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(-) Description

Title :  CRYSTAL STRUCTURE OF APO 3-NITRO-TYROSINE TRNA SYNTHETASE (5B) IN THE OPEN FORM
 
Authors :  R. B. Cooley, C. M. Driggers, P. A. Karplus, R. A. Mehl
Date :  25 Oct 13  (Deposition) - 19 Mar 14  (Release) - 16 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Rossmann Fold, 3-Nitro-Tyrosine Amino-Acyl Trna Synthetase, Trna, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. B. Cooley, J. L. Feldman, C. M. Driggers, T. A. Bundy, A. L. Stokes, P. A. Karplus, R. A. Mehl
Structural Basis Of Improved Second-Generation 3-Nitro-Tyrosine Trna Synthetases.
Biochemistry V. 53 1916 2014
PubMed-ID: 24611875  |  Reference-DOI: 10.1021/BI5001239

(-) Compounds

Molecule 1 - TYROSINE-TRNA LIGASE
    Chains: A
    EC Number: 6.1.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PET28A
    Gene: MJ0389, TYRS, TYRS MJ0389
    Mutation: YES
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 243232
    Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
    Synonym: TYROSYL-TRNA SYNTHETASE, TYRRS

 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, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:70 , LEU A:73 , TYR A:119 , ALA A:147BINDING SITE FOR RESIDUE GOL A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ND6)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ile A:15 -Ser A:16
2Tyr A:251 -Pro A:252

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ND6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ND6)

(-) Exons   (0, 0)

(no "Exon" information available for 4ND6)

(-) Sequences/Alignments

Asymmetric Unit
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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:303
                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d4nd6a_ A: automated matches                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh...eeehhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhhhhh.eeeeeeehhhhhhhh...hhhhhhhhhhhhhhhhhhh....eeee.hhh..hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhh....eeeee........................hhhhhhhhhhh..........hhhhhhhhhhh...eee..hhhhh..eee.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nd6 A   1 MDEFEMIKRNTSEIISEEELREVLKKDEKSAHIGFEPSGKIHLGHYLQIKKMIDLQNAGFDIIILLADLCAYLNNKGELDEIRKIGDYNKKVFEAMGLKAKYVYGSEFQLDKDYTLNVYRLALKTTLKRARRSMELIAENPKVAEVIYPIMQVNSAHYRGVDVAVGGMEQRKIHMLARELLPKKVVCIHNPVLTGLDGEGKMSSSKGNFIAVDDSPEEIRAKIKKAYCPAGVVEGNPIMEIAKYFLEYPLTIKRPEKFGGDLTVNSYEELESLFKNKELHPMDLKNAVAEELIKILEPIRKRL 306
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303   
                                                                                                                                                                   138|                                                                                                                                                                    
                                                                                                                                                                    142
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ND6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ND6)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

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  SYY_METJA | Q57834
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  6.1.1.1
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        SYY_METJA | Q57834: 1j1u 1u7d 1u7x 1zh0 1zh6 2ag6 2hgz 2pxh 2zp1 3d6u 3d6v 3n2y 3qe4 4hjr 4hjx 4hk4 4hpw 4nd7 4nda 4nx2 4pbr 4pbs 4pbt 5u36

(-) Related Entries Specified in the PDB File

4nd7 4nda