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(-) Description

Title :  TERMINAL URIDYLYL TRANSFERASE 4 FROM TRYPANOSOMA BRUCEI WITH BOUND UTP
 
Authors :  H. Luecke, J. Stagno
Date :  02 Oct 06  (Deposition) - 20 Feb 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Tutase, Trypanosoma, Nucleotidyltransferase, Utp-Binding, Rna Editing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Stagno, I. Aphasizheva, A. Rosengarth, H. Luecke, R. Aphasizhev
Utp-Bound And Apo Structures Of A Minimal Rna Uridylyltransferase.
J. Mol. Biol. V. 366 882 2007
PubMed-ID: 17189640  |  Reference-DOI: 10.1016/J.JMB.2006.11.065
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNA URIDYLYL TRANSFERASE
    Chains: A, B
    EC Number: 2.7.7.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: 841358, TB11.01.7300
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 5691

 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, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2UTP1Ligand/IonURIDINE 5'-TRIPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2UTP1Ligand/IonURIDINE 5'-TRIPHOSPHATE
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2UTP-1Ligand/IonURIDINE 5'-TRIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:66 , ASP A:68 , UTP A:501 , HOH A:509 , HOH A:532BINDING SITE FOR RESIDUE MG A 401
2AC2SOFTWAREPHE A:52 , GLY A:53 , SER A:54 , SER A:65 , ASP A:66 , ASP A:68 , GLY A:144 , ASN A:147 , SER A:148 , LYS A:169 , LYS A:173 , THR A:187 , SER A:188 , TYR A:189 , MG A:401 , HOH A:505 , HOH A:527 , HOH A:532 , HOH A:560 , HOH A:627 , HOH A:639 , HOH A:652 , HOH A:657BINDING SITE FOR RESIDUE UTP A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2IKF)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2IKF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2IKF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2IKF)

(-) Exons   (0, 0)

(no "Exon" information available for 2IKF)

(-) 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:326
 aligned with Q381M1_TRYB2 | Q381M1 from UniProtKB/TrEMBL  Length:333

    Alignment length:331
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332 
         Q381M1_TRYB2     3 PSPAVVGRSLVNSFKQFVSKDLHTRHVDATYRLVLDCVAAVDPLMRLYTFGSTVVYGVHEKGSDVDFVVLNKTDVEDGKGGDAATQVAKGLQADILAKLARVIRQKHLSWNVEEVRRTRVPVVRVKGGGAVDFDITAYRRNGVRNSALLRAYFEQNPPCRWLSMSIKRWSKQTGLNASVIGGSITSYGFNLMVVYYLLQRNHLQFVPPSTIDVSRVEPLPPHLPLEEPADEGLELGTQVLDFLHFFLHEFDSDKQVISLNRPGITTKEELDWTKSAEDFARMNGEKVHYQWCIEDPYELNLNVGRNVTPLKRDFLRRHLEKARDTALLTIV 333
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.....-----.hhhhhhhhhhhhhhhhh...eeeeehhhhhhh.......eeeeeehhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh...eeeee......eeeee.....eeeeee..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh......hhhhhhhhhh...............hhhhhhhhhhhhhhhhhh.....eee.......eehhhhh.hhhhhh..ee..ee.....ee..............hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ikf A   3 PSPAVVGRSLVNSFKQFVS-----RHVDATYRLVLDCVAAVDPLMRLYTFGSTVVYGVHEKGSDVDFVVLNKTDVEDGKGGDAATQVAKGLQADILAKLARVIRQKHLSWNVEEVRRTRVPVVRVKGGGAVDFDITAYRRNGVRNSALLRAYFEQNPPCRWLSMSIKRWSKQTGLNASVIGGSITSYGFNLMVVYYLLQRNHLQFVPPSTIDVSRVEPLPPHLPLEEPADEGLELGTQVLDFLHFFLHEFDSDKQVISLNRPGITTKEELDWTKSAEDFARMNGEKVHYQWCIEDPYELNLNVGRNVTPLKRDFLRRHLEKARDTALLTIV 333
                                    12        |-    |   32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332 
                                             21    27                                                                                                                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:310
 aligned with Q381M1_TRYB2 | Q381M1 from UniProtKB/TrEMBL  Length:333

    Alignment length:330
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332
         Q381M1_TRYB2     3 PSPAVVGRSLVNSFKQFVSKDLHTRHVDATYRLVLDCVAAVDPLMRLYTFGSTVVYGVHEKGSDVDFVVLNKTDVEDGKGGDAATQVAKGLQADILAKLARVIRQKHLSWNVEEVRRTRVPVVRVKGGGAVDFDITAYRRNGVRNSALLRAYFEQNPPCRWLSMSIKRWSKQTGLNASVIGGSITSYGFNLMVVYYLLQRNHLQFVPPSTIDVSRVEPLPPHLPLEEPADEGLELGTQVLDFLHFFLHEFDSDKQVISLNRPGITTKEELDWTKSAEDFARMNGEKVHYQWCIEDPYELNLNVGRNVTPLKRDFLRRHLEKARDTALLTI 332
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..--.eeeeehhhhhhh.......eeeeee...-------------.hhhhhhh.hhhhhhhhhhhh...eeee.-----..eeee......eeeee..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh......hhhhh....................hhhhhhhhhhhhhhhhhh.....ee........ee.hhhh.hhhhhhhhhhh........................hhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ikf B   3 PSPAVVGRSLVNSFKQFVSKDLHTRHVDATYRLVLDCVAAVD--MRLYTFGSTVVYGVHEKGSDVDFVVLNKT-------------VAKGLQADILAKLARVIRQKHLSWNVEEV-----PVVRVKGGGAVDFDITAYRRNGVRNSALLRAYFEQNPPCRWLSMSIKRWSKQTGLNASVIGGSITSYGFNLMVVYYLLQRNHLQFVPPSTIDVSRVEPLPPHLPLEEPADEGLELGTQVLDFLHFFLHEFDSDKQVISLNRPGITTKEELDWTKSAEDFARMNGEKVHYQWCIEDPYELNLNVGRNVTPLKRDFLRRHLEKARDTALLTI 332
                                    12        22        32        42 |  |   52        62        72  |      -      | 92       102       112    |    -|      132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332
                                                                    44 47                          75            89                         117   123
   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 2IKF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2IKF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IKF)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q381M1_TRYB2 | Q381M1)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine 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.
cellular component
    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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        Q381M1_TRYB2 | Q381M1: 2nom 2q0c 2q0d 2q0e 2q0f 2q0g 5kal

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