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(-) Description

Title :  CRYSTAL STRUCTURE OF THE E. COLI ASPARTYL-TRNA SYNTHETASE : TRNAASP : ASPARTYL-ADENYLATE COMPLEX
 
Authors :  S. Eiler, A. -C. Dock-Bregeon, L. Moulinier, J. -C. Thierry, D. Moras
Date :  15 Jul 99  (Deposition) - 23 Nov 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Rna Complex, Ligase/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Eiler, A. Dock-Bregeon, L. Moulinier, J. C. Thierry, D. Moras
Synthesis Of Aspartyl-Trna(Asp) In Escherichia Coli--A Snapshot Of The Second Step.
Embo J. V. 18 6532 1999
PubMed-ID: 10562565  |  Reference-DOI: 10.1093/EMBOJ/18.22.6532
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ASPARTYL TRNA
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRC99
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 2 - ASPARTYL TRNA SYNTHETASE
    Chains: A
    EC Number: 6.1.1.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBR322
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: ASPARTATE-TRNA LIGASE, ASPRS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 12)

Asymmetric/Biological Unit (9, 12)
No.NameCountTypeFull Name
14SU1Mod. Nucleotide4-THIOURIDINE-5'-MONOPHOSPHATE
25MU1Mod. Nucleotide5-METHYLURIDINE 5'-MONOPHOSPHATE
3AMO1Ligand/IonASPARTYL-ADENOSINE-5'-MONOPHOSPHATE
4AMP1Ligand/IonADENOSINE MONOPHOSPHATE
5G7M1Mod. NucleotideN7-METHYL-GUANOSINE-5'-MONOPHOSPHATE
6H2U3Mod. Nucleotide5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
7PSU2Mod. NucleotidePSEUDOURIDINE-5'-MONOPHOSPHATE
8QUO1Mod. Nucleotide2-AMINO-7-DEAZA-(2'',3''-DIHYDROXY-CYCLOPENTYLAMINO)-GUANOSINE-5'-MONOPHOSPHATE
9SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREG B:606 , PSU B:665 , C B:666 , C B:667 , HOH B:1245 , HOH B:1502BINDING SITE FOR RESIDUE SO4 B 701
2AC2SOFTWAREPHE A:304 , VAL A:306 , LYS A:347 , GLY A:348 , LEU A:349 , ALA A:350 , ALA A:396 , HOH A:1320 , HOH A:1480BINDING SITE FOR RESIDUE AMP A 800
3AC3SOFTWARESER A:193 , GLN A:195 , LYS A:198 , ARG A:217 , ASP A:224 , ARG A:225 , GLN A:226 , PHE A:229 , GLN A:231 , HIS A:448 , HIS A:449 , GLU A:482 , VAL A:483 , GLY A:484 , GLY A:485 , GLY A:486 , ARG A:489 , GLY A:530 , LEU A:531 , ALA A:532 , GLY A:534 , ARG A:537 , ILE A:548 , HOH A:1003 , HOH A:1131 , HOH A:1133 , A B:676BINDING SITE FOR RESIDUE AMO A 831

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1C0A)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:567 -Pro A:568

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1C0A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1C0A)

(-) Exons   (0, 0)

(no "Exon" information available for 1C0A)

(-) 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:585
 aligned with SYD_ECOLI | P21889 from UniProtKB/Swiss-Prot  Length:590

    Alignment length:585
                                    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       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580     
           SYD_ECOLI      1 MRTEYCGQLRLSHVGQQVTLCGWVNRRRDLGSLIFIDMRDREGIVQVFFDPDRADALKLASELRNEFCIQVTGTVRARDEKNINRDMATGEIEVLASSLTIINRADVLPLDSNHVNTEEARLKYRYLDLRRPEMAQRLKTRAKITSLVRRFMDDHGFLDIETPMLTKATPEGARDYLVPSRVHKGKFYALPQSPQLFKQLLMMSGFDRYYQIVKCFRDEDLRADRQPEFTQIDVETSFMTAPQVREVMEALVRHLWLEVKGVDLGDFPVMTFAEAERRYGSDKPDLRNPMELTDVADLLKSVEFAVFAGPANDPKGRVAALRVPGGASLTRKQIDEYGNFVKIYGAKGLAYIKVNERAKGLEGINSPVAKFLNAEIIEDILDRTAAQDGDMIFFGADNKKIVADAMGALRLKVGKDLGLTDESKWAPLWVIDFPMFEDDGEGGLTAMHHPFTSPKDMTAAELKAAPENAVANAYDMVINGYEVGGGSVRIHNGDMQQTVFGILGINEEEQREKFGFLLDALKYGTPPHAGLAFGLDRLTMLLTGTDNIRDVIAFPKTTAAACLMTEAPSFANPTALAELSIQVVK  585
               SCOP domains d1c0aa1 A:1-106 Aspartyl-tRNA synthetase (AspRS)                                                          d1c0aa3 A:107-287,A:421-585 Aspartyl-tRNA synthetase (AspRS)                                                                                                                         d1c0aa2 A:288-420 Prokaryotic AspRS, insert domain                                                                                   d1c0aa3 A:107-287,A:421-585 Aspartyl-tRNA synthetase (AspRS)                                                                                                          SCOP domains
               CATH domains 1c0aA01 A:1-106 Nucleic acid-binding proteins                                                             --1c0aA02 A:109-270,A:421-585 Bira Bifunctional Protein; Domain 2                                                                                                   1c0aA03 A:271-420  [code=3.30.1360.30, no name defined]                                                                                               1c0aA02 A:109-270,A:421-585 Bira Bifunctional Protein; Domain 2                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh..eeeeeeeeeeeee....eeeeeee..eeeeeeehhhhhhhhhhhh......eeeeeeeeee..............eeeeeeeeeeee.............hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..ee.................eee.......eee....hhhhhhhhhhh...eeeeeeeee...........eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh.......eeehhhhhhhhh...........eeehhhhhh...hhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhhhhhh......eeee.hhhhhhh.ee..hhhhhhhhhhhhhhhhh......eeeeeeeehhhhhhhhhhhhhhhhhhh.........eeeee....eee.....eee...........hhhhhhhh.......eeeeee..eeeeeeee...hhhhhhhhhhhh..hhhhhhhhhhhhhhhh......eeeeeeehhhhhhhhhh..hhhhhh...................hhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1c0a A    1 MRTEYCGQLRLSHVGQQVTLCGWVNRRRDLGSLIFIDMRDREGIVQVFFDPDRADALKLASELRNEFCIQVTGTVRARDEKNINRDMATGEIEVLASSLTIINRADVLPLDSNHVNTEEARLKYRYLDLRRPEMAQRLKTRAKITSLVRRFMDDHGFLDIETPMLTKATPEGARDYLVPSRVHKGKFYALPQSPQLFKQLLMMSGFDRYYQIVKCFRDEDLRADRQPEFTQIDVETSFMTAPQVREVMEALVRHLWLEVKGVDLGDFPVMTFAEAERRYGSDKPDLRNPMELTDVADLLKSVEFAVFAGPANDPKGRVAALRVPGGASLTRKQIDEYGNFVKIYGAKGLAYIKVNERAKGLEGINSPVAKFLNAEIIEDILDRTAAQDGDMIFFGADNKKIVADAMGALRLKVGKDLGLTDESKWAPLWVIDFPMFEDDGEGGLTAMHHPFTSPKDMTAAELKAAPENAVANAYDMVINGYEVGGGSVRIHNGDMQQTVFGILGINEEEQREKFGFLLDALKYGTPPHAGLAFGLDRLTMLLTGTDNIRDVIAFPKTTAAACLMTEAPSFANPTALAELSIQVVK  585
                                    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       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580     


Chain B from PDB  Type:RNA  Length:77
                                                                                                              
                1c0a B  601 GGAGCGGuAGUUCAGuCGGuuAGAAUACCUGCCUgUCACGCAGGGGgUCGCGGGuuCGAGUCCCGuCCGUUCCGCCA  676
                                   610     | 620|      629    |  639      |649    || 659     | 669       
                                 608-4SU 616-H2U|           634-QUO     646-G7M 654-5MU    665-PSU       
                                             620-H2U                             655-PSU                 
                                             620A-H2U
   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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1C0A)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SYD_ECOLI | P21889)
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:0004815    aspartate-tRNA ligase activity    Catalysis of the reaction: ATP + L-aspartate + tRNA(Asp) = AMP + diphosphate + L-aspartyl-tRNA(Asp).
    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:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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:0006422    aspartyl-tRNA aminoacylation    The process of coupling aspartate to aspartyl-tRNA, catalyzed by aspartyl-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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 Related Entries

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

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        SYD_ECOLI | P21889: 1eqr 1il2

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