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(-) Description

Title :  CRYSTAL STRUCTURE OF SERYL-TRNA SYNTHETASE FROM PYROCOCCUS HORIKOSHII COMPLEXED WITH ATP
 
Authors :  Y. Itoh, S. Sekine, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  22 Aug 08  (Deposition) - 09 Sep 08  (Release) - 03 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Coiled-Coil, Homodimer, Aminoacyl-Trna Synthetase, Atp- Binding, Cytoplasm, Ligase, Nucleotide-Binding, Protein Biosynthesis, 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 :  Y. Itoh, S. Sekine, C. Kuroishi, T. Terada, M. Shirouzu, S. Kuramitsu, S. Yokoyama
Crystallographic And Mutational Studies Of Seryl-Trna Synthetase From The Archaeon Pyrococcus Horikoshii
Rna Biol. V. 5 54 2008
PubMed-ID: 18818520
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SERYL-TRNA SYNTHETASE
    Chains: A, B
    EC Number: 6.1.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PH0710
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3
    Synonym: SERYL-TRNA(SER/SEC) SYNTHETASE, SERINE--TRNA LIGASE, SERRS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2SO47Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:283 , GLU A:285 , PHE A:297 , ARG A:298 , VAL A:299 , PHE A:302 , GLU A:370 , VAL A:371 , VAL A:372 , SER A:373 , THR A:406 , ALA A:409 , SER A:411 , ARG A:412BINDING SITE FOR RESIDUE AMP A1001
2AC2SOFTWARESER A:183 , ARG A:184 , ALA A:289 , HIS A:300BINDING SITE FOR RESIDUE SO4 A2001
3AC3SOFTWARELYS A:291 , ASP A:292 , THR A:293 , ARG A:298 , ARG A:369BINDING SITE FOR RESIDUE SO4 A2003
4AC4SOFTWAREPHE A:297 , ARG A:298 , ARG A:369 , GLU A:370 , ARG A:412 , HOH A:2011BINDING SITE FOR RESIDUE SO4 A2005
5AC5SOFTWAREALA A:172 , ASP A:173 , PHE A:174 , ALA A:175BINDING SITE FOR RESIDUE SO4 A2007
6AC6SOFTWAREARG B:283 , GLU B:285 , PHE B:297 , ARG B:298 , VAL B:299 , PHE B:302 , GLU B:370 , VAL B:371 , VAL B:372 , THR B:406 , ALA B:409 , SER B:411 , ARG B:412BINDING SITE FOR RESIDUE AMP B1002
7AC7SOFTWARESER B:183 , ARG B:184 , ALA B:289 , HIS B:300BINDING SITE FOR RESIDUE SO4 B2002
8AC8SOFTWARELYS B:291 , ASP B:292 , THR B:293 , ARG B:298 , ARG B:369BINDING SITE FOR RESIDUE SO4 B2004
9AC9SOFTWAREPHE B:297 , ARG B:298 , ARG B:369 , GLU B:370 , ARG B:412BINDING SITE FOR RESIDUE SO4 B2006

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZR2)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:271 -Pro A:272
2Leu B:271 -Pro B:272

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZR2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZR2)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZR2)

(-) 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:447
 aligned with SYS_PYRHO | O58441 from UniProtKB/Swiss-Prot  Length:455

    Alignment length:447
                                    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       
            SYS_PYRHO     1 MLDIKLIRENPELVKNDLIKRGELEKVKWVDEILKLDTEWRTKLKEINRLRHERNKIAVEIGKRRKKGEPVDELLAKSREIVKRIGELENEVEELKKKIDYYLWRLPNITHPSVPVGKDENDNVPIRFWGKARVWKGHLERFLEQSQGKMEYEILEWKPKLHVDLLEILGGADFARAAKVSGSRFYYLLNEIVILDLALIRFALDRLIEKGFTPVIPPYMVRRFVEEGSTSFEDFEDVIYKVEDEDLYLIPTAEHPLAGMHANEILDGKDLPLLYVGVSPCFRKEAGTAGKDTKGIFRVHQFHKVEQFVYSRPEESWEWHEKIIRNAEELFQELEIPYRVVNICTGDLGYVAAKKYDIEAWMPGQGKFREVVSASNCTDWQARRLNIRFRDRTDEKPRYVHTLNSTAIATSRAIVAILENHQEEDGTVRIPKVLWKYTGFKEIVPVE 447
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhheeeeee.eeeee..hhhhhhhhhh...eeeee.....hhhhhhhhh..eehhhhhhhh.....eeehhhhhhhhhhhhhhhhhhhhh..eeee...eehhhhhhh....hhhhhh.........ee...hhhhhhhh...eeee.....eeeeeeeeee..................eeeeeeeeeee...hhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhh....eeeeeeeee....eeeeeeeeeeeehhhhhhhheeee.......ee.eeeeeeeeehhhhhhhhhhhh......ee.hhhhhhhhh..ee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zr2 A   1 MLDIKLIRENPELVKNDLIKRGELEKVKWVDEILKLDTEWRTKLKEINRLRHERNKIAVEIGKRRKKGEPVDELLAKSREIVKRIGELENEVEELKKKIDYYLWRLPNITHPSVPVGKDENDNVPIRFWGKARVWKGHLERFLEQSQGKMEYEILEWKPKLHVDLLEILGGADFARAAKVSGSRFYYLLNEIVILDLALIRFALDRLIEKGFTPVIPPYMVRRFVEEGSTSFEDFEDVIYKVEDEDLYLIPTAEHPLAGMHANEILDGKDLPLLYVGVSPCFRKEAGTAGKDTKGIFRVHQFHKVEQFVYSRPEESWEWHEKIIRNAEELFQELEIPYRVVNICTGDLGYVAAKKYDIEAWMPGQGKFREVVSASNCTDWQARRLNIRFRDRTDEKPRYVHTLNSTAIATSRAIVAILENHQEEDGTVRIPKVLWKYTGFKEIVPVE 447
                                    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       


Chain B from PDB  Type:PROTEIN  Length:447
 aligned with SYS_PYRHO | O58441 from UniProtKB/Swiss-Prot  Length:455

    Alignment length:447
                                    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       
            SYS_PYRHO     1 MLDIKLIRENPELVKNDLIKRGELEKVKWVDEILKLDTEWRTKLKEINRLRHERNKIAVEIGKRRKKGEPVDELLAKSREIVKRIGELENEVEELKKKIDYYLWRLPNITHPSVPVGKDENDNVPIRFWGKARVWKGHLERFLEQSQGKMEYEILEWKPKLHVDLLEILGGADFARAAKVSGSRFYYLLNEIVILDLALIRFALDRLIEKGFTPVIPPYMVRRFVEEGSTSFEDFEDVIYKVEDEDLYLIPTAEHPLAGMHANEILDGKDLPLLYVGVSPCFRKEAGTAGKDTKGIFRVHQFHKVEQFVYSRPEESWEWHEKIIRNAEELFQELEIPYRVVNICTGDLGYVAAKKYDIEAWMPGQGKFREVVSASNCTDWQARRLNIRFRDRTDEKPRYVHTLNSTAIATSRAIVAILENHQEEDGTVRIPKVLWKYTGFKEIVPVE 447
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Seryl_tRNA_N-2zr2B01 B:1-110                                                                                  ------------------------------------------------------------------------------------tRNA-synt_2b-2zr2B03 B:195-365                                                                                                                                             ---------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) Seryl_tRNA_N-2zr2B02 B:1-110                                                                                  ------------------------------------------------------------------------------------tRNA-synt_2b-2zr2B04 B:195-365                                                                                                                                             ---------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhheeeeee..eeee..hhhhhhhhhh....eeee.....hhhhhhhhhh.eehhhhhhhh.....eeehhhhhhhhhhhhhhhhhhhhh..eeee...eehhhhhhhhh..hhhhhh.........ee...hhhhhhhh...eeee.hhh.eeeeeeeeee..................eeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhh....eeeeeeeee....eeeeeeeeeeeehhhhhhhheeee.......ee.eeeeeeeeehhhhhhhhhhhh......ee.hhhhhhhhh..ee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zr2 B   1 MLDIKLIRENPELVKNDLIKRGELEKVKWVDEILKLDTEWRTKLKEINRLRHERNKIAVEIGKRRKKGEPVDELLAKSREIVKRIGELENEVEELKKKIDYYLWRLPNITHPSVPVGKDENDNVPIRFWGKARVWKGHLERFLEQSQGKMEYEILEWKPKLHVDLLEILGGADFARAAKVSGSRFYYLLNEIVILDLALIRFALDRLIEKGFTPVIPPYMVRRFVEEGSTSFEDFEDVIYKVEDEDLYLIPTAEHPLAGMHANEILDGKDLPLLYVGVSPCFRKEAGTAGKDTKGIFRVHQFHKVEQFVYSRPEESWEWHEKIIRNAEELFQELEIPYRVVNICTGDLGYVAAKKYDIEAWMPGQGKFREVVSASNCTDWQARRLNIRFRDRTDEKPRYVHTLNSTAIATSRAIVAILENHQEEDGTVRIPKVLWKYTGFKEIVPVE 447
                                    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
   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 2ZR2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ZR2)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: tRNA_bind_arm (7)
(-)
Clan: tRNA_synt_II (64)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SYS_PYRHO | O58441)
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: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).
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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  2zr2
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 Related Entries

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

UniProtKB/Swiss-Prot
        SYS_PYRHO | O58441: 2dq0 2zr3

(-) Related Entries Specified in the PDB File

2dq0 THE SAME PROTEIN COMPLEXED WITH SER-SA
2zr3 THE SAME PROTEIN, APO FORM RELATED ID: PHO001000710.2 RELATED DB: TARGETDB