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(-) Description

Title :  CRYSTAL STRUCTURE OF TYROSYL-TRNA SYNTHETASE FROM AEROPYRUM PERNIX
 
Authors :  M. Kuratani, H. Sakai, M. Takahashi, T. Yanagisawa, T. Kobayashi, K. Mu L. Chen, Z. J. Liu, B. C. Wang, C. Kuroishi, S. Kuramitsu, T. Terada, Y. B M. Shirouzu, S. I. Sekine, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  06 Jul 05  (Deposition) - 22 Nov 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Tyrrs, Aminoacylation, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kuratani, H. Sakai, M. Takahashi, T. Yanagisawa, T. Kobayashi, K. Murayama, L. Chen, Z. J. Liu, B. C. Wang, C. Kuroishi, S. Kuramitsu, T. Terada, Y. Bessho, M. Shirouzu, S. I. Sekine, S. Yokoyama
Crystal Structures Of Tyrosyl-Trna Synthetases From Archaea
J. Mol. Biol. V. 355 395 2005
PubMed-ID: 16325203  |  Reference-DOI: 10.1016/J.JMB.2005.10.073

(-) Compounds

Molecule 1 - TYROSYL-TRNA SYNTHETASE
    Chains: A
    EC Number: 6.1.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: AEROPYRUM PERNIX
    Organism Taxid: 56636

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1SO48Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:20 , THR A:22 , GLU A:23 , GLU A:24BINDING SITE FOR RESIDUE SO4 A 1001
2AC2SOFTWAREHIS A:49 , TRP A:52 , MET A:239 , SER A:240 , LYS A:241 , HOH A:1083BINDING SITE FOR RESIDUE SO4 A 1002
3AC3SOFTWAREGLY A:41 , TRP A:55 , GLY A:184 , ASP A:186 , GLN A:187 , HOH A:1113BINDING SITE FOR RESIDUE SO4 A 1003
4AC4SOFTWAREGLN A:270 , VAL A:271 , GLN A:272BINDING SITE FOR RESIDUE SO4 A 1004

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Val A:21 -Thr A:22

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2CYA)

(-) 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:328
 aligned with SYY_AERPE | Q9YA64 from UniProtKB/Swiss-Prot  Length:364

    Alignment length:358
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353        
            SYY_AERPE     4 VDVEERFNRIARNTVEIVTEEELKGLLASGARIKGYIGYEPSGVAHIGWLVWMYKVKDLVEAGVDFSVLEATWHAYINDKLGGDMDLIRAAARIVRRVMEAAGVPVERVRFVDAEELASDKDYWGLVIRVAKRASLARVRRALTIMGRRAEEAEVDASKLIYPLMQVSDIFYMDLDIALGGMDQRKAHMLARDVAEKLGRKKPVAIHTPIISSLQGPGRMEASQGEIDDVLAEVKMSKSKPETAVFVVDSDDDIRRKIRKAYCPAKQVQGNPVLEIARYILFARDGFTLRVDRPAKYGGPVEYTSYEELERDYTDGRLHPLDLKNAVAESLIEVVRPIRGAVLGDPAMKRALEAIEGK 361
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2cyaA01 A:4-214 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                              2cyaA0                2 A:215-361 Tyrosyl-Transfer RNA Synthetase                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh...eeehhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhheeeehhhhhhhhhhhhhhhhhhhh.hhhhhhh..------.hhhhhhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhh.......eeeee.........----------------......hhhhh.....hhhhhhhhhhh..........hhhhhhhhhh........ee..--------.ee.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cya A   4 VDVEERFNRIARNTVEIVTEEELKGLLASGARIKGYIGYEPSGVAHIGWLVWMYKVKDLVEAGVDFSVLEATWHAYINDKLGGDMDLIRAAARIVRRVMEAAGVPVERVRFVDAEELASDKDYWGLVIRVAKRASLARVRRAL------AEEAEVDASKLIYPLMQVSDIFYMDLDIALGGMDQRKAHMLARDVAEKLGRKKPVAIHTPIISSLQGP----------------VKMSKSKPETAVFVVDSDDDIRRKIRKAYCPAKQVQGNPVLEIARYILFARDGFTLRVD--------VEYTSYEELERDYTDGRLHPLDLKNAVAESLIEVVRPIRGAVLGDPAMKRALEAIEGK 361
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143  |    153       163       173       183       193       203       213      |  -         -   |   243       253       263       273       283       293 |       -|      313       323       333       343       353        
                                                                                                                                                                        146    153                                                                220              237                                                       295      304
   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 2CYA)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CYA)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (SYY_AERPE | Q9YA64)
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:0004831    tyrosine-tRNA ligase activity    Catalysis of the reaction: L-tyrosine + ATP + tRNA(Tyr) = L-tyrosyl-tRNA(Tyr) + AMP + diphosphate + 2 H(+).
biological process
    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.
    GO:0006437    tyrosyl-tRNA aminoacylation    The process of coupling tyrosine to tyrosyl-tRNA, catalyzed by tyrosyl-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.
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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