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(-) Description

Title :  STRUCTURE OF THE CYSTEINYL-TRNA SYNTHETASE (CYSS) FROM COXIELLA BURNETII.
 
Authors :  M. Rudolph, J. Cheung, M. C. Franklin, M. Cassidy, E. Gary, F. Burshteyn
Date :  09 Sep 11  (Deposition) - 28 Sep 11  (Release) - 10 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Synthesis, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Franklin, J. Cheung, M. J. Rudolph, F. Burshteyn, M. Cassidy, E. Gary, B. Hillerich, Z. K. Yao, P. R. Carlier, M. Totrov, J. D. Love
Structural Genomics For Drug Design Against The Pathogen Coxiella Burnetii.
Proteins V. 83 2124 2015
PubMed-ID: 26033498  |  Reference-DOI: 10.1002/PROT.24841

(-) Compounds

Molecule 1 - CYSTEINYL-TRNA SYNTHETASE
    Chains: A
    EC Number: 6.1.1.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CYSS, CBU_1487
    Organism Scientific: COXIELLA BURNETII
    Organism Taxid: 777
    Strain: RSA493
    Synonym: CYSTEINE--TRNA LIGASE, CYSRS

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric/Biological Unit (2, 11)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
2ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:29 , CYS A:210 , HIS A:235 , GLU A:239 , HOH A:580BINDING SITE FOR RESIDUE ZN A 461

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TQO)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Thr A:137 -Gly A:138
2Gln A:220 -Pro A:221
3Phe A:233 -Pro A:234

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TQO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TQO)

(-) Exons   (0, 0)

(no "Exon" information available for 3TQO)

(-) 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:387
 aligned with SYC_COXBU | Q83BL7 from UniProtKB/Swiss-Prot  Length:460

    Alignment length:405
                              1                                                                                                                                                                                                                                                                                                                                                                                                                  
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398     
            SYC_COXBU     - --MSVKIFNSLTKQKEIFKPIESGKVKLYVCGMTVYDYMHIGHGRSWIIFDMVVRYLRMRGYEVTFVRNITDIDDKIIKRAGENKESPAALAERFIQILHEDEKALRVLSPDQEPRATQYVPEIIKLIQKLLDNQYAYTGQNGDVFFDVRRFKDYGKLSHRHLDELQAGARVEVSDSKRDPLDFVLWKKAKPGEPKWDSPWGEGRPGWHIECSAMSSSILGQPFDIHGGGLDLKFPHHENEIAQSEAGEEKPFVKLWMHAGLLEINKEKMSKSLGNIISIREALKESDVEVLRYFLLSGHYRNPLSYSKENLENGRLALERFYLALRGLPVVNHEKTSSYTDRFYEAMDDDFNTPIAFALLFEMVREINRFRDNNQIEKAAVLAAELKCLGNIFGLLQYSPEQFL 403
               SCOP domains d3tqoa1 A:-1-316 automated matches                                                                                                                                                                                                                                                                                            d3tqoa2 A:317      -403 automated matches                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee....eeee.......eeeeee.........hhhhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh..eee.....eee.................------------.......eeeeee..............eeehhhhhhhhhhhhhhh..eeeeeee.hhh.hhhhhhhhhhhhhhh...eeeeeee..eee..ee.........hhhhhhhhhhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhhhhhhh....------.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tqo A  -1 NAmSVKIFNSLTKQKEIFKPIESGKVKLYVCGmTVYDYmHIGHGRSWIIFDmVVRYLRmRGYEVTFVRNITDIDDKIIKRAGENKESPAALAERFIQILHEDEKALRVLSPDQEPRATQYVPEIIKLIQKLLDNQYAYTGQNGDVFFDVRRFKDYGKLSHRHLD------------SKRDPLDFVLWKKAKPGEPKWDSPWGEGRPGWHIECSAmSSSILGQPFDIHGGGLDLKFPHHENEIAQSEAGEEKPFVKLWmHAGLLEINKEKmSKSLGNIISIREALKESDVEVLRYFLLSGHYRNPLSYSKENLENGRLALERFYLALRGLPV------SSYTDRFYEAmDDDFNTPIAFALLFEmVREINRFRDNNQIEKAAVLAAELKCLGNIFGLLQYSPEQFL 403
                              |      8        18        28  |     38        48 |      58        68        78        88        98       108       118       128       138       148       158   |     -      |178       188       198       208    |  218       228       238       248       258       268       278       288       298       308       318       328|      338       348       358   |   368       378       388       398     
                              |                            31-MSE |           50-MSE 57-MSE                                                                                                  162          175                                   213-MSE                                    256-MSE     268-MSE                                                      329    336       346-MSE         362-MSE                                     
                              1-MSE                              37-MSE
   Legend:   → Mismatch (orange background)
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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  (2, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TQO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TQO)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SYC_COXBU | Q83BL7)
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:0004817    cysteine-tRNA ligase activity    Catalysis of the reaction: ATP + L-cysteine + tRNA(Cys) = AMP + diphosphate + L-cysteinyl-tRNA(Cys).
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006423    cysteinyl-tRNA aminoacylation    The process of coupling cysteine to cysteinyl-tRNA, catalyzed by cysteinyl-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.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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