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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL PHENYLALANYL-TRNA SYNTHETASE COMPLEXED WITH M-TYROSINE
 
Authors :  L. Klipcan, N. Moor, N. Kessler, M. G. Safro
Date :  12 May 09  (Deposition) - 21 Jul 09  (Release) - 21 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Classii Aarss Fold, Rrm Domain, Trna, Rna Recogntion, Aminoacyl-Trna Synthetase, Atp-Binding, Ligase, Mitochondrion, Nucleotide-Binding, Protein Biosynthesis, Transit Peptide, M-Tyrosine, Polymorphism (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Klipcan, N. Moor, N. Kessler, M. G. Safro
Eukaryotic Cytosolic And Mitochondrial Phenylalanyl-Trna Synthetases Catalyze The Charging Of Trna With The Meta-Tyrosine
Proc. Natl. Acad. Sci. Usa V. 106 11045 2009
PubMed-ID: 19549855  |  Reference-DOI: 10.1073/PNAS.0905212106
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHENYLALANYL-TRNA SYNTHETASE, MITOCHONDRIAL
    ChainsA
    EC Number6.1.1.20
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneFARS2, FARS1, HSPC320
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPHENYLALANINE--TRNA LIGASE, PHERS

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MTY1Ligand/IonMETA-TYROSINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:119 , SER A:121 , GLN A:124 , ARG A:143 , GLN A:157 , GLU A:159 , PHE A:234 , GLY A:254 , CYS A:255 , ALA A:275 , PHE A:276 , GLY A:277 , HOH A:442BINDING SITE FOR RESIDUE MTY A 416

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1His A:236 -Pro A:237

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 6)

Asymmetric/Biological Unit (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_052642S57CSYFM_HUMANPolymorphism34382405AS21C
2UniProtVAR_077044D142YSYFM_HUMANDisease (SPG77)  ---AD106Y
3UniProtVAR_069487Y144CSYFM_HUMANDisease (COXPD14)397514610AY108C
4UniProtVAR_052643N280SSYFM_HUMANPolymorphism11243011AN244S
5UniProtVAR_069488I329TSYFM_HUMANDisease (COXPD14)397514611AI293T
6UniProtVAR_069489D391VSYFM_HUMANDisease (COXPD14)397514612AD355V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FDX_ACBPS51447 Ferredoxin-fold anticodon binding (FDX-ACB) domain profile.SYFM_HUMAN358-450  1A:322-414

(-) Exons   (0, 0)

(no "Exon" information available for 3HFV)

(-) 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:405
 aligned with SYFM_HUMAN | O95363 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:405
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446     
           SYFM_HUMAN    47 PGSVVELLGKSYPQDDHSNLTRKVLTRVGRNLHNQQHHPLWLIKERVKEHFYKQYVGRFGTPLFSVYDNLSPVVTTWQNFDSLLIPADHPSRKKGDNYYLNRTHMLRAHTSAHQWDLLHAGLDAFLVVGDVYRRDQIDSQHYPIFHQLEAVRLFSKHELFAGIKDGESLQLFEQSSRSAHKQETHTMEAVKLVEFDLKQTLTRLMAHLFGDELEIRWVDCYFPFTHPSFEMEINFHGEWLEVLGCGVMEQQLVNSAGAQDRIGWAFGLGLERLAMILYDIPDIRLFWCEDERFLKQFCVSNINQKVKFQPLSKYPAVINDISFWLPSENYAENDFYDLVRTIGGDLVEKVDLIDKFVHPKTHKTSHCYRITYRHMERTLSQREVRHIHQALQEAAVQLLGVEGRF 451
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.......hhhhhh....hhhhh..hhhhhhhhhhhhhhhhhhhhh......eee.....eeehhhhhhhhh....hhhhhhhhh......eee..hhhhhhhhhhhh...eeeeeeeee...........eeeeeeeeeeeehhhhh....hhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..eeeeeeeeeee..eeeeeeeeeeehhhhhhhh....eeeeeeeeehhhhhhhhh...hhhhhhh.hhhhhhhhh..................eeeeeeee......hhhhhhhhhhhhhh..eeeeeeeeeee......eeeeeeeee.......hhhhhhhhhhhhhhhhhhhhh.eeee Sec.struct. author
                 SAPs(SNPs) ----------C------------------------------------------------------------------------------------Y-C---------------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------T-------------------------------------------------------------V------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FDX_ACB  PDB: A:322-414 UniProt: 358-450                                                     - PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hfv A  11 PGSVVELLGKSYPQDDHSNLTRKVLTRVGRNLHNQQHHPLWLIKERVKEHFYKQYVGRFGTPLFSVYDNLSPVVTTWQNFDSLLIPADHPSRKKGDNYYLNRTHMLRAHTSAHQWDLLHAGLDAFLVVGDVYRRDQIDSQHYPIFHQLEAVRLFSKHELFAGIKDGESLQLFEQSSRSAHKQETHTMEAVKLVEFDLKQTLTRLMAHLFGDELEIRWVDCYFPFTHPSFEMEINFHGEWLEVLGCGVMEQQLVNSAGAQDRIGWAFGLGLERLAMILYDIPDIRLFWCEDERFLKQFCVSNINQKVKFQPLSKYPAVINDISFWLPSENYAENDFYDLVRTIGGDLVEKVDLIDKFVHPKTHKTSHCYRITYRHMERTLSQREVRHIHQALQEAAVQLLGVEGRF 415
                                    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     

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 3HFV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SYFM_HUMAN | O95363)
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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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:0004826    phenylalanine-tRNA ligase activity    Catalysis of the reaction: ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + L-phenylalanyl-tRNA(Phe).
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
biological process
    GO:0006432    phenylalanyl-tRNA aminoacylation    The process of coupling phenylalanine to phenylalanyl-tRNA, catalyzed by phenylalanyl-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:0043039    tRNA aminoacylation    The chemical reactions and pathways by which the various amino acids become bonded to their corresponding tRNAs. The most common route for synthesis of aminoacyl tRNA is by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, usually catalyzed by the cognate aminoacyl-tRNA ligase. A given aminoacyl-tRNA ligase aminoacylates all species of an isoaccepting group of tRNA molecules.
    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:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
    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.
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SYFM_HUMAN | O953633cmq 3teg 3tup 5mgh 5mgu 5mgv 5mgw

(-) Related Entries Specified in the PDB File

3cmq