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(-) Description

Title :  CRYSTAL STRUCTURE OF A. AEOLICUS TRNASEC IN COMPLEX WITH M. KANDLERI SERRS
 
Authors :  Y. Itoh, S. Sekine, S. Yokoyama
Date :  27 Dec 12  (Deposition) - 13 Feb 13  (Release) - 07 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Class 2 Aminoacyl-Trna Synthetase, Transfer Rna, Aminoacylation, Selenocysteine Incorporation, Selenium Metabolism, Ligase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Itoh, S. Sekine, S. Suetsugu, S. Yokoyama
Tertiary Structure Of Bacterial Selenocysteine Trna
Nucleic Acids Res. V. 41 6729 2013
PubMed-ID: 23649835  |  Reference-DOI: 10.1093/NAR/GKT321

(-) Compounds

Molecule 1 - TYPE-2 SERINE--TRNA LIGASE
    Chains: A
    EC Number: 6.1.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26B
    Expression System Strain: ROSETTA 2(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SERS
    Mutation: YES
    Organism Scientific: METHANOPYRUS KANDLERI
    Organism Taxid: 190192
    Strain: AV19
    Synonym: SERYL-TRNA SYNTHETASE, SERRS, SERYL-TRNA(SER/SEC) SYNTHETASE
 
Molecule 2 - SELENOCYSTEINE TRNA
    Chains: B
    Engineered: YES
    Organism Scientific: AQUIFEX AEOLICUS VF5
    Organism Taxid: 224324
    Other Details: THE TRNASEC FROM AQUIFEX AEOLICUS VF5 WAS PREPARED BY IN VITRO TRANSCRIPTION WITH T7 RNA POLYMERASE.
    Synthetic: YES

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 33)

Asymmetric Unit (5, 33)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2PT15Ligand/IonPLATINUM (II) ION
3SO48Ligand/IonSULFATE ION
4SSA1Ligand/Ion5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE
5ZN1Ligand/IonZINC ION
Biological Unit 1 (3, 34)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
2PT-1Ligand/IonPLATINUM (II) ION
3SO416Ligand/IonSULFATE ION
4SSA2Ligand/Ion5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE
5ZN-1Ligand/IonZINC ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:319 , GLU A:368 , CYS A:478 , SSA A:2002BINDING SITE FOR RESIDUE ZN A 2001
02AC2SOFTWAREALA A:317 , ARG A:349 , GLU A:351 , VAL A:361 , PHE A:364 , ARG A:366 , GLU A:368 , PHE A:409 , SER A:449 , VAL A:450 , GLY A:451 , SER A:452 , ASN A:454 , CYS A:478 , GLY A:482 , ARG A:485 , ZN A:2001BINDING SITE FOR RESIDUE SSA A 2002
03AC3SOFTWAREPHE A:364 , ARG A:485BINDING SITE FOR RESIDUE PT A 2003
04AC4SOFTWARETYR A:410BINDING SITE FOR RESIDUE PT A 2004
05AC5SOFTWAREU B:47CBINDING SITE FOR RESIDUE PT A 2006
06AC6SOFTWAREHIS A:74BINDING SITE FOR RESIDUE PT A 2007
07AC7SOFTWAREARG A:260 , HIS A:263 , LEU A:416BINDING SITE FOR RESIDUE PT A 2009
08AC8SOFTWAREGLU A:105 , GLU A:131 , ARG A:136BINDING SITE FOR RESIDUE PT A 2010
09AC9SOFTWAREGLY A:194BINDING SITE FOR RESIDUE PT A 2012
10BC1SOFTWAREARG A:166 , SER A:167 , ARG A:414BINDING SITE FOR RESIDUE PT A 2013
11BC2SOFTWAREGLU A:144BINDING SITE FOR RESIDUE PT A 2015
12BC3SOFTWAREGLU A:511 , LYS A:512BINDING SITE FOR RESIDUE PT A 2017
13BC4SOFTWAREARG A:40 , ARG A:83BINDING SITE FOR RESIDUE SO4 A 2018
14BC5SOFTWAREARG A:40 , GLY A:41 , A B:47N , G B:47OBINDING SITE FOR RESIDUE SO4 A 2019
15BC6SOFTWAREMSE A:1 , PHE A:110 , ASP A:111 , ARG A:112 , GLU A:164BINDING SITE FOR RESIDUE SO4 A 2020
16BC7SOFTWAREASN A:296 , GLU A:297BINDING SITE FOR RESIDUE SO4 A 2021
17BC8SOFTWAREARG A:308 , ASP A:309BINDING SITE FOR RESIDUE SO4 A 2022
18BC9SOFTWAREARG A:212 , ARG A:308BINDING SITE FOR RESIDUE SO4 A 2023
19CC1SOFTWAREG B:47BBINDING SITE FOR RESIDUE SO4 B 101
20CC2SOFTWAREC B:47D , C B:47E , C B:47FBINDING SITE FOR RESIDUE SO4 B 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3W3S)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:336 -Pro A:337

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3W3S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3W3S)

(-) Exons   (0, 0)

(no "Exon" information available for 3W3S)

(-) 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:527
 aligned with SYS2_METKA | Q8TVD2 from UniProtKB/Swiss-Prot  Length:527

    Alignment length:527
                                    10        20        30        40        50        60        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       460       470       480       490       500       510       520       
           SYS2_METKA     1 MELKFSAEVELTLSREVDPAEIEPTVEEFVKEANEDLLQRGVPTGKEGAKIESYRVLEDTIEMEITGTRYLRPHEAAMRVRKRLAERLGRKHRVGVRDLKIPRYEVVLRFDREVTRDDVGYVPVADDVVVEDGTVRLTFQDVDEEMLRRHVIDRVIRLVAWAVEERSELVERVTKVEPGTVVDESGPREIRFDGDVTEEARRRGWVKEFPGRGQWIYTPPMAALFEVLRDFLLERVTRKLGFEPALFPKLIPLETMFRMRYLHGLPDGMYYVCPPKRDPELFDDFKRELYVWGELNERTLGSLKEKLRDPGYVLAPAQCEPFYELLRDEVVDPERLPIKLYDCSGWTYRWEGGAAKGLERVNEFQRIEHVWIAEPEEAERIREELLEATKRVAEELELEWKVVVSDDPFYLEGRLLEDRDIELPDVPSYEFEVYLPFKGERSSEEAWISVGSFNVHGEHFVDGFNVKEKSGRTLFTGCAGLGVTRWVVGLLAQHGFEPEEWPEPILERIDEKFGGLPEVPKTLTWPE 527
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh.........eeeeeee...eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee.....hhhhhh......eeee...eeeeeee..hhhhhhhhhhhhhhhhhhhhhh...hhhhh........eeee..........hhhhhhhhh..eee......eeehhhhhhhhhhhhhhhhhhh......ee.....eeehhhhhhhhhhhhhhhhh.ee.....hhhhhhhhhhhhhhhh..hhhhhhhhhhh.....eee.....hhhhhhhh..ee......eeeee...eee..............eeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhh...eeeee.........hhhhhh........eeeeeee.hhhh...hhh.eeeeeeeeeeehhhhhhh..ee......eeeeeeeehhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w3s A   1 mELKFSAEVELTLSREVDPAEIEPTVEEFVKEANEDLLQRGVPTGKEGAKIESYYVLYDTIYmEITGTRYLRPHEAAmRVRKRLAERLGRKHRVGVRDLKIPRYEVVLRFDREVTYDYVGYVPVADDVVVEDGTVRLTFQDVDEEmLRRHVIDRVIRLVAWAVEERSELVERVTKVEPGTVVDESGPRRIRFRGDVTEEARRRGWVKEFPGRGQWIYTPPmAALFEVLRDFLLERVTRKLGFEPALFPKLIPLETmFRmRYLHGLPDGmYYVCPPKRDPELFDDFKRELYVWGELNERTLGSLKEKLRDPGYVLAPAQCEPFYELLRDEVVDPERLPIKLYDCSGWTYRWEGGAAKGLERVNEFQRIEHVWIAEPEEAYRIRRELLEATKRVAEELELEWKVVVSDDPFYLEGRLLEDRDIELPDVPSYEFEVYLPFKGERSSEEAWISVGSFNVHGEHFVDGFNVKEKSGRTLFTGCAGLGVTRWVVGLLAQHGFYPYEWPEPILERIDEKFGGLPEVPKTLTWPE 527
                            |       10        20        30        40        50        60  |     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       460       470       480       490       500       510       520       
                            |                                                            63-MSE         78-MSE                                                             146-MSE                                                                    221-MSE                            256-MSE      269-MSE                                                                                                                                                                                                                                                              
                            1-MSE                                                                                                                                                                                                                                                           259-MSE                                                                                                                                                                                                                                                                        


Chain B from PDB  Type:RNA  Length:98
                                                                                                                                  
                 3w3s B   1 GGGAGAGGUUGGCCGGCUGGUGCCGCCCCGGGACUUCAAAUCCCGUGGGAGGUCCCGCAAGGGAGCUCCGGAGGGUUCGAUUCCCUCCCUCUCCCGCC  75
                                 |   9  |    |19 |      28        38     |  47|||||||47J||||||||48        58       67A        
                                5A    11A   16|  |                     43A  47A||||||47J||||||47S                  67A        
                                             18  |                           47B||||||47K|||||||                              
                                               20A                            47C||||||47L||||||                              
                                                                               47D||||| 47M|||||                              
                                                                                47E||||  47N||||                              
                                                                                 47F|||   47O|||                              
                                                                                  47G||    47P||                              
                                                                                   47H|     47Q|                              
                                                                                    47I      47R
   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 3W3S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3W3S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3W3S)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A   (SYS2_METKA | Q8TVD2)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004812    aminoacyl-tRNA ligase activity    Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0004828    serine-tRNA ligase activity    Catalysis of the reaction: ATP + L-serine + tRNA(Ser) = AMP + diphosphate + L-seryl-tRNA(Ser).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    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: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:0006434    seryl-tRNA aminoacylation    The process of coupling serine to seryl-tRNA, catalyzed by seryl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA.
    GO:0006418    tRNA aminoacylation for protein translation    The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, to be used in ribosome-mediated polypeptide synthesis.
    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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