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(-) Description

Title :  ISOLEUCYL-TRNA SYNTHETASE COMPLEXED WITH ISOLEUCYL-ADENYLATE ANALOGUE
 
Authors :  T. Nakama, O. Nureki, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  17 Sep 01  (Deposition) - 21 Dec 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Aminoacyl-Trna Synthetase, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Nakama, O. Nureki, S. Yokoyama
Structural Basis For The Recognition Of Isoleucyl-Adenylate And An Antibiotic, Mupirocin, By Isoleucyl-Trna Synthetase.
J. Biol. Chem. V. 276 47387 2001
PubMed-ID: 11584022  |  Reference-DOI: 10.1074/JBC.M109089200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ISOLEUCYL-TRNA SYNTHETASE
    Chains: A
    EC Number: 6.1.1.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1ILA1Ligand/IonN-[ISOLEUCINYL]-N'-[ADENOSYL]-DIAMINOSUFONE
2ZN2Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:181 , CYS A:184 , CYS A:389 , CYS A:392BINDING SITE FOR RESIDUE ZN A 1101
2AC2SOFTWARECYS A:461 , CYS A:464 , GLY A:465 , CYS A:502 , CYS A:504BINDING SITE FOR RESIDUE ZN A 1102
3AC3SOFTWAREGLY A:45 , PRO A:46 , HIS A:54 , GLY A:56 , HIS A:57 , GLN A:59 , ASP A:85 , GLU A:550 , GLY A:551 , ASP A:553 , GLN A:554 , TRP A:558 , HIS A:581 , GLY A:582 , LEU A:583 , ILE A:584BINDING SITE FOR RESIDUE ILA A 1301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYI_THET847-58  1A:47-58

(-) Exons   (0, 0)

(no "Exon" information available for 1JZQ)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:821
 aligned with SYI_THET8 | P56690 from UniProtKB/Swiss-Prot  Length:1043

    Alignment length:821
                                    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       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820 
            SYI_THET8     1 MFKEVGEPNFPKLEEEVLAFWKREKIFQKSVENRKGGPRYTVYEGPPTANGLPHVGHAQARSYKDLFPRYKTMRGYYAPRRAGWDTHGLPVELEVEKKLGLKSKREIEAYGIERFNQACRESVFTYEKEWEAFTERIAYWVDLENAYATLEPTYIESIWWSLKNLFDRGLLYRDHKVVPYCPRCGTPLSSHEVALGYKEIQDPSVYVRFPLKEPKKLGLEKASLLIWTTTPWTLPGNVAAAVHPEYTYAAFQVGDEALILEEGLGRKLLGEGTPVLKTFPGKALEGLPYTPPYPQALEKGYFVVLADYVSQEDGTGIVHQAPAFGAEDLETARVYGLPLLKTVDEEGKLLVEPFKGLYFREANRAILRDLRGRGLLFKEESYLHSYPHCWRCSTPLMYYATESWFIKNTLFKDELIRKNQEIHWVPPHIKEGRYGEWLKNLVDWALSRNRYWGTPLPIWVCQACGKEEAIGSFQELKARATKPLPEPFDPHRPYVDQVELACACGGTMRRVPYVIDVWYDSGAMPFASLHYPFEHEEVFRESFPADFIAEGIDQTRGWFNSLHQLGVMLFGSIAFKNVICHGLILDEKGQKMSKSKGNVVDPWDIIREFGADALRWYIYVSAPPEADRRFGPNLVRETVRDYFLTLWNVYSFFVTYANLDRPDLKNPPPPEKRPEMDRWLLARMQDLIQRVTEALEAYDPTTSARALRDFVVEDLSQWYVRRNRRRFWKNEDALDREAAYATLYEALVLVATLAAPFTPFLAEVLWQNLVRSVRPEAKESVHLADWPEADPALADEALVAQMRAVLKVVDLARAARAKSGV 821
               SCOP domains d1jzqa3 A:1-197,A:387-641 Isoleucyl-tRNA synthetase (IleRS)                                                                                                                                          d1jzqa2 A:198-386 Isoleucyl-tRNA synthetase (IleRS)                                                                                                                                          d1jzqa3 A:1-197,A:387-641 Isoleucyl-tRNA synthetase (IleRS)                                                                                                                                                                                                    d1jzqa1 A:642-821 Isoleucyl-tRNA synthetase (IleRS)                                                                                                                                  SCOP domains
               CATH domains 1jzqA01 A:1-195,A:391-630 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                    1jzqA02 A:196-390 Isoleucyl-tRNA Synthetase; Domain 2                                                                                                                                              1jzqA01 A:1-195,A:391-630 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                 1jzqA03 A:631-821 Isoleucyl-tRNA Synthetase; Domain 1                                                                                                                                           CATH domains
               Pfam domains ---------------tRNA-synt_1-1jzqA01 A:16-631                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            ---------------------------------------------Anticodon_1-1jzqA02 A:677-821                                                                                                                     Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhh.........ee...hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........ee..hhhhhhhhhhhhhhhhhhh.eeeeeeeeeee....ee.hhhhhhhheeeeeeeeeeeeee..hhhhhh...eeeeeee.hhhhhhhh.eeee....eeeeeee..eeeeee..hhhhhh.....eeeeee.hhhh.................eee...........eeee....hhhhhhhhhhh...............hhhhh..hhhhhhhhhhhhhhhh..eeeeeeeeeeee.........eeeeeeeeee.hhhhhhhhhhhhhhhee.hhhhh.hhhhhhhhh...ee.............eee..........hhhhhhhhh..........hhhhhh...ee.....eeee.....hhhhhhhhhhhhh......hhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhh......eeeee..ee...............hhhhhhhhhhhhhhhhhhhhh......ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhh..........hhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------AA_TRNA_LIGA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jzq A   1 MFKEVGEPNFPKLEEEVLAFWKREKIFQKSVENRKGGPRYTVYEGPPTANGLPHVGHAQARSYKDLFPRYKTMRGYYAPRRAGWDTHGLPVELEVEKKLGLKSKREIEAYGIERFNQACRESVFTYEKEWEAFTERIAYWVDLEDAYATLEPTYIESIWWSLKNLFDRGLLYRDHKVVPYCPRCGTPLSSHEVALGYKEIQDPSVYVRFPLKEPKKLGLEKASLLIWTTTPWTLPGNVAAAVHPEYTYAAFQVGDEALILEEGLGRKLLGEGTQVLKTFPGKALEGLPYTPPYPQALEKGYFVVLADYVSQEDGTGIVHQAPAFGAEDLETARVYGLPLLKTVDEEGKLLVEPFKGLYFREANRAILRDLRGRGLLFKEESYLHSYPHCWRCSTPLMYYATESWFIKNTLFKDELIRNNQEIHWVPPHIKEGRYGEWLKNLVDWALSRNRYWGTPLPIWVCQACGKEEAIGSFQELKARATKPLPEPFDPHRPYVDQVELACACGGTMRRVPYVIDVWYDSGAMPFASLHYPFEHEEVFRESFPADFIAEGIDQTRGWFNSLHQLGVMLFGSIAFKNVICHGLILDEKGQKMSKSKGNVVDPWDIIRKFGADALRWYIYVSAPPEADRRFGPNLVRETVRDYFLTLWNVYSFFVTYANLDRPDLKNPPPPEKRPEMDRWLLARMQDLIQRVTEALEAYDPTTSARALRDFVVEDLSQWYVRRNRRRFWKNEDALDREAAYATLYEALVLVATLAAPFTPFLAEVLWQNLVRSVRLEAKESVHLADWPEADPALADEALVAQMRAVLKVVDLARAARAKSGV 821
                                    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       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: HUP (230)
(-)
Clan: no clan defined [family: Anticodon_1] (10)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SYI_THET8 | P56690)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0002161    aminoacyl-tRNA editing activity    The hydrolysis of an incorrectly aminoacylated tRNA.
    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:0004822    isoleucine-tRNA ligase activity    Catalysis of the reaction: L-isoleucine + ATP + tRNA(Ile) = L-isoleucyl-tRNA(Ile) + AMP + diphosphate + 2 H(+).
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006428    isoleucyl-tRNA aminoacylation    The process of coupling isoleucine to isoleucyl-tRNA, catalyzed by isoleucyl-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:0006450    regulation of translational fidelity    Any process that modulates the ability of the translational apparatus to interpret the genetic code.
    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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  1jzq
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  6.1.1.5
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 Related Entries

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

UniProtKB/Swiss-Prot
        SYI_THET8 | P56690: 1ile 1jzs 1udz 1ue0 1wk8 1wny 1wnz

(-) Related Entries Specified in the PDB File

1jzs 1JZS CONTAINS THE SAME PROTEIN COMPLEXED WITH MUPIROCIN. RELATED ID: TRT001000219.1 RELATED DB: TARGETDB