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(-) Description

Title :  CRYSTAL STRUCTURE OF A GLUTAMYL-TRNA SYNTHETASE GLURS FROM BORRELIA BURGDORFERI BOUND TO GLUTAMIC ACID AND ZINC
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  24 Aug 12  (Deposition) - 05 Sep 12  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Aminoacyl-Trna Synthetase, Atp- Dependent, Transferase, Aars, Glurs, Trnaglu, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. O. Moen, T. E. Edwards, D. M. Dranow, M. C. Clifton, B. Sankaran, W. C. Van Voorhis, A. Sharma, C. Manoil, B. L. Staker, P. J. Myler, D. D. Lorimer
Ligand Co-Crystallization Of Aminoacyl-Trna Synthetases Fro Infectious Disease Organisms.
Sci Rep V. 7 223 2017
PubMed-ID: 28303005  |  Reference-DOI: 10.1038/S41598-017-00367-6

(-) Compounds

Molecule 1 - GLUTAMATE--TRNA LIGASE
    Chains: A, B
    EC Number: 6.1.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAVA0421
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BB_0372, GLTX
    Organism Scientific: BORRELIA BURGDORFERI
    Organism Taxid: 224326
    Strain: ATCC 35210 / B31 / CIP 102532 / DSM 4680
    Synonym: GLUTAMYL-TRNA SYNTHETASE, GLURS

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GLU2Mod. Amino AcidGLUTAMIC ACID
3ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GLU1Mod. Amino AcidGLUTAMIC ACID
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GLU1Mod. Amino AcidGLUTAMIC ACID
3ZN-1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:107 , TYR A:108 , CYS A:109 , TYR A:130 , CYS A:134BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWAREARG A:7 , ALA A:9 , SER A:11 , GLU A:43 , TYR A:196 , ASN A:200 , ARG A:214 , TRP A:218BINDING SITE FOR RESIDUE GLU A 502
3AC3SOFTWAREGLY A:72 , VAL A:74BINDING SITE FOR RESIDUE CL A 503
4AC4SOFTWARECYS B:107 , TYR B:108 , CYS B:109 , TYR B:130 , CYS B:134BINDING SITE FOR RESIDUE ZN B 501
5AC5SOFTWAREARG B:7 , ALA B:9 , SER B:11 , GLU B:43 , TYR B:196 , ASN B:200 , ARG B:214 , TRP B:218BINDING SITE FOR RESIDUE GLU B 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:80 -Pro A:81
2Lys A:351 -Pro A:352
3Ala B:80 -Pro B:81
4Lys B:351 -Pro B:352

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GRI)

(-) 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:478
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4gria1 A:3-314 automated matches                                                                                                                                                                                                                                                                                       d4gria2 A:315-490 automated matches                                                                                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee........hhhhhhhhhhhhhhhhhh..eeee..........hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhh.............hhhhhhhhhhh....eeee......eeeeee...eeeeee.hhh....eee......hhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhh....eeeee..................hhhhhhhhh.hhhhhhhhhhhh...........hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh.....hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gri A   3 STRVRYAPSPTGLQHIGGIRTALFNYFFAKSCGGKFLLRIEDTDQSRYSPEAENDLYSSLKWLGISFDEGPVVGGDYAPYVQSQRSAIYKQYAKYLIESGHAYYCYCSPERLERIKKIQNINKMPPGYDRHCRNLSNEEVENALIKKIKPVVRFKIPLEGDTSFDDILLGRITWANKDISPDPVILKSDGLPTYHLANVVDDYLMKITHVLRAQEWVSSGPLHVLLYKAFKWKPPIYCHLPMVMGNDGQKLSKRHGSTALRQFIEDGYLPEAIINYVTLLGWSYDDKREFFSKNDLEQFFSIEKINKSPAIFDYHKLDFFNSYYIREKKDEDLFNLLLPFFQKKGYVSKPSTLEENQKLKLLIPLIKSRIKKLSDALNMTKFFYEDIKSWNLDEFKEVCSILELIKPILEGFEKRSSEENDKIFYDFAESNLGEILLPIRIAALGSKVSPPLFDSLKLIGKSKVFERIKLAQEFLRIN 490
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392    || 409       419       429       439||     452       462       472       482        
                                                                                                                                                                                                                                                                                                                                                                                                                                    397|                                440|                                              
                                                                                                                                                                                                                                                                                                                                                                                                                                     405                                 444                                              


Chain B from PDB  Type:PROTEIN  Length:485
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4grib1 B:3-314 automated matches                                                                                                                                                                                                                                                                                       d4grib2 B:315-490 automated matches                                                                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee........hhhhhhhhhhhhhhhhhh..eeee..........hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhh.............hhhhhhhhhhh....eeee......eeeeee...eeeeee.hhh....eee......hhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhh....eeeee..................hhhhhhhhh.hhhhhhhhhhhh...........hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.....hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gri B   3 STRVRYAPSPTGLQHIGGIRTALFNYFFAKSCGGKFLLRIEDTDQSRYSPEAENDLYSSLKWLGISFDEGPVVGGDYAPYVQSQRSAIYKQYAKYLIESGHAYYCYCSPERLERIKKIQNINKMPPGYDRHCRNLSNEEVENALIKKIKPVVRFKIPLEGDTSFDDILLGRITWANKDISPDPVILKSDGLPTYHLANVVDDYLMKITHVLRAQEWVSSGPLHVLLYKAFKWKPPIYCHLPMVMGNDGQKLSKRHGSTALRQFIEDGYLPEAIINYVTLLGWSYDDKREFFSKNDLEQFFSIEKINKSPAIFDYHKLDFFNSYYIREKKDEDLFNLLLPFFQKKGYVSKPSTLEENQKLKLLIPLIKSRIKKLSDALNMTKFFYEDIKSWNLDEFLSRKKTAKEVCSILELIKPILEGFEKRSSEENDKIFYDFAESNLGEILLPIRIAALGSKVSPPLFDSLKLIGKSKVFERIKLAQEFLRIN 490
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       445       455       465       475       485     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                               440|                                              
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                444
   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  (2, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

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(-) Related Entries Specified in the PDB File

4g6z GLURS FROM B. THAILANDENSIS RELATED ID: BOBUA.01348.A RELATED DB: TARGETTRACK