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(-) Description

Title :  THE CRYSTAL STRUCTURE OF SELENOPHOSPHATE SYNTHETASE FROM E. COLI
 
Authors :  N. Noinaj, R. Wattanasak, J. Wally, T. Stadtman, S. K. Buchanan
Date :  28 Sep 11  (Deposition) - 14 Mar 12  (Release) - 14 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Atp Binding Protein, Selenophosphate Synthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Noinaj, R. Wattanasak, D. Y. Lee, J. L. Wally, G. Piszczek, P. B. Chock, T. C. Stadtman, S. K. Buchanan
Structural Insights Into The Catalytic Mechanism Of Escherichia Coli Selenophosphate Synthetase.
J. Bacteriol. V. 194 499 2012
PubMed-ID: 22081394  |  Reference-DOI: 10.1128/JB.06012-11

(-) Compounds

Molecule 1 - SELENIDE, WATER DIKINASE
    Chains: A, B
    EC Number: 2.7.9.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGP1-2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SELD, FDHB, B1764, JW1753
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: SELENIUM DONOR PROTEIN, SELENOPHOSPHATE SYNTHASE

 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
1MG2Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:51 , ASP A:91 , ASP A:227BINDING SITE FOR RESIDUE MG A 401
2AC2SOFTWAREASP B:91 , ASP B:227 , THR B:229BINDING SITE FOR RESIDUE MG B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3U0O)

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Gln A:34 -Ala A:35
2Asn A:41 -Leu A:42
3Asn A:46 -Glu A:47
4Gly A:268 -Ala A:269
5Gly B:18 -Cys B:19
6Ser B:166 -Thr B:167
7Glu B:327 -Leu B:328

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3U0O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3U0O)

(-) Exons   (0, 0)

(no "Exon" information available for 3U0O)

(-) 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:319
 aligned with SELD_ECOLI | P16456 from UniProtKB/Swiss-Prot  Length:347

    Alignment length:319
                                    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         
           SELD_ECOLI    29 ILHSEQAKFVDPNLLVGNETRDDAAVYDLGNGTSVISTTDFFMPIVDNPFDFGRIAATNAISDIFAMGGKPIMAIAILGWPINKLSPEIAREVTEGGRYACRQAGIALAGGHSIDAPEPIFGLAVTGIVPTERVKKNSTAQAGCKLFLTKPLGIGVLTTAEKKSLLKPEHQGLATEVMCRMNIAGASFANIEGVKAMTDVTGFGLLGHLSEMCQGAGVQARVDYEAIPKLPGVEEYIKLGAVPGGTERNFASYGHLMGEMPREVRDLLCDPQTSGGLLLAVMPEAENEVKATAAEFGIELTAIGELVPARGGRAMVEIR 347
               SCOP domains d3u0oa1 A:29-162 automated matches                                                                                                    d3u0oa2 A:163-347 automated matches                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................eeee....eeeeeeeeee.....hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeeeee....eeeeeeeeeee.hhh..........eeee....hhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhh....eeeeee...hhhhhhhhhhhhhhheeeeee........hhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhh.......eeeeehhhhhhhhhhhhhhh.......eeeee.....eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u0o A  29 ILHSEQAKFVDPNLLVGNETRDDAAVYDLGNGTSVISTTDFFMPIVDNPFDFGRIAATNAISDIFAMGGKPIMAIAILGWPINKLSPEIAREVTEGGRYACRQAGIALAGGHSIDAPEPIFGLAVTGIVPTERVKKNSTAQAGCKLFLTKPLGIGVLTTAEKKSLLKPEHQGLATEVMCRMNIAGASFANIEGVKAMTDVTGFGLLGHLSEMCQGAGVQARVDYEAIPKLPGVEEYIKLGAVPGGTERNFASYGHLMGEMPREVRDLLCDPQTSGGLLLAVMPEAENEVKATAAEFGIELTAIGELVPARGGRAMVEIR 347
                                    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         


Chain B from PDB  Type:PROTEIN  Length:335
 aligned with SELD_ECOLI | P16456 from UniProtKB/Swiss-Prot  Length:347

    Alignment length:335
                                    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       342     
           SELD_ECOLI    13 HGAGCGCKISPKVLETILHSEQAKFVDPNLLVGNETRDDAAVYDLGNGTSVISTTDFFMPIVDNPFDFGRIAATNAISDIFAMGGKPIMAIAILGWPINKLSPEIAREVTEGGRYACRQAGIALAGGHSIDAPEPIFGLAVTGIVPTERVKKNSTAQAGCKLFLTKPLGIGVLTTAEKKSLLKPEHQGLATEVMCRMNIAGASFANIEGVKAMTDVTGFGLLGHLSEMCQGAGVQARVDYEAIPKLPGVEEYIKLGAVPGGTERNFASYGHLMGEMPREVRDLLCDPQTSGGLLLAVMPEAENEVKATAAEFGIELTAIGELVPARGGRAMVEIR 347
               SCOP domains d3u0ob1 B:13-162 automated matches                                                                                                                    d3u0ob2 B:163-347 automated matches                                                                                                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhh................eeee....eeeeeeeeee.....hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeeeee....eeeeeeeeeeehhhhhh........eeee....hhhhhhhhh..........hhhhhhhh....hhhhhh....eeeeee...hhhhhhhhhhhhh..eeeee.........hhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhh.......eeeee...hhhhhhhhhhhh....eeeeeeee.......eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u0o B  13 HGAGCGCKISPKVLETILHSEQAKFVDPNLLVGNETRDDAAVYDLGNGTSVISTTDFFMPIVDNPFDFGRIAATNAISDIFAMGGKPIMAIAILGWPINKLSPEIAREVTEGGRYACRQAGIALAGGHSIDAPEPIFGLAVTGIVPTERVKKNSTAQAGCKLFLTKPLGIGVLTTAEKKSLLKPEHQGLATEVMCRMNIAGASFANIEGVKAMTDVTGFGLLGHLSEMCQGAGVQARVDYEAIPKLPGVEEYIKLGAVPGGTERNFASYGHLMGEMPREVRDLLCDPQTSGGLLLAVMPEAENEVKATAAEFGIELTAIGELVPARGGRAMVEIR 347
                                    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       342
   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 3U0O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3U0O)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SELD_ECOLI | P16456)
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.
    GO:0070329    tRNA seleno-modification    The substitution of a selenium atom for a sulfur atom in a ribonucleotide in a tRNA molecule.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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