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(-) Description

Title :  CRYSTAL STRUCTURE OF SEP-TRNA:CYS-TRNA SYNTHASE FROM ARCHAEOGLOBUS FULGIDUS
 
Authors :  R. Fukunaga, S. Yokoyama, Riken Structural Genomics/Proteomics I (Rsgi)
Date :  10 Jan 07  (Deposition) - 17 Jul 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Seven-Stranded Bete-Strand, Lyase, 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 :  R. Fukunaga, S. Yokoyama
Structural Insights Into The Second Step Of Rna-Dependent Cysteine Biosynthesis In Archaea: Crystal Structure Of Sep-Trna:Cys-Trna Synthase From Archaeoglobus Fulgidus
J. Mol. Biol. V. 370 128 2007
PubMed-ID: 17512006  |  Reference-DOI: 10.1016/J.JMB.2007.04.050

(-) Compounds

Molecule 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26B
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234
    Synonym: HYPOTHETICAL PROTEIN AF_0028

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): A 
Biological Unit 2 (2x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
2SO45Ligand/IonSULFATE ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
2SO46Ligand/IonSULFATE ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1PLP-1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
2SO44Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY B:77 , ALA B:78 , ARG B:79 , SER B:206 , HIS B:208BINDING SITE FOR RESIDUE SO4 B 601
2AC2SOFTWARELYS A:20 , ARG A:267 , ARG A:270BINDING SITE FOR RESIDUE SO4 A 602
3AC3SOFTWARELYS B:20 , HIS B:263 , ARG B:267 , ARG B:270 , GLY B:350BINDING SITE FOR RESIDUE SO4 B 603
4AC4SOFTWAREHIS A:56 , HOH A:1234BINDING SITE FOR RESIDUE SO4 A 604
5AC5SOFTWAREARG A:79 , HIS A:103 , TYR A:104 , HOH A:1259BINDING SITE FOR RESIDUE SO4 A 605
6AC6SOFTWAREGLY A:77 , ALA A:78 , ARG A:79 , LYS A:82 , HIS A:103 , SER A:105 , ASN A:183 , ALA A:185 , TYR A:186 , SER A:206 , HIS A:208 , LYS A:209BINDING SITE FOR RESIDUE PLP A 1209

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2E7I)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Tyr A:125 -Pro A:126
2Tyr A:155 -Pro A:156
3Asn A:296 -Pro A:297
4Tyr B:125 -Pro B:126
5Tyr B:155 -Pro B:156
6Asn B:296 -Pro B:297

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2E7I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2E7I)

(-) Exons   (0, 0)

(no "Exon" information available for 2E7I)

(-) 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:344
 aligned with SPSS1_ARCFU | O30207 from UniProtKB/Swiss-Prot  Length:371

    Alignment length:364
                                    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       337       347       357       367    
          SPSS1_ARCFU     8 DFINIDPLQTGGKLTEEARQALLEWGDGYSVCDFCTTGRLDEIKTPPIHDFIHNQLPKFLGCDVARVTNGAREAKFAVMHSLAKKDAWVVMDENCHYSSYVAAERAGLNIALVPKTDYPDYAITPENFAQTIEETKKRGEVVLALITYPDGNYGNLPDVKKIAKVCSEYDVPLLVNGAYAIGRMPVSLKEIGADFIVGSGHKSMAASGPIGVMGMKEEWAEIVLRRSEKYKNKEVELLGCTARGATIITLMASFPHVRERIKRWDEEVEKARRFAAEMEKLGIKQLGDNPHNHDLMFFHAEVLYEISKKAKGGRFFLYRELKSRKIHGIKPGLTRYFKLSTYGLSDEEVDYVLNAFKEIIEKYS 371
               SCOP domains d2e7ia1 A:8-371 Selenocys                    teinyl-tRNA synthase (SepSecS)                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhh...hhhhhhhhhhh--------------------.hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeeee...hhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhhh.eeeeeee..........hhhhhhhhhhh....eeee.hhh......hhhhhh..eeeee...........eeeee...hhhhhh.........hhhhh.....hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..eee........eeeeehhhhhhhh....hhhhhhhhhhhh..ee........eeeee....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e7i A   8 DFINIDPLQTGGKLTEEARQALLEW--------------------PPIHDFIHNQLPKFLGCDVARVTNGAREAKFAVMHSLAKKDAWVVMDENCHYSSYVAAERAGLNIALVPKTDYPDYAITPENFAQTIEETKKRGEVVLALITYPDGNYGNLPDVKKIAKVCSEYDVPLLVNGAYAIGRMPVSLKEIGADFIVGSGHKSMAASGPIGVMGMKEEWAEIVLRRSEKYKNKEVELLGCTARGATIITLMASFPHVRERIKRWDEEVEKARRFAAEMEKLGIKQLGDNPHNHDLMFFHAEVLYEISKKAKGGRFFLYRELKSRKIHGIKPGLTRYFKLSTYGLSDEEVDYVLNAFKEIIEKYS 371
                                    17        27    |    -         -     |  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       337       347       357       367    
                                                   32                   53                                                                                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:344
 aligned with SPSS1_ARCFU | O30207 from UniProtKB/Swiss-Prot  Length:371

    Alignment length:364
                                    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       337       347       357       367    
          SPSS1_ARCFU     8 DFINIDPLQTGGKLTEEARQALLEWGDGYSVCDFCTTGRLDEIKTPPIHDFIHNQLPKFLGCDVARVTNGAREAKFAVMHSLAKKDAWVVMDENCHYSSYVAAERAGLNIALVPKTDYPDYAITPENFAQTIEETKKRGEVVLALITYPDGNYGNLPDVKKIAKVCSEYDVPLLVNGAYAIGRMPVSLKEIGADFIVGSGHKSMAASGPIGVMGMKEEWAEIVLRRSEKYKNKEVELLGCTARGATIITLMASFPHVRERIKRWDEEVEKARRFAAEMEKLGIKQLGDNPHNHDLMFFHAEVLYEISKKAKGGRFFLYRELKSRKIHGIKPGLTRYFKLSTYGLSDEEVDYVLNAFKEIIEKYS 371
               SCOP domains d2e7ib_ B: Selenocysteiny                    l-tRNA synthase (SepSecS)                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh...hhhhhhhhhhh--------------------.hhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhh...eeeeee...hhhhhhhhhh...eeeee..........hhhhhhhhhhhhhh..eeeeeee...........hhhhhhhhhhh....eee.hhhh......hhhhhh..eeeeehhhhh......eeeee...hhhhhh.........hhhhh.....hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.eee........eeeeehhhhhhhhhhh.hhhhhhhhhhhhh...........eeeee....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e7i B   8 DFINIDPLQTGGKLTEEARQALLEW--------------------PPIHDFIHNQLPKFLGCDVARVTNGAREAKFAVMHSLAKKDAWVVMDENCHYSSYVAAERAGLNIALVPKTDYPDYAITPENFAQTIEETKKRGEVVLALITYPDGNYGNLPDVKKIAKVCSEYDVPLLVNGAYAIGRMPVSLKEIGADFIVGSGHKSMAASGPIGVMGMKEEWAEIVLRRSEKYKNKEVELLGCTARGATIITLMASFPHVRERIKRWDEEVEKARRFAAEMEKLGIKQLGDNPHNHDLMFFHAEVLYEISKKAKGGRFFLYRELKSRKIHGIKPGLTRYFKLSTYGLSDEEVDYVLNAFKEIIEKYS 371
                                    17        27    |    -         -     |  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       337       347       357       367    
                                                   32                   53
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2E7I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2E7I)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SPSS1_ARCFU | O30207)
molecular function
    GO:0043766    Sep-tRNA:Cys-tRNA synthase activity    Catalysis of the reaction: O-phospho-L-seryl-tRNACys + sulfide = L-cysteinyl-tRNACys + phosphate.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0071952    conversion of O-phosphoseryl-tRNA to cysteinyl-tRNA    The modification process that results in the conversion of O-phosphoserine charged on a tRNA(Cys) to cysteinyl-tRNA.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.

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 Related Entries

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

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        SPSS1_ARCFU | O30207: 2e7j

(-) Related Entries Specified in the PDB File

2e7j RELATED ID: AR_001000847.2 RELATED DB: TARGETDB