROM AQUIFEX AEOLICUS COMPLEXED WITH AMPCPP
 
Authors :  Y. Itoh, S. Sekine, E. Matsumoto, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  29 Apr 07  (Deposition) - 29 Apr 08  (Release) - 22 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Full-Length Selenophosphate Synthetase Complex With Atp-Analog, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (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: 511693
    Expression System Vector Type: PLASMID
    Gene: AQ_1030
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 224324
    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  (3, 13)

Asymmetric/Biological Unit (3, 13)
No.NameCountTypeFull Name
1APC2Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2CO10Ligand/IonCOBALT (II) ION
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:60 , HOH A:931 , HIS B:132BINDING SITE FOR RESIDUE CO B 701
02AC2SOFTWAREASP A:44 , ASP A:83 , ASP A:219 , HOH A:859 , HOH A:918BINDING SITE FOR RESIDUE CO A 702
03AC3SOFTWAREASP A:60 , ASP A:83 , HOH A:859 , HOH A:932BINDING SITE FOR RESIDUE CO A 703
04AC4SOFTWAREASP A:44 , THR A:58 , ASP A:60 , ASP A:83 , HOH A:804 , HOH A:860 , HOH A:931BINDING SITE FOR RESIDUE CO A 704
05AC5SOFTWAREASP A:43 , ASP A:44 , ALA A:86 , MET A:87 , ILE A:155 , CYS A:217BINDING SITE FOR RESIDUE CO A 705
06AC6SOFTWAREHIS A:132 , ASP B:60 , HOH B:991BINDING SITE FOR RESIDUE CO A 801
07AC7SOFTWAREASP B:44 , ASP B:83 , ASP B:219 , HOH B:902 , HOH B:1049BINDING SITE FOR RESIDUE CO B 802
08AC8SOFTWAREASP B:60 , ASP B:83 , HOH B:1027 , HOH B:1049BINDING SITE FOR RESIDUE CO B 803
09AC9SOFTWAREASP B:44 , THR B:58 , ASP B:60 , ASP B:83 , HOH B:903 , HOH B:917 , HOH B:991BINDING SITE FOR RESIDUE CO B 804
10BC1SOFTWAREASP B:43 , ASP B:44 , ALA B:86 , MET B:87 , ILE B:155 , CYS B:217BINDING SITE FOR RESIDUE CO B 805
11BC2SOFTWARELYS A:259 , LYS B:179 , GLU B:183 , LYS B:260 , ILE B:261 , TYR B:262BINDING SITE FOR RESIDUE PO4 B 901
12BC3SOFTWARELYS A:16 , LEU A:22 , LEU A:26 , GLY A:42 , ASP A:43 , ASP A:44 , ASP A:60 , ASP A:83 , THR A:221 , GLY A:222 , PHE A:223 , HOH A:833 , HOH A:859 , HOH A:860 , HOH A:918 , HOH A:928 , HOH A:931 , HOH A:932 , ALA B:96 , SER B:98 , GLY B:130 , GLY B:131 , HIS B:132 , THR B:133 , HOH B:921 , HOH B:1048BINDING SITE FOR RESIDUE APC A 501
13BC4SOFTWAREALA A:96 , SER A:98 , GLY A:130 , GLY A:131 , HIS A:132 , THR A:133 , HOH A:822 , HOH A:929 , LEU B:22 , LEU B:26 , GLY B:42 , ASP B:43 , ASP B:44 , ASP B:60 , ASP B:83 , THR B:221 , GLY B:222 , HOH B:902 , HOH B:917 , HOH B:935 , HOH B:942 , HOH B:944 , HOH B:949 , HOH B:982 , HOH B:991 , HOH B:1049BINDING SITE FOR RESIDUE APC B 601

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:103 -B:13

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YYE)

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

    Alignment length:339
                               1                                                                                                                                                                                                                                                                                                                                               
                               |     7        17        27        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     - ---MVELLKLVRSSGUAAKVGPGDLQEILKGFNIYTDESTLVSIGDDAGVYEHNGIIWVYTVDIITPVVNDPYLWGAISTANALSDVYAMGGIPVNALAISCFNNCELDIEIFREVIRGALDKLREAKTVLLGGHTIDDKEPKFGLSVAGICPEGKYITQSGAQVGQLLILTKPIGTGILIKGLKEGILKEEDINEAIENMLALNDKARNLMLSLDATACTDVTGFGLLGHAWNICKNSNIGARIFFEKVPYYQLSENLVKKKIYPKGAIENLNFVKNYLKSNLDNWKLILLSDPVTSGGLLFTINKEKLEKIDETAKELEVNYWIIGETIAENVLEVL 336
               SCOP domains ---d2yyea1 A:1-154 Selenide, water dikinase SelD                                                                                                             d2yyea2 A:155-336 Selenide, water dikinase SelD                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh...........hhhhhhhhh........eee......eeeee..eeeeeeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeeeeeee......hhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeee.hhhh...........eeee....hhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhh....eee...hhhhhhhhhhhhhhh.eeeee.hhh..hhhhhhhhh....hhhhhhhhhhhh..ee...hhhhhhhhhh......eeeeehhhhhhhhhhhhhhhh...eeeeeee....eeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yye A  -6 GGIMVELLKLVRSSGCAAKVGPGDLQEILKGFNIYTDESTLVSIGDDAGVYEHNGIIWVYTVDIITPVVNDPYLWGAISTANALSDVYAMGGIPVNALAISCFNNCELDIEIFREVIRGALDKLREAKTVLLGGHTIDDKEPKFGLSVAGICPEGKYITQSGAQVGQLLILTKPIGTGILIKGLKEGILKEEDINEAIENMLALNDKARNLMLSLDATACTDVTGFGLLGHAWNICKNSNIGARIFFEKVPYYQLSENLVKKKIYPKGAIENLNFVKNYLKSNLDNWKLILLSDPVTSGGLLFTINKEKLEKIDETAKELEVNYWIIGETIAENVLEVL 336
                              ||     7        17        27        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         
                             -4|                                                                                                                                                                                                                                                                                                                                               
                               1                                                                                                                                                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:343
 aligned with SELD_AQUAE | O67139 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:343
                                   1                                                                                                                                                                                                                                                                                                                                               
                                   | 3        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       313       323       333   
           SELD_AQUAE     - -------MVELLKLVRSSGUAAKVGPGDLQEILKGFNIYTDESTLVSIGDDAGVYEHNGIIWVYTVDIITPVVNDPYLWGAISTANALSDVYAMGGIPVNALAISCFNNCELDIEIFREVIRGALDKLREAKTVLLGGHTIDDKEPKFGLSVAGICPEGKYITQSGAQVGQLLILTKPIGTGILIKGLKEGILKEEDINEAIENMLALNDKARNLMLSLDATACTDVTGFGLLGHAWNICKNSNIGARIFFEKVPYYQLSENLVKKKIYPKGAIENLNFVKNYLKSNLDNWKLILLSDPVTSGGLLFTINKEKLEKIDETAKELEVNYWIIGETIAENVLEVL 336
               SCOP domains d2yyeb1 B:-6-154 Selenide, water dikinase SelD                                                                                                                   d2yyeb2 B:155-336 Selenide, water dikinase SelD                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------AIRS-2yyeB01 B:42-133                                                                       ---------------------------AIRS_C-2yyeB03 B:161-336                                                                                                                                                         Pfam domains (1)
           Pfam domains (2) ------------------------------------------------AIRS-2yyeB02 B:42-133                                                                       ---------------------------AIRS_C-2yyeB04 B:161-336                                                                                                                                                         Pfam domains (2)
         Sec.struct. author .........hhhhhh...........hhhhhhhhhh.......eee......eeeee..eeeeeeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeeeeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeeeeee....eeeeeeeee.hhhh..........eeeee....hhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhh...eeee...hhhhhhhhhhhhhh..eeeee.hhh..hhhhhhhhhh...hhhhhhhhhhh...ee...hhhhhhhhhh......eeeeee..hhhhhhhhhhhhh...eeeeeee....eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yye B  -6 GGIEGRHMVELLKLVRSSGCAAKVGPGDLQEILKGFNIYTDESTLVSIGDDAGVYEHNGIIWVYTVDIITPVVNDPYLWGAISTANALSDVYAMGGIPVNALAISCFNNCELDIEIFREVIRGALDKLREAKTVLLGGHTIDDKEPKFGLSVAGICPEGKYITQSGAQVGQLLILTKPIGTGILIKGLKEGILKEEDINEAIENMLALNDKARNLMLSLDATACTDVTGFGLLGHAWNICKNSNIGARIFFEKVPYYQLSENLVKKKIYPKGAIENLNFVKNYLKSNLDNWKLILLSDPVTSGGLLFTINKEKLEKIDETAKELEVNYWIIGETIAENVLEVL 336
                                     3        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       313       323       333
   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 2YYE)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: AIRS] (11)
(-)
Family: AIRS (11)
(-)
Aquifex aeolicus (2)
1aAIRS-2yyeB01B:42-133
1bAIRS-2yyeB02B:42-133
(-)
Clan: no clan defined [family: AIRS_C] (13)
(-)
Family: AIRS_C (13)
(-)
Aquifex aeolicus (2)
2aAIRS_C-2yyeB03B:161-336
2bAIRS_C-2yyeB04B: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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  2yye
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  SELD_AQUAE | O67139
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  2.7.9.3
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

2e0b AN N-TERMINALLY TRUNCATED FRAGMENT, CORRESPONDING TO RESIDUES 26-336 OF THE FULL-LENGTH PROTEIN.
2zau AN N-TERMINALLY TRUNCATED FRAGMENT, CORRESPONDING TO RESIDUES 26-336 OF THE FULL-LENGTH SPS
2zod THE FULL-LENGTH SPS, APO FORM RELATED ID: AAE001001030.3 RELATED DB: TARGETDB