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(-) Description

Title :  CRYSTAL STRUCTURE OF APO S. AUREUS HISTIDYL-TRNA SYNTHETASE
 
Authors :  X. Qiu, C. A. Janson, M. N. Blackburn, I. K. Chohan, M. Hibbs, S. S. Abdel-
Date :  12 Jul 99  (Deposition) - 12 Jul 00  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Class Ii Trna Synthetase, Beta Sheet, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Qiu, C. A. Janson, M. N. Blackburn, I. K. Chhohan, M. Hibbs, S. S. Abdel-Meguid
Cooperative Structural Dynamics And A Novel Fidelity Mechanism In Histidyl-Trna Synthetases.
Biochemistry V. 38 12296 1999
PubMed-ID: 10493797  |  Reference-DOI: 10.1021/BI990482V

(-) Compounds

Molecule 1 - HISTIDINE--TRNA LIGASE
    Chains: A, B
    EC Number: 6.1.1.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDB575
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: HISS
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Synonym: HISTIDYL-TRNA SYNTHETASE,HISRS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1QE0)

(-) Sites  (0, 0)

(no "Site" information available for 1QE0)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:191 -A:194

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gln A:100 -Pro A:101
2Gln B:100 -Pro B:101

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QE0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1QE0)

(-) Exons   (0, 0)

(no "Exon" information available for 1QE0)

(-) 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:390
 aligned with SYH_STAAU | P60911 from UniProtKB/Swiss-Prot  Length:420

    Alignment length:420
                                    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       330       340       350       360       370       380       390       400       410       420
            SYH_STAAU     1 MIKIPRGTQDILPEDSKKWRYIENQLDELMTFYNYKEIRTPIFESTDLFARGVGDSTDVVQKEMYTFKDKGDRSITLRPEGTAAVVRSYIEHKMQGNPNQPIKLYYNGPMFRYERKQKGRYRQFNQFGVEAIGAENPSVDAEVLAMVMHIYQSFGLKHLKLVINSVGDMASRKEYNEALVKHFEPVIHEFCSDCQSRLHTNPMRILDCKVDRDKEAIKTAPRITDFLNEESKAYYEQVKAYLDDLGIPYIEDPNLVRGLDYYTHTAFELMMDNPNYDGAITTLCGGGRYNGLLELLDGPSETGIGFALSIERLLLALEEEGIELDIEENLDLFIVTMGDQADRYAVKLLNHLRHNGIKADKDYLQRKIKGQMKQADRLGAKFTIVIGDQELENNKIDVKNMTTGESETIELDALVEYFKK 420
               SCOP domains d1qe0a2 A:1-325 Histidyl-tRNA synthetase (HisRS)                                                                                                                                                                                                                                                                                     d1qe0a1 A:326-420 Histidyl-tRNA synthetase (HisRS), C-terminal domain                           SCOP domains
               CATH domains 1qe0A01 A:1-326 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                                                                                   1qe0A02 A:327-417  [code=3.40.50.800, no name defined]                                     --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhhh.ee.....eeehhhhh.-----------..eeehhhhhh.eee...hhhhhhhhhhhhhhhhh....eeeeeeeeee..-------..eeeeeeeeee...hhhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh------------...hhhhh...hhhhhhhhhhhhhhhhh...ee..........eeeeeeeeeee.......eeeeeeeeeeehhhhhh.....eeeeeeeehhhhhhhhhhh...........eeeeehhhhhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhh...eeeeehhhhhhhh.eeeee.....eeee..hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qe0 A   1 MIKIPRGTQDILPEDSKKWRYIENQLDELMTFYNYKEIRTPIFESTDLFAR-----------EMYTFKDKGDRSITLRPEGTAAVVRSYIEHKMQGNPNQPIKLYYNGPMFRY-------YRQFNQFGVEAIGAENPSVDAEVLAMVMHIYQSFGLKHLKLVINSVGDMASRKEYNEALVKHFEPVIHEFCSDCQSRLHTDPMRIL------------TAPRITDFLNEESKAYYEQVKAYLDDLGIPYTEDPNLVRGLDYYTHTAFELMMDNPNYDGAITTLCGGGRYNGLLELLDGPSETGIGFALSIERLLLALEEEGIELDIEENLDLFIVTMGDQADRYAVKLLNHLRHNGIKADKDYLQRKIKGQMKQADRLGAKFTIVIGDQELENNKIDVKNMTTGESETIELDALVEYFKK 420
                                    10        20        30        40        50|        -  |     70        80        90       100       110  |      -|      130       140       150       160       170       180       190       200     |   -       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420
                                                                             51          63                                               113     121                                                                                  206          219                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:342
 aligned with SYH_STAAU | P60911 from UniProtKB/Swiss-Prot  Length:420

    Alignment length:419
                                    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       330       340       350       360       370       380       390       400       410         
            SYH_STAAU     1 MIKIPRGTQDILPEDSKKWRYIENQLDELMTFYNYKEIRTPIFESTDLFARGVGDSTDVVQKEMYTFKDKGDRSITLRPEGTAAVVRSYIEHKMQGNPNQPIKLYYNGPMFRYERKQKGRYRQFNQFGVEAIGAENPSVDAEVLAMVMHIYQSFGLKHLKLVINSVGDMASRKEYNEALVKHFEPVIHEFCSDCQSRLHTNPMRILDCKVDRDKEAIKTAPRITDFLNEESKAYYEQVKAYLDDLGIPYIEDPNLVRGLDYYTHTAFELMMDNPNYDGAITTLCGGGRYNGLLELLDGPSETGIGFALSIERLLLALEEEGIELDIEENLDLFIVTMGDQADRYAVKLLNHLRHNGIKADKDYLQRKIKGQMKQADRLGAKFTIVIGDQELENNKIDVKNMTTGESETIELDALVEYFK 419
               SCOP domains d1qe0b2 B:1-325 Histidyl-tRNA synthetase (HisRS)                                                                                                                                                                                                                                                                                     d1qe0b1 B:326-419 Histidyl-tRNA synthetase (HisRS), C-terminal domain                          SCOP domains
               CATH domains 1qe0B01 B:1-326 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                                                                                   1qe0B02 B:327-416  [code=3.40.50.800, no name defined]                                    --- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhhh.ee.....eeehhhhhh-----------...eehhhhhh.eee...hhhhhhhhhhhhhhhhh....eeeeeeeeee..-------..eeeeeeeeee...hhhhhhhhhhhhhhhhhh.....eeeeeee......-----------------------------------------------------------hhhhhhhhhhhhhhhh..eee.............eeeeeeee.......eeeeeeeeeeehhhhhh.....eeeeeeeehhhhhhhhhhh...........eeeeehhhhhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhh...eeeeehhhhhhhheeeeee.....eeeee.hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qe0 B   1 MIKIPRGTQDILPEDSKKWRYIENQLDELMTFYNYKEIRTPIFESTDLFAR-----------EMYTFKDKGDRSITLRPEGTAAVVRSYIEHKMQGNPNQPIKLYYNGPMFRY-------YRQFNQFGVEAIGAENPSVDAEVLAMVMHIYQSFGLKHLKLVINSVGDMAS-----------------------------------------------------------SKAYYEQVKAYLDDLGIPYTEDPNLVRGLDYYTHTAFELMMDNPNYDGAITTLCGGGRYNGLLELLDGPSETGIGFALSIERLLLALEEEGIELDIEENLDLFIVTMGDQADRYAVKLLNHLRHNGIKADKDYLQRKIKGQMKQADRLGAKFTIVIGDQELENNKIDVKNMTTGESETIELDALVEYFK 419
                                    10        20        30        40        50|        -  |     70        80        90       100       110  |      -|      130       140       150       160       170|        -         -         -         -         -         -|      240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410         
                                                                             51          63                                               113     121                                               171                                                         231
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1QE0)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SYH_STAAU | P60911)
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:0004821    histidine-tRNA ligase activity    Catalysis of the reaction: ATP + L-histidine + tRNA(His) = AMP + diphosphate + L-histidyl-tRNA(His).
    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.
biological process
    GO:0006427    histidyl-tRNA aminoacylation    The process of coupling histidine to histidyl-tRNA, catalyzed by histidyl-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.

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