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(-) Description

Title :  LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM COMPLEXED WITH LYSINE AND ATP AND MN2+
 
Authors :  G. Desogus, F. Todone, P. Brick, S. Onesti
Date :  16 May 00  (Deposition) - 28 Jul 00  (Release) - 24 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Ligase, Aminoacyl-Trna Synthetase, Protein Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Desogus, F. Todone, P. Brick, S. Onesti
Active Site Of Lysyl-Trna Synthetase: Structural Studies Of The Adenylation Reaction
Biochemistry V. 39 8418 2000
PubMed-ID: 10913247  |  Reference-DOI: 10.1021/BI0006722

(-) Compounds

Molecule 1 - LYSYL-TRNA SYNTHETASE
    Cellular Location: CYTOPLASM
    Chains: A
    EC Number: 6.1.1.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: LYSU
    Expression System Plasmid: PXLYS5
    Expression System Strain: TG2
    Expression System Taxid: 562
    Gene: LYSU
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2GOL2Ligand/IonGLYCEROL
3LYS1Mod. Amino AcidLYSINE
4MN3Ligand/IonMANGANESE (II) ION
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2GOL4Ligand/IonGLYCEROL
3LYS2Mod. Amino AcidLYSINE
4MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:414 , GLU A:421 , ATP A:512 , MN A:517BINDING SITE FOR RESIDUE MN A 515
2AC2SOFTWAREATP A:512BINDING SITE FOR RESIDUE MN A 516
3AC3SOFTWAREGLU A:421 , ATP A:512 , MN A:515BINDING SITE FOR RESIDUE MN A 517
4AC4SOFTWAREGLY A:216 , ALA A:217 , GLU A:240 , ARG A:262 , GLU A:278 , TYR A:280 , ASN A:424 , PHE A:426 , GLU A:428 , GLY A:473 , ATP A:512 , HOH A:2355BINDING SITE FOR RESIDUE LYS A 510
5AC5SOFTWAREARG A:262 , GLU A:264 , ARG A:269 , HIS A:270 , ASN A:271 , PHE A:274 , MET A:276 , GLU A:421 , ILE A:422 , ASN A:424 , GLY A:477 , ARG A:480 , ILE A:491 , LYS A:510 , MN A:515 , MN A:516 , MN A:517 , HOH A:2198 , HOH A:2200 , HOH A:2356 , HOH A:2358 , HOH A:2359BINDING SITE FOR RESIDUE ATP A 512
6AC6SOFTWARELEU A:190 , ARG A:194 , GLU A:204 , GLU A:206 , ILE A:257 , ASN A:258 , HOH A:2165 , HOH A:2196BINDING SITE FOR RESIDUE GOL A 520
7AC7SOFTWAREPRO A:214 , GLY A:215 , ALA A:217 , SER A:218 , ALA A:219 , ILE A:237 , LYS A:446 , GLU A:452 , ALA A:453 , MET A:454 , PHE A:455BINDING SITE FOR RESIDUE GOL A 521

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1E24)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1E24)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1E24)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1E24)

(-) Exons   (0, 0)

(no "Exon" information available for 1E24)

(-) 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:486
 aligned with SYK2_ECO57 | P0A8N6 from UniProtKB/Swiss-Prot  Length:505

    Alignment length:494
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501    
           SYK2_ECO57    12 AIDFNDELRNRREKLAALRQQGVAFPNDFRRDHTSDQLHEEFDAKDNQELESLNIEVSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQTGELSIHCTELRLLTKALRPLPDKFHGLQDQEVRYRQRYLDLIANDKSRQTFVVRSKILAAIRQFMVARGFMEVETPMMQVIPGGASARPFITHHNALDLDMYLRIAPELYLKRLVVGGFERVFEINRNFRNEGISVRHNPEFTMMELYMAYADYHDLIELTESLFRTLAQEVLGTTKVTYGEHVFDFGKPFEKLTMREAIKKYRPETDMADLDNFDAAKALAESIGITVEKSWGLGRIVTEIFDEVAEAHLIQPTFITEYPAEVSPLARRNDVNPEITDRFEFFIGGREIGNGFSELNDAEDQAERFQEQVNAKAAGDDEAMFYDEDYVTALEYGLPPTAGLGIGIDRMIMLFTNSHTIRDVILFPAMRPQK 505
               SCOP domains d1e24a1 A:11-153 Lysyl-tRNA synthetase (LysRS)                                                                                                 -------d1e24a2 A:161-502 Lysyl-tRNA synthetase (LysRS)                                                                                                                                                                                                                                                                                                       -- SCOP domains
               CATH domains ---1e24A01 A:14-153 Nucleic acid-binding proteins                                                                                              -------1e24A02 A:161-501 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                                                                                                --- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhh..hhhhhhhhh.eeeeeeeeeeeee...eeeeeeee..eeeeeeee......hhhhhhhhhh....eeeeeeeeee.....eeeee.eeeeee.......-------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......................eeee....eeee....hhhhhhhhhhhh..eeeeeeeee...........eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh..eeee..eeee.....eeeehhhhhhhhh...hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...eeee....hhh..............eeeeee..eeeeeeee...hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh..eeeeeeehhhhhhhhh...hhhhh........-. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e24 A  11 AIDFNDELRNRREKLAALRQQGVAFPNDFRRDHTSDQLHEEFDAKDNQELESLNIEVSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQTGELSIHCTELRLLTKALRPLP-------DQEVRYRQRYLDLIANDKSRQTFVVRSKILAAIRQFMVARGFMEVETPMMQVIPGGASARPFITHHNALDLDMYLRIAPELYLKRLVVGGFERVFEINRNFRNEGISVRHNPEFTMMELYMAYADYHDLIELTESLFRTLAQEVLGTTKVTYGEHVFDFGKPFEKLTMREAIKKYRPETDMADLDNFDAAKALAESIGITVEKSWGLGRIVTEIFDEVAEAHLIQPTFITEYPAEVSPLARRNDVNPEITDRFEFFIGGREIGNGFSELNDAEDQAERFQEQVNAKAAGDDEAMFYDEDYVTALEYGLPPTAGLGIGIDRMIMLFTNSHTIRDVILFPAMRP-K 510
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150  |      -|      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 | |
                                                                                                                                                                        153     161                                                                                                                                                                                                                                                                                                                                                  502 |
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       510


Chain A from PDB  Type:PROTEIN  Length:486
 aligned with SYK2_ECOLI | P0A8N5 from UniProtKB/Swiss-Prot  Length:505

    Alignment length:494
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501    
           SYK2_ECOLI    12 AIDFNDELRNRREKLAALRQQGVAFPNDFRRDHTSDQLHEEFDAKDNQELESLNIEVSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQTGELSIHCTELRLLTKALRPLPDKFHGLQDQEVRYRQRYLDLIANDKSRQTFVVRSKILAAIRQFMVARGFMEVETPMMQVIPGGASARPFITHHNALDLDMYLRIAPELYLKRLVVGGFERVFEINRNFRNEGISVRHNPEFTMMELYMAYADYHDLIELTESLFRTLAQEVLGTTKVTYGEHVFDFGKPFEKLTMREAIKKYRPETDMADLDNFDAAKALAESIGITVEKSWGLGRIVTEIFDEVAEAHLIQPTFITEYPAEVSPLARRNDVNPEITDRFEFFIGGREIGNGFSELNDAEDQAERFQEQVNAKAAGDDEAMFYDEDYVTALEYGLPPTAGLGIGIDRMIMLFTNSHTIRDVILFPAMRPQK 505
               SCOP domains d1e24a1 A:11-153 Lysyl-tRNA synthetase (LysRS)                                                                                                 -------d1e24a2 A:161-502 Lysyl-tRNA synthetase (LysRS)                                                                                                                                                                                                                                                                                                       -- SCOP domains
               CATH domains ---1e24A01 A:14-153 Nucleic acid-binding proteins                                                                                              -------1e24A02 A:161-501 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                                                                                                --- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhh..hhhhhhhhh.eeeeeeeeeeeee...eeeeeeee..eeeeeeee......hhhhhhhhhh....eeeeeeeeee.....eeeee.eeeeee.......-------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......................eeee....eeee....hhhhhhhhhhhh..eeeeeeeee...........eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh..eeee..eeee.....eeeehhhhhhhhh...hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...eeee....hhh..............eeeeee..eeeeeeee...hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh..eeeeeeehhhhhhhhh...hhhhh........-. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e24 A  11 AIDFNDELRNRREKLAALRQQGVAFPNDFRRDHTSDQLHEEFDAKDNQELESLNIEVSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQTGELSIHCTELRLLTKALRPLP-------DQEVRYRQRYLDLIANDKSRQTFVVRSKILAAIRQFMVARGFMEVETPMMQVIPGGASARPFITHHNALDLDMYLRIAPELYLKRLVVGGFERVFEINRNFRNEGISVRHNPEFTMMELYMAYADYHDLIELTESLFRTLAQEVLGTTKVTYGEHVFDFGKPFEKLTMREAIKKYRPETDMADLDNFDAAKALAESIGITVEKSWGLGRIVTEIFDEVAEAHLIQPTFITEYPAEVSPLARRNDVNPEITDRFEFFIGGREIGNGFSELNDAEDQAERFQEQVNAKAAGDDEAMFYDEDYVTALEYGLPPTAGLGIGIDRMIMLFTNSHTIRDVILFPAMRP-K 510
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150  |      -|      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 | |
                                                                                                                                                                        153     161                                                                                                                                                                                                                                                                                                                                                  502 |
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       510
   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, 2)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1E24)

(-) Gene Ontology  (14, 26)

Asymmetric Unit(hide GO term definitions)
Chain A   (SYK2_ECO57 | P0A8N6)
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.

Chain A   (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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 Related Entries

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

UniProtKB/Swiss-Prot
        SYK2_ECO57 | P0A8N6: 1e1t 1e22
        SYK2_ECOLI | P0A8N5: 1e1o 1e1t 1e22 1lyl

(-) Related Entries Specified in the PDB File

1e1o LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM, COMPLEXED WITH LYSINE
1e1t LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM COMPLEXED WITH THE LYSYL_ADENYLATE INTERMEDIATE
1e22 LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM COMPLEXED WITH LYSINE AND THE NON-HYDROLYSABLE ATP ANALOGUE AMP-PCP
1lyl LYSYL-TRNA SYNTHETASE (LYSU) (E.C.6.1.1.6) COMPLEXED WITH LYSINE