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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DEPENTAMERIZED MUTANT OF N-TERMINAL TRUNCATED SELENOCYSTEINE SYNTHASE SELA
 
Authors :  Y. Itoh, S. Sekine, S. Yokoyama
Date :  29 May 13  (Deposition) - 22 Jan 14  (Release) - 30 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Fold-Type-I Pyridoxal 5'-Phosphate (Plp) Dependent Enzyme, Homodimer, L-Seryl-Trna(Sec) Selenium Transferase, Selenocysteine Synthesis, Selenium Metabolism, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Itoh, M. J. Brocker, S. Sekine, D. Soll, S. Yokoyama
Dimer-Dimer Interaction Of The Bacterial Selenocysteine Synthase Sela Promotes Functional Active-Site Formation And Catalytic Specificity
J. Mol. Biol. V. 426 1723 2014
PubMed-ID: 24456689  |  Reference-DOI: 10.1016/J.JMB.2014.01.003

(-) Compounds

Molecule 1 - L-SERYL-TRNA(SEC) SELENIUM TRANSFERASE
    Chains: A, B
    EC Number: 2.9.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: ROSETTA 2(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 62-452
    Gene: AQ_1031, SELA
    Mutation: YES
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 224324
    Strain: VF5
    Synonym: SELENOCYSTEINE SYNTHASE, SEC SYNTHASE, SELENOCYSTEINYL- TRNA(SEC) SYNTHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 20)

Asymmetric/Biological Unit (3, 20)
No.NameCountTypeFull Name
1LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
2MSE13Mod. Amino AcidSELENOMETHIONINE
3THJ5Ligand/IonTHIOSULFATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:116 , ARG A:312 , ARG A:315 , SER B:172 , ARG B:174BINDING SITE FOR RESIDUE THJ A 3001
2AC2SOFTWARESER A:118 , ARG A:119 , ARG A:315 , ARG B:174BINDING SITE FOR RESIDUE THJ A 3002
3AC3SOFTWARELYS A:91 , ARG A:343 , ASN B:102BINDING SITE FOR RESIDUE THJ A 3003
4AC4SOFTWARESER A:172 , ARG A:174 , ARG B:116 , ARG B:312 , ARG B:315 , HOH B:1040BINDING SITE FOR RESIDUE THJ B 501
5AC5SOFTWAREARG A:174 , SER B:118 , ARG B:119 , ILE B:120 , ARG B:315BINDING SITE FOR RESIDUE THJ B 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:415 -Pro A:416
2Glu B:415 -Pro B:416

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3WCO)

(-) 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:385
 aligned with SELA_AQUAE | O67140 from UniProtKB/Swiss-Prot  Length:452

    Alignment length:392
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450  
           SELA_AQUAE    61 IKSLMKPNIKRVINATGVVINTNLGRAPLSKDVINFISEIANGYSNLEYNLEEGKRGSRIAHIEKYLNELTGAESSFVVNNNAGAVFLVLNTLAEGKEVIISRGELVEIGGSFRIPDIMKKSGAILREVGTTNKTKVSDYEGAINQNTALLMKVHKSNFYMEGFVEEVKLEDLVKLGHKYGIPTYYDAGSGLLINLKEFGISVDEPNFRDCISLGIDLVSGSGDKLLGGPQAGIIVGKKNLIEKIKKNPIARALRIDKLTLSGLEMTLKLYFEKRYEDIPVIRMLTQDEKALRQKAKRLEKLLKDIPGLKISVIKDKAKPGGGSLPELELPTYCVAIRHDRLSSQELSRRLRLAEPPIVCRIREDQLLFDMRTVFHEDLKTIKKTLQELLSI 452
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee.....hhhhh....hhhhhhhhhhhhh.ee...ee....ee.hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhh...eeeee......hhhhhhhh....eeeeeee...-------....hhhhhhhhhhhhh..eeeeee.....hhhhhh......hhhhhhhh...eeeee..........eeeeehhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhhh.....eeeeeeeeee...........eeeeeeeeee...hhhhhhhhhhhh...eeeeee..eeeee....hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wco A  61 mKSLmKPNIKRVINATGVVINTNLGRAPLSKDVINFISEIANGYSNLEYNLEEGKRGSRIAHIEKYLNELTGAESSFVVNNNAGAVFLVLNTLAEGKEVIISRGELVEIGGSFRIPDImKKSGAILREVGYYNKTKVSRYEGAINQNTALLmKVHKS-------VEEVKLEDLVKLGHKYGIPTYYDAGSGLLINLKEFGISVDEPNFRDCISLGIDLVSGSGDkLLGGPQAGIIVGKKNLIEKIKKNPIARALRIDKLTLSGLEmTLKLYFEKRYEDIPVIRmLTQDEKALRQKAKRLEKLLKDIPGLKISVIKDKAKPGGGSLPELELPTYCVAIRHDRLSSQELSRRLRLAEPPIVCRIREDQLLFDmRTVFHEDLKTIKKTLQELLSI 452
                            |   |   70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 |    |  -    |  230       240       250       260       270       280    |  290       300       310       320     | 330       340   |   350       360       370       380       390       400       410       420       430|      440       450  
                            |   |                                                                                                               179-MSE                          212-MSE7     225                                                         285-LLP                                  326-MSE           344-MSE                                                                                431-MSE                 
                           61-MSE                                                                                                                                                                                                                                                                                                                                                                                                   
                               65-MSE                                                                                                                                                                                                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:382
 aligned with SELA_AQUAE | O67140 from UniProtKB/Swiss-Prot  Length:452

    Alignment length:390
                                    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       352       362       372       382       392       402       412       422       432       442       452
           SELA_AQUAE    63 SLMKPNIKRVINATGVVINTNLGRAPLSKDVINFISEIANGYSNLEYNLEEGKRGSRIAHIEKYLNELTGAESSFVVNNNAGAVFLVLNTLAEGKEVIISRGELVEIGGSFRIPDIMKKSGAILREVGTTNKTKVSDYEGAINQNTALLMKVHKSNFYMEGFVEEVKLEDLVKLGHKYGIPTYYDAGSGLLINLKEFGISVDEPNFRDCISLGIDLVSGSGDKLLGGPQAGIIVGKKNLIEKIKKNPIARALRIDKLTLSGLEMTLKLYFEKRYEDIPVIRMLTQDEKALRQKAKRLEKLLKDIPGLKISVIKDKAKPGGGSLPELELPTYCVAIRHDRLSSQELSRRLRLAEPPIVCRIREDQLLFDMRTVFHEDLKTIKKTLQELLSI 452
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeee..............hhhhhhhhhhhhh......ee....ee.hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhh..eeeee.....hhhhh.hhhhhhhhh..eeeee......hhhhhhh.....eeeeeee...--------...hhhhhhhhhhhhh..eeeeee.....hhhhhh......hhhhhhhh...eeeee..........eeeeehhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....eeeeeeeeee...........eeeeeeeeee...hhhhhhhhhhh....eeeeee..eeeee....hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3wco B  63 SLmKPNIKRVINATGVVINTNLGRAPLSKDVINFISEIANGYSNLEYNLEEGKRGSRIAHIEKYLNELTGAESSFVVNNNAGAVFLVLNTLAEGKEVIISRGELVEIGGSFRIPDImKKSGAILREVGYYNKTKVSRYEGAINQNTALLmKVHKS--------EEVKLEDLVKLGHKYGIPTYYDAGSGLLINLKEFGISVDEPNFRDCISLGIDLVSGSGDkLLGGPQAGIIVGKKNLIEKIKKNPIARALRIDKLTLSGLEmTLKLYFEKRYEDIPVIRmLTQDEKALRQKAKRLEKLLKDIPGLKISVIKDKAKPGGGSLPELELPTYCVAIRHDRLSSQELSRRLRLAEPPIVCRIREDQLLFDmRTVFHEDLKTIKKTLQELLSI 452
                              |     72        82        92       102       112       122       132       142       152       162       172      |182       192       202       212    |    -   |   232       242       252       262       272       282  |    292       302       312       322   |   332       342 |     352       362       372       382       392       402       412       422       432       442       452
                             65-MSE                                                                                                           179-MSE                          212-MSE7      226                                                        285-LLP                                  326-MSE           344-MSE                                                                                431-MSE
   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  (0, 0)

(no "SCOP Domain" information available for 3WCO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WCO)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SELA_AQUAE | O67140)
molecular function
    GO:0004125    L-seryl-tRNASec selenium transferase activity    Catalysis of the reaction: L-seryl-tRNA(Sec) + selenophosphate = L-selenocysteinyl-tRNA(Sec) + H2O + 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:0001514    selenocysteine incorporation    The incorporation of selenocysteine into a peptide; uses a special tRNA that recognizes the UGA codon as selenocysteine, rather than as a termination codon. Selenocysteine is synthesized from serine before its incorporation; it is not a posttranslational modification of peptidyl-cysteine.
    GO:0097056    selenocysteinyl-tRNA(Sec) biosynthetic process    The chemical reactions and pathways resulting in the formation of selenocysteinyl-tRNA(Sec). This process occurs through the following steps: a unique serine-tRNA with a UGA recognizing anticodon is first aminoacylated with serine; this is then phosphorylated by phosphoseryl-tRNA[Ser]Sec kinase; lastly, selenium is swapped for the phosphate on the serine.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SELA_AQUAE | O67140: 3w1h 3w1i 3w1j 3w1k 3wcn

(-) Related Entries Specified in the PDB File

3w1h DECAMERIC SELA (FULL LENGTH)
3w1i DECAMERIC SELA (N-TERMINAL TRUNCATED)
3w1j DECAMERIC SELA (N-TERMINAL TRUNCATED) IN COMPLEX WITH THIOSULFATE
3w1k DECAMERIC SELA (FULL LENGTH) IN COMPLEX WITH TRNA(SEC)
3wcn