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(-) Description

Title :  CRYSTAL STRUCTURE OF SERYL-TRNA SYNTHETASE FROM CANDIDA ALBICANS
 
Authors :  R. Rocha, M. A. Santos, P. J. B. Pereira, S. Macedo-Ribeiro
Date :  09 Feb 11  (Deposition) - 03 Aug 11  (Release) - 10 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Class-Ii Aminoacyl-Trna Synthetase Family, Type-1 Seryl-Trna Synthetase Subfamily, Aminoacyl-Trna Synthetase, Serine, Trna, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Rocha, P. J. Pereira, M. A. Santos, S. Macedo-Ribeiro
Unveiling The Structural Basis For Translational Ambiguity Tolerance In A Human Fungal Pathogen.
Proc. Natl. Acad. Sci. Usa V. 108 14091 2011
PubMed-ID: 21825144  |  Reference-DOI: 10.1073/PNAS.1102835108
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SERYL-TRNA SYNTHETASE, CYTOPLASMIC
    Chains: A
    EC Number: 6.1.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: P7-7
    Gene: SES1, CAO19.7901
    Organism Common: YEAST
    Organism Scientific: CANDIDA ALBICANS
    Organism Taxid: 5476
    Synonym: SERINE--TRNA LIGASE, SERRS, SERYL-TRNA(SER/SEC) SYNTHETASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2SSA2Ligand/Ion5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2SSA4Ligand/Ion5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:246 , GLU A:248 , ARG A:279 , GLU A:281 , PHE A:293 , ARG A:294 , VAL A:295 , PHE A:298 , LYS A:300 , GLU A:302 , GLU A:366 , LEU A:367 , VAL A:368 , SER A:369 , ASN A:402 , THR A:404 , ALA A:407 , ARG A:410 , MG A:487 , HOH A:554 , HOH A:559 , HOH A:561 , HOH A:705BINDING SITE FOR RESIDUE SSA A 486
2AC2SOFTWAREGLU A:366 , SER A:369 , SSA A:486 , HOH A:556 , HOH A:719 , HOH A:743BINDING SITE FOR RESIDUE MG A 487
3AC3SOFTWAREPRO A:133 , GLU A:134 , ALA A:145 , GLN A:328 , SER A:329 , LEU A:330 , GLY A:331 , TYR A:419 , VAL A:426 , ILE A:427 , GLU A:429 , ARG A:432 , HOH A:654 , HOH A:655 , HOH A:691BINDING SITE FOR RESIDUE SSA A 488
4AC4SOFTWARELEU A:344 , HOH A:495 , HOH A:496 , HOH A:497 , HOH A:575 , HOH A:601BINDING SITE FOR RESIDUE MG A 489

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QO8)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asp A:72 -Ala A:73
2Leu A:267 -Pro A:268

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QO8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QO8)

(-) Exons   (0, 0)

(no "Exon" information available for 3QO8)

(-) 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:441
 aligned with SYSC_CANAL | Q9HGT6 from UniProtKB/Swiss-Prot  Length:462

    Alignment length:451
                                    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 
           SYSC_CANAL     1 MLDINAFLVEKGGDPEIIKASQKKRGDSVELVDEIIAEYKEWVKLRFDLDEHNKKLNSVQKEIGKRFKAKEDAKDLIAEKEKLSNEKKEIIEKEAEADKNLRSKINQVGNIVHESVVDSQDEENNELVRTWTPENYKKPEQIAAATGAPAKLSHHEVLLRLDGYDPERGVRIVGHRGYFLRNYGVFLNQALINYGLSFLSSKGYVPLQAPVMMNKEVMAKTAQLSQFDEELYKVIDGEDEKYLIATSEQPISAYHAGEWFESPAEQLPVRYAGYSSCFRREAGSHGKDAWGIFRVHAFEKIEQFVLTEPEKSWEEFDRMIGCSEEFYQSLGLPYRVVGIVSGELNNAAAKKYDLEAWFPFQQEYKELVSCSNCTDYQSRNLEIRCGIKQQNQQEKKYVHCLNSTLSATERTICCILENYQKEDGLVIPEVLRKYIPGEPEFIPYIKELPKN 451
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..---.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhheeeeee.....................hhhhhhhhh..eehhhhhhhhh....ee.hhhhhhhhhhhhhhhhhhhh...eeee...eeehhhhh...hhhhhhhh..eeee..eeeee...hhhhhhh.....ee.hhhhhh.eeeeeeeeee..................eeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh.....eeeeeeeee....eeeeeeeeee..hhhhhhhh.ee..-------....eeeeeeeeehhhhhhhhhhhhee..eee.hhhhhhhh.....eee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qo8 A   1 MLDINAFLVEKGGDPEIIKASQKKRGDSVELVDEIIAEYKEWVKLRFDLDEHNKKLNSVQKEIGKRFK---DAKDLIAEKEKLSNEKKEIIEKEAEADKNLRSKINQVGNIVHESVVDSQDEENNELVRTWTPENYKKPEQIAAATGAPAKLSHHEVLLRLDGYDPERGVRIVGHRGYFLRNYGVFLNQALINYGLSFLSSKGYVPLQAPVMMNKEVMAKTAQLSQFDEELYKVIDGEDEKYLIATSEQPISAYHAGEWFESPAEQLPVRYAGYSSCFRREAGSHGKDAWGIFRVHAFEKIEQFVLTEPEKSWEEFDRMIGCSEEFYQSLGLPYRVVGIVSGELNNAAAKKYDLEAWFPFQQEYKELVSCSNCTDYQSRNLEIRCGI-------KKYVHCLNSTLSATERTICCILENYQKEDGLVIPEVLRKYIPGEPEFIPYIKELPKN 451
                                    10        20        30        40        50        60       | - |      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      |  -    |  400       410       420       430       440       450 
                                                                                              68  72                                                                                                                                                                                                                                                                                                                        387     395
   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 3QO8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QO8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3QO8)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (SYSC_CANAL | Q9HGT6)
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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        SYSC_CANAL | Q9HGT6: 3qne 3qo5 3qo7

(-) Related Entries Specified in the PDB File

3qne APO-ENZYME (MAJOR ISOFORM: CUG CODON TRANSLATED AS A SERINE)
3qo5 APO-ENZYME (MINOR ISOFORM: CUG CODON TRANSLATED AS A LEUCINE)
3qo7 COMPLEX WITH ATP (MAJOR ISOFORM: CUG CODON TRANSLATED AS A SERINE)