Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  LEISHMANIA MAJOR METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH METHIONYLADENYLATE AND PYROPHOSPHATE
 
Authors :  E. T. Larson, E. A. Merritt, Medical Structural Genomics Of Pathog Protozoa (Msgpp)
Date :  27 Oct 09  (Deposition) - 27 Oct 10  (Release) - 23 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Leishmania, Parasite, Aminoacyl-Trna Synthetase, Trna Ligase, Aars, Metrs, Methionine, Translation, Atp-Binding, Nucleotide-Binding, Structural Genomics, Msgpp, Ligase, Medical Structural Genomics Of Pathogenic Protozoa (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. T. Larson, J. E. Kim, F. H. Zucker, A. Kelley, N. Mueller, A. J. Napuli C. L. Verlinde, E. Fan, F. S. Buckner, W. C. Van Voorhis, E. A. Merritt, W. G. Hol
Structure Of Leishmania Major Methionyl-Trna Synthetase In Complex With Intermediate Products Methionyladenylate And Pyrophosphate.
Biochimie V. 93 570 2011
PubMed-ID: 21144880  |  Reference-DOI: 10.1016/J.BIOCHI.2010.11.015

(-) Compounds

Molecule 1 - METHIONYL-TRNA SYNTHETASE
    Chains: A
    EC Number: 6.1.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 206-747
    Gene: LMJF21.0810, METRS
    Organism Scientific: LEISHMANIA MAJOR
    Organism Taxid: 5664

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 15)

Asymmetric/Biological Unit (6, 15)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2FMT4Ligand/IonFORMIC ACID
3ME81Ligand/Ion[[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL] (2S)-2-AZANYL-4-METHYLSULFANYL-BUTANOATE
4MG1Ligand/IonMAGNESIUM ION
5POP1Ligand/IonPYROPHOSPHATE 2-
6ZN1Ligand/IonZINC ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:216 , ILE A:217 , TYR A:218 , TYR A:219 , HIS A:225 , GLY A:227 , HIS A:228 , SER A:231 , ASP A:256 , TRP A:443 , ALA A:446 , ASN A:449 , TYR A:450 , GLY A:484 , ASP A:486 , ILE A:487 , HIS A:491 , HIS A:513 , GLY A:514 , TRP A:515 , TRP A:516 , LYS A:522 , ILE A:523 , LYS A:525 , POP A:802 , MG A:803 , HOH A:1058BINDING SITE FOR RESIDUE ME8 A 801
02AC2SOFTWAREASN A:221 , HIS A:225 , HIS A:228 , LYS A:261 , LYS A:522 , SER A:524 , LYS A:525 , SER A:526 , ME8 A:801 , MG A:803 , EDO A:811 , HOH A:1002 , HOH A:1057 , HOH A:1118BINDING SITE FOR RESIDUE POP A 802
03AC3SOFTWAREME8 A:801 , POP A:802 , HOH A:1057 , HOH A:1058 , HOH A:1118BINDING SITE FOR RESIDUE MG A 803
04AC4SOFTWAREHIS A:258 , GLU A:307 , HOH A:1211 , HOH A:1212BINDING SITE FOR RESIDUE ZN A 804
05AC5SOFTWAREHIS A:364 , LYS A:522 , SER A:524 , SER A:526 , LEU A:527 , POP A:802 , HOH A:1118BINDING SITE FOR RESIDUE EDO A 811
06AC6SOFTWARETYR A:230 , GLY A:514 , ASN A:554 , PHE A:555 , ASP A:557BINDING SITE FOR RESIDUE EDO A 812
07AC7SOFTWAREARG A:240 , ARG A:243 , ASP A:294BINDING SITE FOR RESIDUE EDO A 813
08AC8SOFTWARETHR A:341 , ASP A:415 , TYR A:494 , FMT A:822BINDING SITE FOR RESIDUE EDO A 814
09AC9SOFTWAREGLU A:361 , ASP A:486 , LEU A:488 , LYS A:489 , FMT A:821 , HOH A:1187BINDING SITE FOR RESIDUE EDO A 815
10BC1SOFTWAREASP A:694 , ARG A:703BINDING SITE FOR RESIDUE EDO A 816
11BC2SOFTWARETHR A:278 , SER A:282 , LYS A:285BINDING SITE FOR RESIDUE EDO A 817
12BC3SOFTWAREGLU A:404 , THR A:408 , LYS A:489 , EDO A:815BINDING SITE FOR RESIDUE FMT A 821
13BC4SOFTWARELEU A:413 , EDO A:814 , HOH A:1064BINDING SITE FOR RESIDUE FMT A 822
14BC5SOFTWAREHIS A:631BINDING SITE FOR RESIDUE FMT A 823
15BC6SOFTWAREASP A:638BINDING SITE FOR RESIDUE FMT A 824

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Val A:397 -Pro A:398
2Trp A:476 -Pro A:477
3Leu A:626 -Pro A:627

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KFL)

(-) 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:530
 aligned with Q4QCD2_LEIMA | Q4QCD2 from UniProtKB/TrEMBL  Length:747

    Alignment length:530
                                   216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736
         Q4QCD2_LEIMA   207 KQKVFFATTPIYYVNASPHIGHVYSTLIVDVLGRYHRVKGEEVFVMTGTDEHGQKVAEAAAKQGVSPMDFTTSVSSEFKQCFQEMNYDMNYFIRTTNPTHEKLVQDIWKKLAAKGDIYLGKYEGWYSVSDESFLTAQNVADGVDRDGKPCKVSLESGHVVTWVEEENYMFRLSAFRERLLKYFHDHPNCIVPEFRRREVIKTVEKGLFDLSISRKRESVMNWSIPVPGDERHCIYVWLDALFNYYTGALTRVATDGTETLDEDHHALNRWPADVHVVGKDILKFHAIYWPAFLMSAELPLPERLVSHGWWTKDHKKISKSLGNAFDPVEKAKEFGIDALKYFLMRESNFQDDGDYSDKNMVARLNGELADTLGNLVSRCVAPKINVNGMWPEPAEYSESDKTLIASLNNLAGTVDHYYCLPDIQHALIAIFDVLRSLNAYVTENAPWKLVKMDTARLGTVLYVTMEGLRICTMFLQPVMPQKAKEIMDALGVPEAARVGMENYLFGIVKPGTKIAGLAEGQVVFQKVTLP 736
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----tRNA-synt_1g-3kflA01 A:211-586                                                                                                                                                                                                                                                                                                                                                          ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhhh.eeeeeeeeeee....eeehhh.eeeee.....eeeee.......eeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhh...ee.eee.hhhh....ee..eeeeeehhhhhhhhhhhhhhheee.....eee.............eeeee..hhhhhhhhhhhhhhhh.......eeee..eee..ee.........hhhhhhhhhhhhhhhhhhhhhh.....ee.hhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhh.hhhhh........................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kfl A 207 KQKVFFATTPIYYVNASPHIGHVYSTLIVDVLGRYHRVKGEEVFVMTGTDEHGQKVAEAAAKQGVSPMDFTTSVSSEFKQCFQEMNYDMNYFIRTTNPTHEKLVQDIWKKLAAKGDIYLGKYEGWYSVSDESFLTAQNVADGVDRDGKPCKVSLESGHVVTWVEEENYMFRLSAFRERLLKYFHDHPNCIVPEFRRREVIKTVEKGLFDLSISRKRESVMNWSIPVPGDERHCIYVWLDALFNYYTGALTRVATDGTETLDEDHHALNRWPADVHVVGKDILKFHAIYWPAFLMSAELPLPERLVSHGWWTKDHKKISKSLGNAFDPVEKAKEFGIDALKYFLMRESNFQDDGDYSDKNMVARLNGELADTLGNLVSRCVAPKINVNGMWPEPAEYSESDKTLIASLNNLAGTVDHYYCLPDIQHALIAIFDVLRSLNAYVTENAPWKLVKMDTARLGTVLYVTMEGLRICTMFLQPVMPQKAKEIMDALGVPEAARVGMENYLFGIVKPGTKIAGLAEGQVVFQKVTLP 736
                                   216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736
   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 3KFL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: HUP (230)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q4QCD2_LEIMA | Q4QCD2)
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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0004825    methionine-tRNA ligase activity    Catalysis of the reaction: ATP + L-methionine + tRNA(Met) = AMP + diphosphate + L-methionyl-tRNA(Met).
    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:0006431    methionyl-tRNA aminoacylation    The process of coupling methionine to methionyl-tRNA, catalyzed by methionyl-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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FMT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ME8  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    POP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:626 - Pro A:627   [ RasMol ]  
    Trp A:476 - Pro A:477   [ RasMol ]  
    Val A:397 - Pro A:398   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3kfl
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q4QCD2_LEIMA | Q4QCD2
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  6.1.1.10
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q4QCD2_LEIMA | Q4QCD2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3KFL)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3KFL)