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(-) Description

Title :  CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS TILS IN A COMPLEX WITH ATP, MAGNESIUM ION, AND L-LYSINE
 
Authors :  M. Kuratani, Y. Yoshikawa, S. Takahashi, S. Yokoyama, Riken Structur Genomics/Proteomics Initiative (Rsgi)
Date :  19 Jan 07  (Deposition) - 13 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Rossmann-Fold, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kuratani, Y. Yoshikawa, Y. Bessho, K. Higashijima, T. Ishii, R. Shibata, S. Takahashi, K. Yutani, S. Yokoyama
Structural Basis Of The Initial Binding Of Trna(Ile) Lysidine Synthetase Tils With Atp And L-Lysine
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRNA(ILE)-LYSIDINE SYNTHASE
    Chains: A, B, C, D
    EC Number: 6.3.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Synonym: TRNA(ILE)-LYSIDINE SYNTHETASE, TRNA(ILE)-2-LYSYL-CYTIDINE SYNTHASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1ATP4Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2LYS1Mod. Amino AcidLYSINE
3MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2LYS1Mod. Amino AcidLYSINE
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2LYS-1Mod. Amino AcidLYSINE
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP C:36 , ALA C:132 , HIS C:134 , ASP C:137 , ATP C:902 , HOH C:932BINDING SITE FOR RESIDUE MG C 601
2AC2SOFTWAREVAL B:35 , LYS B:182 , TRP B:188 , VAL B:189 , ASP B:191BINDING SITE FOR RESIDUE LYS B 950
3AC3SOFTWAREALA A:30 , PHE A:31 , SER A:32 , ALA A:59 , PHE A:61 , ARG A:110 , ARG A:113 , THR A:131 , ALA A:132 , HIS A:133 , ARG A:201BINDING SITE FOR RESIDUE ATP A 900
4AC4SOFTWAREALA B:30 , PHE B:31 , SER B:32 , ALA B:59 , HIS B:60 , PHE B:61 , ARG B:110 , ARG B:113 , THR B:131 , ALA B:132 , HIS B:133 , ARG B:201BINDING SITE FOR RESIDUE ATP B 901
5AC5SOFTWAREALA C:30 , PHE C:31 , SER C:32 , ALA C:59 , HIS C:60 , PHE C:61 , ARG C:110 , ARG C:113 , THR C:131 , ALA C:132 , HIS C:133 , MG C:601BINDING SITE FOR RESIDUE ATP C 902
6AC6SOFTWAREALA D:30 , PHE D:31 , SER D:32 , ASP D:36 , ALA D:59 , HIS D:60 , PHE D:61 , ARG D:113 , THR D:131 , ALA D:132 , HIS D:133 , ARG D:201BINDING SITE FOR RESIDUE ATP D 903

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:253 -A:312
2B:253 -B:312
3C:253 -C:312
4D:253 -D:312

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2E89)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2E89)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2E89)

(-) Exons   (0, 0)

(no "Exon" information available for 2E89)

(-) 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:317
 aligned with TILS_AQUAE | O67728 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:317
                                    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       
           TILS_AQUAE     1 MNPESRVIRKVLALQNDEKIFSGERRVLIAFSGGVDSVVLTDVLLKLKNYFSLKEVALAHFNHMLRESAERDEEFCKEFAKERNMKIFVGKEDVRAFAKENRMSLEEAGRFLRYKFLKEILESEGFDCIATAHHLNDLLETSLLFFTRGTGLDGLIGFLPKEEVIRRPLYYVKRSEIEEYAKFKGLRWVEDETNYEVSIPRNRIRHRVIPELKRINENLEDTFLKMVKVLRAEREFLEEEAQKLYKEVKKGNCLDVKKLKEKPLALQRRVIRKFIGEKDYEKVELVRSLLEKGGEVNLGKGKVLKRKERWLCFSPEV 317
               SCOP domains d2e89a1 A:1-216 TilS-like protein Aq_1887                                                                                                                                                                               d2e89a2 A:217-317 TilS-like protein Aq_1887                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhh......eeeeeeee....hhhhhhhhhhhhhhhhh..eeeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhhh.hhhhhhh...ee..ee......hhhhhhhhhhhh..............hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee..eeehhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhh.....eee.....eeee...eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e89 A   1 MNPESRVIRKVLALQNDEKIFSGERRVLIAFSGGVDSVVLTDVLLKLKNYFSLKEVALAHFNHMLRESAERDEEFCKEFAKERNMKIFVGKEDVRAFAKENRMSLEEAGRFLRYKFLKEILESEGFDCIATAHHLNDLLETSLLFFTRGTGLDGLIGFLPKEEVIRRPLYYVKRSEIEEYAKFKGLRWVEDETNYEVSIPRNRIRHRVIPELKRINENLEDTFLKMVKVLRAEREFLEEEAQKLYKEVKKGNCLDVKKLKEKPLALQRRVIRKFIGEKDYEKVELVRSLLEKGGEVNLGKGKVLKRKERWLCFSPEV 317
                                    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       


Chain B from PDB  Type:PROTEIN  Length:315
 aligned with TILS_AQUAE | O67728 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:316
                                    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      
           TILS_AQUAE     1 MNPESRVIRKVLALQNDEKIFSGERRVLIAFSGGVDSVVLTDVLLKLKNYFSLKEVALAHFNHMLRESAERDEEFCKEFAKERNMKIFVGKEDVRAFAKENRMSLEEAGRFLRYKFLKEILESEGFDCIATAHHLNDLLETSLLFFTRGTGLDGLIGFLPKEEVIRRPLYYVKRSEIEEYAKFKGLRWVEDETNYEVSIPRNRIRHRVIPELKRINENLEDTFLKMVKVLRAEREFLEEEAQKLYKEVKKGNCLDVKKLKEKPLALQRRVIRKFIGEKDYEKVELVRSLLEKGGEVNLGKGKVLKRKERWLCFSPE 316
               SCOP domains d2e89b1 B:1-216 TilS-like protein Aq_1887                                                                                                                                                                               d2e89b2 B:217-314 TilS-like protein Aq_1887                                                       -- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhh.......eeeeeeee.....hhhhhhhhhhhhhhhh...eeeee.hhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...eee...hhhhhhhhhhhhhhhh.hhhhhhh...ee..ee......hhhhhhhhhhhh..............hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhh....eeee.....eeee....eee.-. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e89 B   1 MNPESRVIRKVLALQNDEKIFSGERRVLIAFSGGVDSVVLTDVLLKLKNYFSLKEVALAHFNHMLRESAERDEEFCKEFAKERNMKIFVGKEDVRAFAKENRMSLEEAGRFLRYKFLKEILESEGFDCIATAHHLNDLLETSLLFFTRGTGLDGLIGFLPKEEVIRRPLYYVKRSEIEEYAKFKGLRWVEDETNYEVSIPRNRIRHRVIPELKRINENLEDTFLKMVKVLRAEREFLEEEAQKLYKEVKKGNCLDVKKLKEKPLALQRRVIRKFIGEKDYEKVELVRSLLEKGGEVNLGKGKVLKRKERWLCFS-K 950
                                    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   | |
                                                                                                                                                                                                                                                                                                                                                   314 |
                                                                                                                                                                                                                                                                                                                                                     950


Chain C from PDB  Type:PROTEIN  Length:314
 aligned with TILS_AQUAE | O67728 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:314
                                    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    
           TILS_AQUAE     1 MNPESRVIRKVLALQNDEKIFSGERRVLIAFSGGVDSVVLTDVLLKLKNYFSLKEVALAHFNHMLRESAERDEEFCKEFAKERNMKIFVGKEDVRAFAKENRMSLEEAGRFLRYKFLKEILESEGFDCIATAHHLNDLLETSLLFFTRGTGLDGLIGFLPKEEVIRRPLYYVKRSEIEEYAKFKGLRWVEDETNYEVSIPRNRIRHRVIPELKRINENLEDTFLKMVKVLRAEREFLEEEAQKLYKEVKKGNCLDVKKLKEKPLALQRRVIRKFIGEKDYEKVELVRSLLEKGGEVNLGKGKVLKRKERWLCFS 314
               SCOP domains d2e89c1 C:1-216 TilS-like protein Aq_1887                                                                                                                                                                               d2e89c2 C:217-314 TilS-like protein Aq_1887                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhhh.hhhhhhh...ee..ee......hhhhhhhhhhhh.......hhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee..eeehhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhh.....eee.....eeee...eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e89 C   1 MNPESRVIRKVLALQNDEKIFSGERRVLIAFSGGVDSVVLTDVLLKLKNYFSLKEVALAHFNHMLRESAERDEEFCKEFAKERNMKIFVGKEDVRAFAKENRMSLEEAGRFLRYKFLKEILESEGFDCIATAHHLNDLLETSLLFFTRGTGLDGLIGFLPKEEVIRRPLYYVKRSEIEEYAKFKGLRWVEDETNYEVSIPRNRIRHRVIPELKRINENLEDTFLKMVKVLRAEREFLEEEAQKLYKEVKKGNCLDVKKLKEKPLALQRRVIRKFIGEKDYEKVELVRSLLEKGGEVNLGKGKVLKRKERWLCFS 314
                                    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    


Chain D from PDB  Type:PROTEIN  Length:313
 aligned with TILS_AQUAE | O67728 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:313
                                    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   
           TILS_AQUAE     1 MNPESRVIRKVLALQNDEKIFSGERRVLIAFSGGVDSVVLTDVLLKLKNYFSLKEVALAHFNHMLRESAERDEEFCKEFAKERNMKIFVGKEDVRAFAKENRMSLEEAGRFLRYKFLKEILESEGFDCIATAHHLNDLLETSLLFFTRGTGLDGLIGFLPKEEVIRRPLYYVKRSEIEEYAKFKGLRWVEDETNYEVSIPRNRIRHRVIPELKRINENLEDTFLKMVKVLRAEREFLEEEAQKLYKEVKKGNCLDVKKLKEKPLALQRRVIRKFIGEKDYEKVELVRSLLEKGGEVNLGKGKVLKRKERWLCF 313
               SCOP domains d2e89d1 D:1-216 TilS-like protein Aq_1887                                                                                                                                                                               d2e89d2 D:217-313 TilS-like protein Aq_1887                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhh.......eee..eee....hhhhhhhhhhhhhhhhhh....eee..hhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhhh.hhhhhhh...ee..ee......hhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhh....eeee..eee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e89 D   1 MNPESRVIRKVLALQNDEKIFSGERRVLIAFSGGVDSVVLTDVLLKLKNYFSLKEVALAHFNHMLRESAERDEEFCKEFAKERNMKIFVGKEDVRAFAKENRMSLEEAGRFLRYKFLKEILESEGFDCIATAHHLNDLLETSLLFFTRGTGLDGLIGFLPKEEVIRRPLYYVKRSEIEEYAKFKGLRWVEDETNYEVSIPRNRIRHRVIPELKRINENLEDTFLKMVKVLRAEREFLEEEAQKLYKEVKKGNCLDVKKLKEKPLALQRRVIRKFIGEKDYEKVELVRSLLEKGGEVNLGKGKVLKRKERWLCF 313
                                    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
   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, 8)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2E89)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2E89)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (TILS_AQUAE | O67728)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0016879    ligase activity, forming carbon-nitrogen bonds    Catalysis of the joining of two molecules, or two groups within a single molecule, via a carbon-nitrogen bond, 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:0006400    tRNA modification    The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
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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  2e89
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  TILS_AQUAE | O67728
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  6.3.4.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        TILS_AQUAE | O67728: 1wy5 2e21

(-) Related Entries Specified in the PDB File

2e21 RELATED ID: AAE001001887.3 RELATED DB: TARGETDB