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(-) Description

Title :  CRYSTAL STRUCTURE OF ASPARTYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED TO TRNAASP FROM ESCHERICHIA COLI
 
Authors :  C. Briand, A. Poterszman, S. Eiler, G. Webster, J. -C. Thierry, D. Moras
Date :  10 Feb 00  (Deposition) - 19 Jun 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Aspartyl-Trna Synthetase, Trna, Protein/Rna Complex, Ligase/Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Briand, A. Poterszman, S. Eiler, G. Webster, J. Thierry, D. Moras
An Intermediate Step In The Recognition Of Trna(Asp) By Aspartyl-Trna Synthetase.
J. Mol. Biol. V. 299 1051 2000
PubMed-ID: 10843857  |  Reference-DOI: 10.1006/JMBI.2000.3819
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ASPARTYL-TRNA
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 2 - ASPARTYL-TRNA SYNTHETASE
    Chains: A, B
    EC Number: 6.1.1.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    Synonym: ASPARTATE - TRNA LIGASE, ASPRS

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 20)

Asymmetric Unit (7, 20)
No.NameCountTypeFull Name
12MA2Mod. Nucleotide2-METHYLADENOSINE-5'-MONOPHOSPHATE
24SU2Mod. Nucleotide4-THIOURIDINE-5'-MONOPHOSPHATE
35MU2Mod. Nucleotide5-METHYLURIDINE 5'-MONOPHOSPHATE
4G7M2Mod. NucleotideN7-METHYL-GUANOSINE-5'-MONOPHOSPHATE
5H2U6Mod. Nucleotide5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
6PSU4Mod. NucleotidePSEUDOURIDINE-5'-MONOPHOSPHATE
7QUO2Mod. Nucleotide2-AMINO-7-DEAZA-(2'',3''-DIHYDROXY-CYCLOPENTYLAMINO)-GUANOSINE-5'-MONOPHOSPHATE
Biological Unit 1 (7, 10)
No.NameCountTypeFull Name
12MA1Mod. Nucleotide2-METHYLADENOSINE-5'-MONOPHOSPHATE
24SU1Mod. Nucleotide4-THIOURIDINE-5'-MONOPHOSPHATE
35MU1Mod. Nucleotide5-METHYLURIDINE 5'-MONOPHOSPHATE
4G7M1Mod. NucleotideN7-METHYL-GUANOSINE-5'-MONOPHOSPHATE
5H2U3Mod. Nucleotide5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
6PSU2Mod. NucleotidePSEUDOURIDINE-5'-MONOPHOSPHATE
7QUO1Mod. Nucleotide2-AMINO-7-DEAZA-(2'',3''-DIHYDROXY-CYCLOPENTYLAMINO)-GUANOSINE-5'-MONOPHOSPHATE
Biological Unit 2 (7, 10)
No.NameCountTypeFull Name
12MA1Mod. Nucleotide2-METHYLADENOSINE-5'-MONOPHOSPHATE
24SU1Mod. Nucleotide4-THIOURIDINE-5'-MONOPHOSPHATE
35MU1Mod. Nucleotide5-METHYLURIDINE 5'-MONOPHOSPHATE
4G7M1Mod. NucleotideN7-METHYL-GUANOSINE-5'-MONOPHOSPHATE
5H2U3Mod. Nucleotide5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
6PSU2Mod. NucleotidePSEUDOURIDINE-5'-MONOPHOSPHATE
7QUO1Mod. Nucleotide2-AMINO-7-DEAZA-(2'',3''-DIHYDROXY-CYCLOPENTYLAMINO)-GUANOSINE-5'-MONOPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 1EFW)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:272 -Pro A:273
2Ala A:561 -Pro A:562
3Leu B:272 -Pro B:273
4Ala B:561 -Pro B:562

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1EFW)

(-) 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:580
 aligned with SYD_THETH | P36419 from UniProtKB/Swiss-Prot  Length:580

    Alignment length:580
                                    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_THETH     1 MRRTHYAGSLRETHVGEEVVLEGWVNRRRDLGGLIFLDLRDREGLVQLVAHPASPAYATAERVRPEWVVRAKGLVRLRPEPNPRLATGRVEVELSALEVLAEAKTPPFPVDAGWRGEEEKEASEELRLKYRYLDLRRRRMQENLRLRHRVIKAIWDFLDREGFVQVETPFLTKSTPEGARDFLVPYRHEPGLFYALPQSPQLFKQMLMVAGLDRYFQIARCFRDEDLRADRQPDFTQLDLEMSFVEVEDVLELNERLMAHVFREALGVELPLPFPRLSYEEAMERYGSDKPDLRFGLELKEVGPLFRQSGFRVFQEAESVKALALPKALSRKEVAELEEVAKRHKAQGLAWARVEEGGFSGGVAKFLEPVREALLQATEARPGDTLLFVAGPRKVAATALGAVRLRAADLLGLKREGFRFLWVVDFPLLEWDEEEEAWTYMHHPFTSPHPEDLPLLEKDPGRVRALAYDLVLNGVEVGGGSIRIHDPRLQARVFRLLGIGEEEQREKFGFFLEALEYGAPPHGGIAWGLDRLLALMTGSPSIREVIAFPKNKEGKDPLTGAPSPVPEEQLRELGLMVVRP 580
               SCOP domains d1efwa1 A:1-104 Aspartyl-tRNA synthetase (AspRS)                                                        d1efwa3 A:105-294,A:415-580 Aspartyl-tRNA synthetase (AspRS)                                                                                                                                  d1efwa2 A:295-414 Prokaryotic AspRS, insert domain                                                                      d1efwa3 A:105-294,A:415-580 Aspartyl-tRNA synthetase (AspRS)                                                                                                           SCOP domains
               CATH domains 1efwA01 A:1-106 Nucleic acid-binding proteins                                                             ------------------------------1efwA02 A:137-277,A:416-580 Bira Bifunctional Protein; Domain 2                                                                              1efwA03 A:278-415  [code=3.30.1360.30, no name defined]                                                                                   1efwA02 A:137-277,A:416-580 Bira Bifunctional Protein; Domain 2                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh......................................hhhhhhhhhh...............................................hhhhhh......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..ee.................eee.......eee....hhhhhhhhhhh...eeeeeeeee...........eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh.........eeehhhhhhhhh..............hhhhhh...hhhhhh..eeeeeee....hhhhhhhhhhhhhhh.....eeeeee..eee..hhhhhh.hhhhhhhhhh.....eeeeeeehhhhhhhhhhhhhhhhhhhhh.......eeeee....ee........ee.............hhhhhh........eeeee..eeeee......hhhhhhhhhhhh..hhhhhhhhhhhhhhhh......eeeeeehhhhhhhhhhh..hhhhhh...................hhhhhhh..eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1efw A   1 MRRTHYAGSLRETHVGEEVVLEGWVNRRRDLGGLIFLDLRDREGLVQLVAHPASPAYATAERVRPEWVVRAKGLVRLRPEPNPRLATGRVEVELSALEVLAEAKTPPFPVDAGWRGEEEKEASEELRLKYRYLDLRRRRMQENLRLRHRVIKAIWDFLDREGFVQVETPFLTKSTPEGARDFLVPYRHEPGLFYALPQSPQLFKQMLMVAGLDRYFQIARCFRDEDLRADRQPDFTQLDLEMSFVEVEDVLELNERLMAHVFREALGVELPLPFPRLSYEEAMERYGSDKPDLRFGLELKEVGPLFRQSGFRVFQEAESVKALALPKALSRKEVAELEEVAKRHKAQGLAWARVEEGGFSGGVAKFLEPVREALLQATEARPGDTLLFVAGPRKVAATALGAVRLRAADLLGLKREGFRFLWVVDFPLLEWDEEEEAWTYMHHPFTSPHPEDLPLLEKDPGRVRALAYDLVLNGVEVGGGSIRIHDPRLQARVFRLLGIGEEEQREKFGFFLEALEYGAPPHGGIAWGLDRLLALMTGSPSIREVIAFPKNKEGKDPLTGAPSPVPEEQLRELGLMVVRP 580
                                    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:PROTEIN  Length:580
 aligned with SYD_THETH | P36419 from UniProtKB/Swiss-Prot  Length:580

    Alignment length:580
                                    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_THETH     1 MRRTHYAGSLRETHVGEEVVLEGWVNRRRDLGGLIFLDLRDREGLVQLVAHPASPAYATAERVRPEWVVRAKGLVRLRPEPNPRLATGRVEVELSALEVLAEAKTPPFPVDAGWRGEEEKEASEELRLKYRYLDLRRRRMQENLRLRHRVIKAIWDFLDREGFVQVETPFLTKSTPEGARDFLVPYRHEPGLFYALPQSPQLFKQMLMVAGLDRYFQIARCFRDEDLRADRQPDFTQLDLEMSFVEVEDVLELNERLMAHVFREALGVELPLPFPRLSYEEAMERYGSDKPDLRFGLELKEVGPLFRQSGFRVFQEAESVKALALPKALSRKEVAELEEVAKRHKAQGLAWARVEEGGFSGGVAKFLEPVREALLQATEARPGDTLLFVAGPRKVAATALGAVRLRAADLLGLKREGFRFLWVVDFPLLEWDEEEEAWTYMHHPFTSPHPEDLPLLEKDPGRVRALAYDLVLNGVEVGGGSIRIHDPRLQARVFRLLGIGEEEQREKFGFFLEALEYGAPPHGGIAWGLDRLLALMTGSPSIREVIAFPKNKEGKDPLTGAPSPVPEEQLRELGLMVVRP 580
               SCOP domains d1efwb1 B:1-104 Aspartyl-tRNA synthetase (AspRS)                                                        d1efwb3 B:105-294,B:415-580 Aspartyl-tRNA synthetase (AspRS)                                                                                                                                  d1efwb2 B:295-414 Prokaryotic AspRS, insert domain                                                                      d1efwb3 B:105-294,B:415-580 Aspartyl-tRNA synthetase (AspRS)                                                                                                           SCOP domains
               CATH domains 1efwB01 B:1-106 Nucleic acid-binding proteins                                                             ------------------------------1efwB02 B:137-277,B:416-580 Bira Bifunctional Protein; Domain 2                                                                              1efwB03 B:278-415  [code=3.30.1360.30, no name defined]                                                                                   1efwB02 B:137-277,B:416-580 Bira Bifunctional Protein; Domain 2                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh....eeeeeeeeeee....eeeeeee..eeeeeee....hhhhhh.......eeeee..eee............eeee..eeeeee..........hhhhh......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..ee.................eee.......eee....hhhhhhhhhhh...eeeeeeeee...........eeeeeeeeee..hhhhhhhhhhhhhhhhhhhh..........eeehhhhhhhhh..............hhhhhh...hhhhhhh.eeeeeee.....hhhhhhhhhhhhhh........eee..eee..hhhhhhhhhhhhhhhh......eeeeeeehhhhhhhhhhhhhhhhhhhh........eeeee....ee........ee...........hhhhh..hhhhh...eeeeee..eeeeeee....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhh...hhhhhh...................hhhhhh...eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1efw B   1 MRRTHYAGSLRETHVGEEVVLEGWVNRRRDLGGLIFLDLRDREGLVQLVAHPASPAYATAERVRPEWVVRAKGLVRLRPEPNPRLATGRVEVELSALEVLAEAKTPPFPVDAGWRGEEEKEASEELRLKYRYLDLRRRRMQENLRLRHRVIKAIWDFLDREGFVQVETPFLTKSTPEGARDFLVPYRHEPGLFYALPQSPQLFKQMLMVAGLDRYFQIARCFRDEDLRADRQPDFTQLDLEMSFVEVEDVLELNERLMAHVFREALGVELPLPFPRLSYEEAMERYGSDKPDLRFGLELKEVGPLFRQSGFRVFQEAESVKALALPKALSRKEVAELEEVAKRHKAQGLAWARVEEGGFSGGVAKFLEPVREALLQATEARPGDTLLFVAGPRKVAATALGAVRLRAADLLGLKREGFRFLWVVDFPLLEWDEEEEAWTYMHHPFTSPHPEDLPLLEKDPGRVRALAYDLVLNGVEVGGGSIRIHDPRLQARVFRLLGIGEEEQREKFGFFLEALEYGAPPHGGIAWGLDRLLALMTGSPSIREVIAFPKNKEGKDPLTGAPSPVPEEQLRELGLMVVRP 580
                                    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 C from PDB  Type:RNA  Length:73
                                                                                                         
                 1efw C   1 GGAGCGGuAGUUCAGuCGGuuAGAAUACCUGCCUgUCaCGCAGGGGgUCGCGGGuuCGAGUCCCGuCCGUUCC  72
                                   |10     |  20|       29    |  |39      | 49    ||  59     |  69   
                                   8-4SU  16-H2U|            34-QUO      46-G7M  54-5MU     65-PSU   
                                              20-H2U            37-2MA            55-PSU             
                                              20A-H2U                                                


Chain D from PDB  Type:RNA  Length:73
                                                                                                         
                 1efw D   1 GGAGCGGuAGUUCAGuCGGuuAGAAUACCUGCCUgUCaCGCAGGGGgUCGCGGGuuCGAGUCCCGuCCGUUCC  72
                                   |10     |  20|       29    |  |39      | 49    ||  59     |  69   
                                   8-4SU  16-H2U|            34-QUO      46-G7M  54-5MU     65-PSU   
                                              20-H2U            37-2MA            55-PSU             
                                              20A-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, 6)

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

(-) CATH Domains  (3, 6)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SYD_THETH | P36419)
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: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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  1efw
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 Related Entries

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

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        SYD_THETH | P36419: 1g51 1l0w

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