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(-) Description

Title :  CRYSTAL STRUCTURE OF F2YRS COMPLEXED WITH F2Y
 
Authors :  J. Wang, C. Tian, W. Gong, F. Li, P. Shi, J. Li, W. Ding
Date :  14 Oct 12  (Deposition) - 13 Mar 13  (Release) - 22 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.91
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aminoacyl-Trna Synthetase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Li, P. Shi, J. Li, F. Yang, T. Wang, W. Zhang, F. Gao, W. Ding, D. Li, J. Li, Y. Xiong, J. Sun, W. Gong, C. Tian, J. Wang
A Genetically Encoded 19F Nmr Probe For Tyrosine Phosphorylation.
Angew. Chem. Int. Ed. Engl. V. 52 3958 2013
PubMed-ID: 23450644  |  Reference-DOI: 10.1002/ANIE.201300463

(-) Compounds

Molecule 1 - TYROSINE-TRNA LIGASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TYRS, MJ0389
    Mutation: YES
    Organism Scientific: METHANOCOCCUS JANNASCHII DSM 2661
    Organism Taxid: 243232
    Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
    Synonym: TYROSYL-TRNA SYNTHETASE, 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
1F2Y2Ligand/Ion3,5-DIFLUORO-L-TYROSINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:32 , GLY A:34 , GLU A:36 , ALA A:67 , ILE A:137 , TYR A:151 , GLN A:155 , ASN A:158 , GLN A:173 , HOH A:529BINDING SITE FOR RESIDUE F2Y A 401
2AC2SOFTWAREARG B:32 , GLY B:34 , GLU B:36 , ALA B:67 , ILE B:137 , TYR B:151 , GLN B:155 , ASN B:158 , GLN B:173 , HOH B:523BINDING SITE FOR RESIDUE F2Y B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HJX)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ile A:15 -Ser A:16
2Tyr A:251 -Pro A:252
3Ile B:15 -Ser B:16
4Tyr B:251 -Pro B:252

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HJX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HJX)

(-) Exons   (0, 0)

(no "Exon" information available for 4HJX)

(-) 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:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4hjxa_ A: automated matches                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh...eeehhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhhhhh.eeeeeeehhhhhhhh...hhhhhhhhhhhhhhhhhhh....eeee......hhhhhhhhhhhhh..hhhhhhhhh...........hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhh....eeeee........................hhhhhhhhhhhh.........hhhhhhhhhh....eee..hhhhh..eee.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hjx A   1 MDEFEMIKRNTSEIISEEELREVLKKDEKSARIGFEPSGKIHLGHYLQIKKMIDLQNAGFDIIIYLADLGAYLNQKGELDEIRKIGDYNKKVFEAMGLKAKYVYGSENCLDKDYTLNVYRLALKTTLKRARRSMELIAREDENPKVAEVIYPIMQVNNIHYSGVDVAVGGMEQRKIHMLARELLPKKVVCIHNPVLTGLDGEGKMSSSKGNFIAVDDSPEEIRAKIKKAYCPAGVVEGNPIMEIAKYFLEYPLTIKRPEKFGGDLTVNSYEELESLFKNKELHPMDLKNAVAEELIKILEPIRKRL 306
                                    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      


Chain B from PDB  Type:PROTEIN  Length:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4hjxb_ B: automated matches                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh...eeehhhhhhhhh....eeeeeee......hhhhhhhhhhhhhhhhh.eeeeeeehhhhhhhh...hhhhhhhhhhhhhhhhhhh....eeee......hhhhhhhhhhhhh..hhhhhhhhh...........hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhh....eeeee........................hhhhhhhhhhh..........hhhhhhhhhh....eee..hhhhh..eee.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hjx B   1 MDEFEMIKRNTSEIISEEELREVLKKDEKSARIGFEPSGKIHLGHYLQIKKMIDLQNAGFDIIIYLADLGAYLNQKGELDEIRKIGDYNKKVFEAMGLKAKYVYGSENCLDKDYTLNVYRLALKTTLKRARRSMELIAREDENPKVAEVIYPIMQVNNIHYSGVDVAVGGMEQRKIHMLARELLPKKVVCIHNPVLTGLDGEGKMSSSKGNFIAVDDSPEEIRAKIKKAYCPAGVVEGNPIMEIAKYFLEYPLTIKRPEKFGGDLTVNSYEELESLFKNKELHPMDLKNAVAEELIKILEPIRKRL 306
                                    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
   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  (0, 0)

(no "CATH Domain" information available for 4HJX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HJX)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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    Ile A:15 - Ser A:16   [ RasMol ]  
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    Tyr B:251 - Pro B:252   [ RasMol ]  
 

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  SYY_METJA | Q57834
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 Related Entries

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

UniProtKB/Swiss-Prot
        SYY_METJA | Q57834: 1j1u 1u7d 1u7x 1zh0 1zh6 2ag6 2hgz 2pxh 2zp1 3d6u 3d6v 3n2y 3qe4 4hjr 4hk4 4hpw 4nd6 4nd7 4nda 4nx2 4pbr 4pbs 4pbt 5u36

(-) Related Entries Specified in the PDB File

4hjr CRYSTAL STRUCTURE OF F2YRS