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(-) Description

Title :  STRUCTURE AND MECHANISM OF RNA LIGASE
 
Authors :  C. K. Ho, L. K. Wang, C. D. Lima, S. Shuman
Date :  22 Jan 04  (Deposition) - 24 Feb 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Ribonucleic Acid Ligase, Rna Repair, T4 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. K. Ho, L. K. Wang, C. D. Lima, S. Shuman
Structure And Mechanism Of Rna Ligase.
Structure V. 12 327 2004
PubMed-ID: 14962393  |  Reference-DOI: 10.1016/S0969-2126(04)00023-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNA LIGASE 2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET16B
    Expression System Strain: BL21 DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN (RESIDUES 1-249)
    Gene: Y10A, 24.1
    Organism Scientific: ENTEROBACTERIA PHAGE T4
    Organism Taxid: 10665

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:5 , GLU A:34 , LYS A:35 , ILE A:36 , ASN A:40 , ARG A:55 , GLU A:99 , PHE A:119 , ALA A:150 , VAL A:207 , LYS A:225 , LYS A:227 , HOH A:317 , HOH A:355BINDING SITE FOR RESIDUE AMP A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1S68)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1S68)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S68)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1S68)

(-) Exons   (0, 0)

(no "Exon" information available for 1S68)

(-) 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:233
 aligned with RLIG2_BPT4 | P32277 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:233
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230   
           RLIG2_BPT4     1 MFKKYSSLENHYNSKFIEKLYSLGLTGGEWVAREKIHGTNFSLIIERDKVTCAKRTGPILPAEDFFGYEIILKNYADSIKAVQDIMETSAVVSYQVFGEFAGPGIQKNVDYCDKDFYVFDIIVTTESGDVTYVDDYMMESFCNTFKFKMAPLLGRGKFEELIKLPNDLDSVVQDYNFTVDHAGLVDANKCVWNAEAKGEVFTAEGYVLKPCYPSWLRNGNRVAIKCKNSKFSE 233
               SCOP domains d1s68a_ A: RNA ligase 2, N-terminal domain                                                                                                                                                                                                SCOP domains
               CATH domains ------1s68A01 A:7-37,A:151-233       1s68A02 A:38-150 DNA ligase/mRNA capping enzyme                                                                  1s68A01 A:7-37,A:151-233  [code=3.30.1490.70, no name defined]                      CATH domains
               Pfam domains ---------------------------RNA_ligase-1s68A01 A:28-227                                                                                                                                                                             ------ Pfam domains
         Sec.struct. author ........ee..hhhhhhhhhhhh.....eeeee....eeeeeeee...eeeee..ee.........hhhhhhhhhhhhhhhhhhhhhhheeeeeeeeeee.............eeeeeeeeeee....eee.hhhhhhhhhhhhh.ee..eeeeehhhhhh........hhhhhhhhhhhhhhhhhhhh..............eeeeee.............eeee.hhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s68 A   1 MFKKYSSLENHYNSKFIEKLYSLGLTGGEWVAREKIHGTNFSLIIERDKVTCAKRTGPILPAEDFFGYEIILKNYADSIKAVQDIMETSAVVSYQVFGEFAGPGIQKNVDYCDKDFYVFDIIVTTESGDVTYVDDYMMESFCNTFKFKMAPLLGRGKFEELIKLPNDLDSVVQDYNFTVDHAGLVDANKCVWNAEAKGEVFTAEGYVLKPCYPSWLRNGNRVAIKCKNSKFSE 233
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
   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  (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  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: DNA_ligase (17)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RLIG2_BPT4 | P32277)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0042245    RNA repair    Any process that results in the repair of damaged RNA.

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  1s68
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 Related Entries

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

UniProtKB/Swiss-Prot
        RLIG2_BPT4 | P32277: 2hvq 2hvr 2hvs

(-) Related Entries Specified in the PDB File

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