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(-) Description

Title :  LEISHMANIA MAJOR TYROSYL-TRNA SYNTHETASE IN COMPLEX WITH TYROSINOL, CUBIC CRYSTAL FORM
 
Authors :  E. A. Merritt, E. T. Larson, Medical Structural Genomics Of Pathog Protozoa (Msgpp)
Date :  28 Sep 10  (Deposition) - 23 Mar 11  (Release) - 01 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.13
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Aminoacyl-Trna Synthetase, Trna Ligase, Aars, Tyrrs, Pseudodimer, Translation, Atp-Binding, Nucleotide-Binding, Ligase, Structural Genomics, Medical Structural Genomics Of Pathogenic Protozoa, Msgpp (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. T. Larson, J. E. Kim, L. J. Castaneda, A. J. Napuli, Z. Zhang, E. Fan, F. H. Zucker, C. L. Verlinde, F. S. Buckner, W. C. Van Voorhis, W. G. Hol E. A. Merritt
The Double-Length Tyrosyl-Trna Synthetase From The Eukaryot Leishmania Major Forms An Intrinsically Asymmetric Pseudo-Dimer.
J. Mol. Biol. V. 409 159 2011
PubMed-ID: 21420975  |  Reference-DOI: 10.1016/J.JMB.2011.03.026

(-) Compounds

Molecule 1 - TYROSYL-TRNA SYNTHETASE
    Chains: A, B
    EC Number: 6.1.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BG1861
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LMJF14.1370
    Organism Scientific: LEISHMANIA MAJOR
    Organism Taxid: 5664

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 39)

Asymmetric Unit (2, 39)
No.NameCountTypeFull Name
1MSE37Mod. Amino AcidSELENOMETHIONINE
2TYE2Ligand/Ion4-[(2S)-2-AMINO-3-HYDROXYPROPYL]PHENOL
Biological Unit 1 (2, 21)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE
2TYE1Ligand/Ion4-[(2S)-2-AMINO-3-HYDROXYPROPYL]PHENOL
Biological Unit 2 (2, 18)
No.NameCountTypeFull Name
1MSE17Mod. Amino AcidSELENOMETHIONINE
2TYE1Ligand/Ion4-[(2S)-2-AMINO-3-HYDROXYPROPYL]PHENOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:36 , GLY A:38 , GLU A:40 , TRP A:70 , PHE A:75 , ILE A:148 , TYR A:163 , GLN A:167 , ASP A:170 , GLN A:185BINDING SITE FOR RESIDUE TYE A 701
2AC2SOFTWARETYR B:36 , GLY B:38 , GLU B:40 , TRP B:70 , PHE B:75 , ILE B:148 , TYR B:163 , GLN B:167 , ASP B:170 , GLN B:185BINDING SITE FOR RESIDUE TYE B 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P0I)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Thr A:359 -Leu A:360

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P0I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P0I)

(-) Exons   (0, 0)

(no "Exon" information available for 3P0I)

(-) 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:673
 aligned with Q4QFJ7_LEIMA | Q4QFJ7 from UniProtKB/TrEMBL  Length:682

    Alignment length:682
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678  
         Q4QFJ7_LEIMA     - --MNTDERYKLLRSVGEECIQESELRNLIEKKPLIRCYDGFEPSGRMHIAQGIFKAVNVNKCTAAGCEFVFWVADWFALMNDKVGGELEKIRIVGRYLIEVWKAAGMDMDKVLFLWSSEEITSHADTYWRMVLDIGRQNTIARIKKCCTIMGKTEGTLTAAQVLYPLMQCCDIFFLKADICQLGLDQRKVNMLAREYCDLIGRKLKPVILSHHMLAGLKQGQAKMSKSDPDSAIFMEDTEEDVARKIRQAYCPRVKQSASAITDDGAPVATDDRNPVLDYFQCVVYARPGAAATIDGTTYATYEDLEQAFVSDEVSEDALKSCLIDEVNALLEPVRQHFASNEEAHELLEAVKSYRKDGATLPLAETALPAAPAKPHACMWMPALLKVPLDVAEGMIKVTKDFIAAHPEGTVTLVLPDWSAVASDEITGVEKDISAALQVNCALLKAYGLPSSVKIVTENEVILGNCDDFWVSVIGIARKNLLSHVEELYGGEVRNAGQVIAALMRVATALMLSVSHVISTSLDGHINAFAREYTKERIDCVQTLEGRIPALHRPGAAPAVLGADDVLYLDDNDMDIRRKIKKAYSAPNEEANPVISVAQHLLAQHGALSIERGEANGGNVSYNTPEALVADCGSGALHPADLKAAVLQLLLDRSAQARALLNGELKKNMTVLRNAEKKMAK 680
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh..eeehhhhhhhhhhhh..eeeeeee......hhhhhhhhhhhhhhhhhh.eeeeeeehhhhhhhh........hhhhhhhhhhhhhhhhh.hhh.eeeeehhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh..........hhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhh.....eeee.................hhhhh.....hhhhhhhhhhh.........................hhhhhhhhhhh.......eee..eee.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...................eeeee.......hhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhh....hhhhhhhhhhhhhhhhhhh......eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...eeee.......hhhhhhhh....eeee............---------........hhhhhhhhhhhh........hhhhhhhhhhhhhhh.eee.........eee..hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p0i A  -1 HHmNTDERYKLLRSVGEECIQESELRNLIEKKPLIRCYDGFEPSGRmHIAQGIFKAVNVNKCTAAGCEFVFWVADWFALmNDKVGGELEKIRIVGRYLIEVWKAAGmDmDKVLFLWSSEEITSHADTYWRmVLDIGRQNTIARIKKCCTImGKTEGTLTAAQVLYPLmQCCDIFFLKADICQLGLDQRKVNmLAREYCDLIGRKLKPVILSHHmLAGLKQGQAKmSKSDPDSAIFmEDTEEDVARKIRQAYCPRVKQSASAITDDGAPVATDDRNPVLDYFQCVVYARPGAAATIDGTTYATYEDLEQAFVSDEVSEDALKSCLIDEVNALLEPVRQHFASNEEAHELLEAVKSYRKDGATLPLAETALPAAPAKPHACmWmPALLKVPLDVAEGmIKVTKDFIAAHPEGTVTLVLPDWSAVASDEITGVEKDISAALQVNCALLKAYGLPSSVKIVTENEVILGNCDDFWVSVIGIARKNLLSHVEELYGGEVRNAGQVIAALmRVATALmLSVSHVISTSLDGHINAFAREYTKERIDCVQTLEGRIPALHRP---------DDVLYLDDNDmDIRRKIKKAYSAPNEEANPVISVAQHLLAQHGALSIERGEANGGNVSYNTPEALVADCGSGALHPADLKAAVLQLLLDRSAQARALLNGELKKNmTVLRNAEKKmAK 680
                              |      8        18        28        38      | 48        58        68        78        88        98      |108       118       128|      138       148|      158       168       178       188 |     198       208   |   218    |  228     | 238       248       258       268       278       288       298       308       318       328       338       348       358       368       378 |     388     | 398       408       418       428       438       448       458       468       478       488       498    |  508 |     518       528       538       548    |    -    |  568    |  578       588       598       608       618       628       638       648       658       668       678  
                              |                                          45-MSE                           78-MSE                    105-MSE                 129-MSE             149-MSE          166-MSE                 190-MSE               212-MSE    223-MSE    234-MSE                                                                                                                                         378-MSE         394-MSE                                                                                                      503-MSE  |                                        553       563       573-MSE                                                                                        668-MSE   678-MSE
                              1-MSE                                                                                                   107-MSE                                                                                                                                                                                                                                                                          380-MSE                                                                                                                           510-MSE                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:536
 aligned with Q4QFJ7_LEIMA | Q4QFJ7 from UniProtKB/TrEMBL  Length:682

    Alignment length:546
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538      
         Q4QFJ7_LEIMA     - --MNTDERYKLLRSVGEECIQESELRNLIEKKPLIRCYDGFEPSGRMHIAQGIFKAVNVNKCTAAGCEFVFWVADWFALMNDKVGGELEKIRIVGRYLIEVWKAAGMDMDKVLFLWSSEEITSHADTYWRMVLDIGRQNTIARIKKCCTIMGKTEGTLTAAQVLYPLMQCCDIFFLKADICQLGLDQRKVNMLAREYCDLIGRKLKPVILSHHMLAGLKQGQAKMSKSDPDSAIFMEDTEEDVARKIRQAYCPRVKQSASAITDDGAPVATDDRNPVLDYFQCVVYARPGAAATIDGTTYATYEDLEQAFVSDEVSEDALKSCLIDEVNALLEPVRQHFASNEEAHELLEAVKSYRKDGATLPLAETALPAAPAKPHACMWMPALLKVPLDVAEGMIKVTKDFIAAHPEGTVTLVLPDWSAVASDEITGVEKDISAALQVNCALLKAYGLPSSVKIVTENEVILGNCDDFWVSVIGIARKNLLSHVEELYGGEVRNAGQVIAALMRVATALMLSVSHVISTSLDGHINAFAREYTKERIDCVQTLE 544
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----------------------------tRNA-synt_1b-3p0iB01 B:28-331                                                                                                                                                                                                                                                                                   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------tRNA-synt_1b-3p0iB02 B:28-331                                                                                                                                                                                                                                                                                   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhh..eeehhhhhhhhhhhh..eeeeeee......hhhhhhhhhhhhhhhhhh.eeeeeeehhhhhhhh........hhhhhhhhhhhhhhhhh.hhh.eeeeehhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh..........hhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhh.....eeee.................hhhhh.....hhhhhhhhhhh.........................hhhhhhhhhhh.......eee..eee.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh----------.........eeeee.......hhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhh....hhhhhhhhhhhhhhhhhhh......eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...eeee.......hhhhhhhh....eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3p0i B  -1 HHmNTDERYKLLRSVGEECIQESELRNLIEKKPLIRCYDGFEPSGRmHIAQGIFKAVNVNKCTAAGCEFVFWVADWFALmNDKVGGELEKIRIVGRYLIEVWKAAGmDmDKVLFLWSSEEITSHADTYWRmVLDIGRQNTIARIKKCCTImGKTEGTLTAAQVLYPLmQCCDIFFLKADICQLGLDQRKVNmLAREYCDLIGRKLKPVILSHHmLAGLKQGQAKmSKSDPDSAIFmEDTEEDVARKIRQAYCPRVKQSASAITDDGAPVATDDRNPVLDYFQCVVYARPGAAATIDGTTYATYEDLEQAFVSDEVSEDALKSCLIDEVNALLEPVRQHFASNEEAHELLEAVKSYRK----------ALPAAPAKPHACmWmPALLKVPLDVAEGmIKVTKDFIAAHPEGTVTLVLPDWSAVASDEITGVEKDISAALQVNCALLKAYGLPSSVKIVTENEVILGNCDDFWVSVIGIARKNLLSHVEELYGGEVRNAGQVIAALmRVATALmLSVSHVISTSLDGHINAFAREYTKERIDCVQTLE 544
                              |      8        18        28        38      | 48        58        68        78        88        98      |108       118       128|      138       148|      158       168       178       188 |     198       208   |   218    |  228     | 238       248       258       268       278       288       298       308       318       328       338       348      |  -       368       378 |     388     | 398       408       418       428       438       448       458       468       478       488       498    |  508 |     518       528       538      
                              |                                          45-MSE                           78-MSE                    105-MSE                 129-MSE             149-MSE          166-MSE                 190-MSE               212-MSE    223-MSE    234-MSE                                                                                                                  355        366         378-MSE         394-MSE                                                                                                      503-MSE  |                                  
                              1-MSE                                                                                                   107-MSE                                                                                                                                                                                                                                                                          380-MSE                                                                                                                           510-MSE
   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  (0, 0)

(no "SCOP Domain" information available for 3P0I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P0I)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: HUP (230)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q4QFJ7_LEIMA | Q4QFJ7)
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: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:0004831    tyrosine-tRNA ligase activity    Catalysis of the reaction: L-tyrosine + ATP + tRNA(Tyr) = L-tyrosyl-tRNA(Tyr) + AMP + diphosphate + 2 H(+).
    GO:0004832    valine-tRNA ligase activity    Catalysis of the reaction: L-valine + ATP + tRNA(Val) = L-valyl-tRNA(Val) + AMP + diphosphate + 2 H(+).
biological process
    GO:0006418    tRNA aminoacylation for protein translation    The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, to be used in ribosome-mediated polypeptide synthesis.
    GO:0006438    valyl-tRNA aminoacylation    The process of coupling valine to valyl-tRNA, catalyzed by valyl-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.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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        Q4QFJ7_LEIMA | Q4QFJ7: 3p0h 3p0j

(-) Related Entries Specified in the PDB File

3p0h 3p0j