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(-) Description

Title :  HIGH RESOLUTION CRYSTAL STRUCTURE OF AN EDITOSOME ENZYME FROM TRYPANOSOMA BRUCEI: RNA EDITING LIGASE 1
 
Authors :  J. Deng, A. Schnaufer, R. Salavati, K. D. Stuart, W. G. Hol
Date :  07 Sep 04  (Deposition) - 07 Dec 04  (Release) - 10 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Rna Editing, Ligase, Trypanosoma Brucei, (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Deng, A. Schnaufer, R. Salavati, K. D. Stuart, W. G. Hol
High Resolution Crystal Structure Of A Key Editosome Enzyme From Trypanosoma Brucei: Rna Editing Ligase 1.
J. Mol. Biol. V. 343 601 2004
PubMed-ID: 15465048  |  Reference-DOI: 10.1016/J.JMB.2004.08.041

(-) Compounds

Molecule 1 - RNA EDITING LIGASE MP52
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSKB3
    Expression System Strain: BL21GOLD DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: ADENYLATION DOMAIN
    Gene: MP52
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 5691

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREATP A:501 , HOH A:514 , HOH A:520 , HOH A:528 , HOH A:530BINDING SITE FOR RESIDUE MG A 502
2AC2SOFTWARETYR A:58 , ILE A:59 , GLU A:60 , ILE A:61 , GLU A:86 , LYS A:87 , VAL A:88 , ASN A:92 , ARG A:111 , GLU A:159 , PHE A:209 , VAL A:286 , LYS A:307 , ARG A:309 , MG A:502 , HOH A:514 , HOH A:520 , HOH A:528 , HOH A:530 , HOH A:536 , HOH A:587 , HOH A:634 , HOH A:650 , HOH A:777 , HOH A:829 , HOH A:871 , HOH A:886BINDING SITE FOR RESIDUE ATP A 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:197 -Pro A:198

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1XDN)

(-) 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:265
 aligned with RLGM1_TRYB2 | P86927 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:265
                                    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     
          RLGM1_TRYB2    52 QSDFSPYIEIDLPSESRIQSLHKSGLAAQEWVACEKVHGTNFGIYLINQGDHEVVRFAKRSGIMDPNENFFGYHILIDEFTAQIRILNDLLKQKYGLSRVGRLVLNGELFGAKYKHPLVPKSEKWCTLPNGKKFPIAGVQIQREPFPQYSPELHFFAFDIKYSVSGAEEDFVLLGYDEFVEFSSKVPNLLYARALVRGTLDECLAFDVENFMTPLPALLGLGNYPLEGNLAEGVVIRHVRRGDPAVEKHNVSTIIKLRCSSFMEL 316
               SCOP domains d1xdna_ A: RNA editing ligase MP52                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1xdnA01 A:52-89,A:245-316             1xdnA02 A:90-244 DNA ligase/mRNA capping enzyme                                                                                                            1xdnA01 A:52-89,A:245-316  [code=3.30.1490.70, no name defined]          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhh.eeeeee...eeeeeeeeee..eeeeeeee..ee........hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeeee...........eee.....eee.hhh..........eeeeeeeeeeeeee...hhh.eee.hhhhhhhhhhh....ee....eeehhhhhhh.hhhhh..hhhhhh.............eeeeee....hhhhhh.....eeeeehhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xdn A  52 QSDFSPYIEIDLPSESRIQSLHKSGLAAQEWVACEKVHGTNFGIYLINQGDHEVVRFAKRSGImDPNENFFGYHILIDEFTAQIRILNDLLKQKYGLSRVGRLVLNGELFGAKYKHPLVPKSEKWCTLPNGKKFPIAGVQIQREPFPQYSPELHFFAFDIKYSVSGAEEDFVLLGYDEFVEFSSKVPNLLYARALVRGTLDECLAFDVENFmTPLPALLGLGNYPLEGNLAEGVVIRHVRRGDPAVEKHNVSTIIKLRCSSFmEL 316
                                    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  |  
                                                                                         115-MSE                                                                                                                                             263-MSE                                            314-MSE
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RLGM1_TRYB2 | P86927)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003972    RNA ligase (ATP) activity    Catalysis of the reaction: ATP + ribonucleotide(n) + ribonucleotide(m) = AMP + diphosphate + ribonucleotide(n+m).
    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.
biological process
    GO:0009451    RNA modification    The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically.
cellular component
    GO:0031019    mitochondrial mRNA editing complex    An mRNA editing complex found in the mitochondrion. The best characterized example is that of Trypanosoma brucei, which catalyzes the insertion and deletion of uridylates.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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