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(-) Description

Title :  LYSYL-TRNA SYNTHETASE (LYSU) (E.C.6.1.1.6) COMPLEXED WITH LYSINE
 
Authors :  S. Onesti, P. Brick
Date :  03 May 95  (Deposition) - 15 Oct 95  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B  (2x)
Keywords :  Ligase (Synthetase) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Onesti, A. D. Miller, P. Brick
The Crystal Structure Of The Lysyl-Trna Synthetase (Lysu) From Escherichia Coli
Structure V. 3 163 1995
PubMed-ID: 7735833  |  Reference-DOI: 10.1016/S0969-2126(01)00147-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LYSYL-TRNA SYNTHETASE (LYSU)
    Chains: A, B, C
    EC Number: 6.1.1.6
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A C
Biological Unit 2 (2x):  B 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1LYS3Mod. Amino AcidLYSINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1LYS2Mod. Amino AcidLYSINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1LYS2Mod. Amino AcidLYSINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:216 , GLU A:240 , ARG A:262 , MET A:276 , GLU A:278 , TYR A:280 , ASN A:424 , PHE A:426 , GLU A:428 , GLY A:473BINDING SITE FOR RESIDUE LYS A 505
2AC2SOFTWAREGLY B:216 , ALA B:238 , GLU B:240 , ARG B:262 , GLU B:278 , TYR B:280 , ASN B:424 , PHE B:426 , GLU B:428 , GLY B:473BINDING SITE FOR RESIDUE LYS B 505
3AC3SOFTWAREGLY C:216 , GLU C:240 , GLU C:278 , TYR C:280 , ASN C:424 , PHE C:426 , GLU C:428 , GLY C:473 , GLY C:475BINDING SITE FOR RESIDUE LYS C 505

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1LYL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1LYL)

(-) 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:483
 aligned with SYK2_ECOLI | P0A8N5 from UniProtKB/Swiss-Prot  Length:505

    Alignment length:491
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504 
           SYK2_ECOLI    15 FNDELRNRREKLAALRQQGVAFPNDFRRDHTSDQLHEEFDAKDNQELESLNIEVSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQTGELSIHCTELRLLTKALRPLPDKFHGLQDQEVRYRQRYLDLIANDKSRQTFVVRSKILAAIRQFMVARGFMEVETPMMQVIPGGASARPFITHHNALDLDMYLRIAPELYLKRLVVGGFERVFEINRNFRNEGISVRHNPEFTMMELYMAYADYHDLIELTESLFRTLAQEVLGTTKVTYGEHVFDFGKPFEKLTMREAIKKYRPETDMADLDNFDAAKALAESIGITVEKSWGLGRIVTEIFDEVAEAHLIQPTFITEYPAEVSPLARRNDVNPEITDRFEFFIGGREIGNGFSELNDAEDQAERFQEQVNAKAAGDDEAMFYDEDYVTALEYGLPPTAGLGIGIDRMIMLFTNSHTIRDVILFPAMRPQK 505
               SCOP domains d1lyla1 A:14-153 Lysyl-tRNA synthetase (LysRS)                                                                                              -------d1lyla2 A:161-502 Lysyl-tRNA synthetase (LysRS)                                                                                                                                                                                                                                                                                                       -- SCOP domains
               CATH domains 1lylA01 A:14-153 Nucleic acid-binding proteins                                                                                              -------1lylA02 A:161-502 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                                                                                                 -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.............hhhhhhhh....hhhhhh...eeeeeeeeeeeee...eeeeeeee..eeeeeeee.......hhhh.hhh.....eeeeeeeeeee...eeeeee.eeeeee.......-------.hhhhhh.hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh......................eee......eee.....hhhhhhhhh....eeeeeeeee...........eeeeeeeeee...hhhhhhhhhhhhhhhhhhhh...eeee..eeee.....eeeehhhhhhhh.....hhhhh.hhhhhhhhhhh.........hhhhhhhhhhhh.hhh....eeee...hhh...............eeeeee..eeeeeeee....hhhhhhhhhhhhhhhh..........hhhhhhhhh....eeeeeeehhhhhhhhh....hhh.........-. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lyl A  14 FNDELRNRREKLAALRQQGVAFPNDFRRDHTSDQLHEEFDAKDNQELESLNIEVSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQTGELSIHCTELRLLTKALRPLP-------DQEVRYRQRYLDLIANDKSRQTFVVRSKILAAIRQFMVARGFMEVETPMMQVIPGGASARPFITHHNALDLDMYLRIAPELYLKRLVVGGFERVFEINRNFRNEGISVRHNPEFTMMELYMAYADYHDLIELTESLFRTLAQEVLGTTKVTYGEHVFDFGKPFEKLTMREAIKKYRPETDMADLDNFDAAKALAESIGITVEKSWGLGRIVTEIFDEVAEAHLIQPTFITEYPAEVSPLARRNDVNPEITDRFEFFIGGREIGNGFSELNDAEDQAERFQEQVNAKAAGDDEAMFYDEDYVTALEYGLPPTAGLGIGIDRMIMLFTNSHTIRDVILFPAMRP-K 505
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493        |-|
                                                                                                                                                                     153     161                                                                                                                                                                                                                                                                                                                                                  502 |
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    505


Chain B from PDB  Type:PROTEIN  Length:484
 aligned with SYK2_ECOLI | P0A8N5 from UniProtKB/Swiss-Prot  Length:505

    Alignment length:490
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504
           SYK2_ECOLI    15 FNDELRNRREKLAALRQQGVAFPNDFRRDHTSDQLHEEFDAKDNQELESLNIEVSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQTGELSIHCTELRLLTKALRPLPDKFHGLQDQEVRYRQRYLDLIANDKSRQTFVVRSKILAAIRQFMVARGFMEVETPMMQVIPGGASARPFITHHNALDLDMYLRIAPELYLKRLVVGGFERVFEINRNFRNEGISVRHNPEFTMMELYMAYADYHDLIELTESLFRTLAQEVLGTTKVTYGEHVFDFGKPFEKLTMREAIKKYRPETDMADLDNFDAAKALAESIGITVEKSWGLGRIVTEIFDEVAEAHLIQPTFITEYPAEVSPLARRNDVNPEITDRFEFFIGGREIGNGFSELNDAEDQAERFQEQVNAKAAGDDEAMFYDEDYVTALEYGLPPTAGLGIGIDRMIMLFTNSHTIRDVILFPAMRPQ 504
               SCOP domains d1lylb1 B:14-153 Lysyl-tRNA synthetase (LysRS)                                                                                              d      1lylb2 B:154-502 Lysyl-tRNA synthetase (LysRS)                                                                                                                                                                                                                                                                                                        - SCOP domains
               CATH domains 1lylB01 B:14-153 Nucleic acid-binding proteins                                                                                              -------1lylB02 B:161-501 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                                                                                                -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.............hhhhhhhh....hhhhhh...eeeeeeeeeeeee...eeeeeeee..eeeeeeee.......hhhh.hhh.....eeeeeeeeee.....eeeee.eeeeee........------.hhhhhh.hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh......................eeee....eeee.....hhhhhhhhhh...eeeeeeeee...........eeeeeeeeee...hhhhhhhhhhhhhhhhhhh....eeee..eeee.....eeeehhhhhhhh.....hhhhh.hhhhhhhhhhh.........hhhhhhhhhhhh.hhh....eeee...hhh...............eeeeee..eeeeeeee....hhhhhhhhhhhhhhhh..........hhhhhhhhh....eeeeeeehhhhhhhhh....hhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lyl B  14 FNDELRNRREKLAALRQQGVAFPNDFRRDHTSDQLHEEFDAKDNQELESLNIEVSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQTGELSIHCTELRLLTKALRPLPD------DQEVRYRQRYLDLIANDKSRQTFVVRSKILAAIRQFMVARGFMEVETPMMQVIPGGASARPFITHHNALDLDMYLRIAPELYLKRLVVGGFERVFEINRNFRNEGISVRHNPEFTMMELYMAYADYHDLIELTESLFRTLAQEVLGTTKVTYGEHVFDFGKPFEKLTMREAIKKYRPETDMADLDNFDAAKALAESIGITVEKSWGLGRIVTEIFDEVAEAHLIQPTFITEYPAEVSPLARRNDVNPEITDRFEFFIGGREIGNGFSELNDAEDQAERFQEQVNAKAAGDDEAMFYDEDYVTALEYGLPPTAGLGIGIDRMIMLFTNSHTIRDVILFPAMRPK 505
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153|      163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       505
                                                                                                                                                                      154    161                                                                                                                                                                                                                                                                                                                                                  502|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   505


Chain C from PDB  Type:PROTEIN  Length:483
 aligned with SYK2_ECOLI | P0A8N5 from UniProtKB/Swiss-Prot  Length:505

    Alignment length:490
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504
           SYK2_ECOLI    15 FNDELRNRREKLAALRQQGVAFPNDFRRDHTSDQLHEEFDAKDNQELESLNIEVSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQTGELSIHCTELRLLTKALRPLPDKFHGLQDQEVRYRQRYLDLIANDKSRQTFVVRSKILAAIRQFMVARGFMEVETPMMQVIPGGASARPFITHHNALDLDMYLRIAPELYLKRLVVGGFERVFEINRNFRNEGISVRHNPEFTMMELYMAYADYHDLIELTESLFRTLAQEVLGTTKVTYGEHVFDFGKPFEKLTMREAIKKYRPETDMADLDNFDAAKALAESIGITVEKSWGLGRIVTEIFDEVAEAHLIQPTFITEYPAEVSPLARRNDVNPEITDRFEFFIGGREIGNGFSELNDAEDQAERFQEQVNAKAAGDDEAMFYDEDYVTALEYGLPPTAGLGIGIDRMIMLFTNSHTIRDVILFPAMRPQ 504
               SCOP domains d1lylc1 C:14-153 Lysyl-tRNA synthetase (LysRS)                                                                                              -------d1lylc2 C:161-502 Lysyl-tRNA synthetase (LysRS)                                                                                                                                                                                                                                                                                                       - SCOP domains
               CATH domains 1lylC01 C:14-153 Nucleic acid-binding proteins                                                                                              -------1lylC02 C:161-501 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                                                                                                -- CATH domains
           Pfam domains (1) -----------------------------------------------------tRNA_anti-1lylC01 C:67-145                                                     ---------------tRNA-synt_2-1lylC04 C:161-502                                                                                                                                                                                                                                                                                                                         - Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------tRNA_anti-1lylC02 C:67-145                                                     ---------------tRNA-synt_2-1lylC05 C:161-502                                                                                                                                                                                                                                                                                                                         - Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------tRNA_anti-1lylC03 C:67-145                                                     ---------------tRNA-synt_2-1lylC06 C:161-502                                                                                                                                                                                                                                                                                                                         - Pfam domains (3)
         Sec.struct. author .hhhhhhhhhhhhhhhh..............hhhhhhhh....hhhhhh...eeeeeeeeeeeee...eeeeeeee..eeeeeeeehhh....hhhh.hhh.....eeeeeeeeee.....eeeee.eeeeee.......-------.hhhhhh.hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh......................eeee....eeee.....hhhhhhhhh....eeeeeeeee...........eeeeeeeeee...hhhhhhhhhhhhhhhhhhh....eeee..eeee.....eeeehhhhhhhh.....hhhhh.hhhhhhhhhhh.........hhhhhhhhhhhh.hhh....eeee...hhh...............eeeeee..eeeeeeee....hhhhhhhhhhhhhhhh..........hhhhhhhhh....eeeeeeehhhhhhhhh....hhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lyl C  14 FNDELRNRREKLAALRQQGVAFPNDFRRDHTSDQLHEEFDAKDNQELESLNIEVSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQTGELSIHCTELRLLTKALRPLP-------DQEVRYRQRYLDLIANDKSRQTFVVRSKILAAIRQFMVARGFMEVETPMMQVIPGGASARPFITHHNALDLDMYLRIAPELYLKRLVVGGFERVFEINRNFRNEGISVRHNPEFTMMELYMAYADYHDLIELTESLFRTLAQEVLGTTKVTYGEHVFDFGKPFEKLTMREAIKKYRPETDMADLDNFDAAKALAESIGITVEKSWGLGRIVTEIFDEVAEAHLIQPTFITEYPAEVSPLARRNDVNPEITDRFEFFIGGREIGNGFSELNDAEDQAERFQEQVNAKAAGDDEAMFYDEDYVTALEYGLPPTAGLGIGIDRMIMLFTNSHTIRDVILFPAMRPK 505
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       505
                                                                                                                                                                     153     161                                                                                                                                                                                                                                                                                                                                                  502|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   505
   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, 6)

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

(-) CATH Domains  (2, 6)

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

(-) Pfam Domains  (2, 6)

Asymmetric Unit
(-)
Clan: OB (224)
(-)
Clan: tRNA_synt_II (64)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (SYK2_ECOLI | P0A8N5)
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: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:0004824    lysine-tRNA ligase activity    Catalysis of the reaction: ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys).
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0006430    lysyl-tRNA aminoacylation    The process of coupling lysine to lysyl-tRNA, catalyzed by lysyl-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.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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  1lyl
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 Related Entries

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        SYK2_ECOLI | P0A8N5: 1e1o 1e1t 1e22 1e24

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1LYL)