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(-) Description

Title :  CRYSTAL STRUCTURE OF TYROSYL-TRNA SYNTHETASE COMPLEXED WITH L-TYROSINE FROM ARCHAEOGLOBUS FULGIDUS
 
Authors :  M. Kuratani, H. Sakai, M. Takahashi, T. Yanagisawa, T. Kobayashi, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  06 Jul 05  (Deposition) - 22 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann-Fold, 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. Sekine, S. Yokoyama
Crystal Structures Of Tyrosyl-Trna Synthetases From Archaea
J. Mol. Biol. V. 355 395 2006
PubMed-ID: 16325203  |  Reference-DOI: 10.1016/J.JMB.2005.10.073
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TYROSYL-TRNA SYNTHETASE
    Chains: A, B
    EC Number: 6.1.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET41A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234
    Synonym: TYROSINE--TRNA LIGASE, TYRRS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1TYR2Mod. Amino AcidTYROSINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:36 , GLY A:38 , LEU A:69 , HIS A:74 , VAL A:144 , TYR A:158 , GLN A:162 , ASP A:165 , GLN A:180 , HOH B:530 , HOH B:612 , HOH B:626BINDING SITE FOR RESIDUE TYR B 401
2AC2SOFTWARETYR B:36 , GLY B:38 , LEU B:69 , ALA B:71 , HIS B:74 , VAL B:144 , TYR B:158 , GLN B:162 , ASP B:165 , GLN B:180 , HOH B:522 , HOH B:560 , HOH B:634 , HOH B:640BINDING SITE FOR RESIDUE TYR B 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Val A:18 -Thr A:19
2Val B:18 -Thr B:19

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYY_ARCFU41-50
 		  2A:41-50
B:41-50

(-) Exons   (0, 0)

(no "Exon" information available for 2CYB)

(-) 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:319
 aligned with SYY_ARCFU | O29482 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:319
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311         
            SYY_ARCFU     2 DITEKLRLITRNAEEVVTEEELRQLIETKEKPRAYVGYEPSGEIHLGHMMTVQKLMDLQEAGFEIIVLLADIHAYLNEKGTFEEIAEVADYNKKVFIALGLDESRAKFVLGSEYQLSRDYVLDVLKMARITTLNRARRSMDEVSRRKEDPMVSQMIYPLMQALDIAHLGVDLAVGGIDQRKIHMLARENLPRLGYSSPVCLHTPILVGLDGQKMSSSKGNYISVRDPPEEVERKIRKAYCPAGVVEENPILDIAKYHILPRFGKIVVERDAKFGGDVEYASFEELAEDFKSGQLHPLDLKIAVAKYLNMLLEDARKRLG 320
               SCOP domains d2cyba_ A: automated matches                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2cybA01 A:2-207 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                         2cybA02 A:208-320 Tyrosyl-Transfer RNA Synthetase                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh...eeehhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhh...hhhhhhhhhhhhhhhhhhh.......eeee.hhh..hhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhh....eeeee.......................hhhhhhhhhhh..........hhhhhhhhhhhhhhhh.eee..hhhhh..eee.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------AA_TRNA_LI------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cyb A   2 DITEKLRLITRNAEEVVTEEELRQLIETKEKPRAYVGYEPSGEIHLGHMMTVQKLMDLQEAGFEIIVLLADIHAYLNEKGTFEEIAEVADYNKKVFIALGLDESRAKFVLGSEYQLSRDYVLDVLKMARITTLNRARRSMDEVSRRKEDPMVSQMIYPLMQALDIAHLGVDLAVGGIDQRKIHMLARENLPRLGYSSPVCLHTPILVGLDGQKMSSSKGNYISVRDPPEEVERKIRKAYCPAGVVEENPILDIAKYHILPRFGKIVVERDAKFGGDVEYASFEELAEDFKSGQLHPLDLKIAVAKYLNMLLEDARKRLG 320
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311         


Chain B from PDB  Type:PROTEIN  Length:319
 aligned with SYY_ARCFU | O29482 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:323
                                    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   
            SYY_ARCFU     1 MDITEKLRLITRNAEEVVTEEELRQLIETKEKPRAYVGYEPSGEIHLGHMMTVQKLMDLQEAGFEIIVLLADIHAYLNEKGTFEEIAEVADYNKKVFIALGLDESRAKFVLGSEYQLSRDYVLDVLKMARITTLNRARRSMDEVSRRKEDPMVSQMIYPLMQALDIAHLGVDLAVGGIDQRKIHMLARENLPRLGYSSPVCLHTPILVGLDGQKMSSSKGNYISVRDPPEEVERKIRKAYCPAGVVEENPILDIAKYHILPRFGKIVVERDAKFGGDVEYASFEELAEDFKSGQLHPLDLKIAVAKYLNMLLEDARKRLGVSV 323
               SCOP domains d2cybb_ B: automated matches                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2cybB01 B:1-207 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                          2cybB02 B:208-320 Tyrosyl-Transfer RNA Synthetase                                                                - - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...eeehhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhh...hhhhhhhhhhhhhhhhhhh.......eeee.hhh..hhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhh....eeeee.......................hhhhhhhhhhhh.........hhhhhhhhhhhhhhhh.eee....---..eee.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.-. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------AA_TRNA_LI--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cyb B   1 MDITEKLRLITRNAEEVVTEEELRQLIETKEKPRAYVGYEPSGEIHLGHMMTVQKLMDLQEAGFEIIVLLADIHAYLNEKGTFEEIAEVADYNKKVFIALGLDESRAKFVLGSEYQLSRDYVLDVLKMARITTLNRARRSMDEVSRRKEDPMVSQMIYPLMQALDIAHLGVDLAVGGIDQRKIHMLARENLPRLGYSSPVCLHTPILVGLDGQKMSSSKGNYISVRDPPEEVERKIRKAYCPAGVVEENPILDIAKYHILPRFGKIVVERDA---GDVEYASFEELAEDFKSGQLHPLDLKIAVAKYLNMLLEDARKRLGY-Y 501
                                    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| |
                                                                                                                                                                                                                                                                                                         272 276                                         320| |
                                                                                                                                                                                                                                                                                                                                                          401 |
                                                                                                                                                                                                                                                                                                                                                            501
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SYY_ARCFU | O29482)
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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