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(-) Description

Title :  CRYSTAL STRUCTURE OF RTCA.ATP.MN TERNARY COMPLEX
 
Authors :  A. K. Chakravarty, P. Smith, S. Shuman
Date :  19 Sep 11  (Deposition) - 28 Dec 11  (Release) - 18 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Cyclization Of Rna 3'-Phosphate Ends, Transferase, Cyclase Family (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. K. Chakravarty, P. Smith, S. Shuman
Structures Of Rna 3'-Phosphate Cyclase Bound To Atp Reveal The Mechanism Of Nucleotidyl Transfer And Metal-Assisted Catalysis.
Proc. Natl. Acad. Sci. Usa V. 108 21034 2011
PubMed-ID: 22167800  |  Reference-DOI: 10.1073/PNAS.1115560108

(-) Compounds

Molecule 1 - RNA 3'-TERMINAL PHOSPHATE CYCLASE
    ChainsA
    EC Number6.5.1.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneB4475, JW5688, RTCA, YHGJ, YHGK
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    StrainK12
    SynonymRNA CYCLASE, RNA-3'-PHOSPHATE CYCLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

Asymmetric/Biological Unit (5, 6)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2EDO2Ligand/Ion1,2-ETHANEDIOL
3GOL1Ligand/IonGLYCEROL
4MN1Ligand/IonMANGANESE (II) ION
5SO41Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:14 , GLY A:16 , GLY A:17 , GLN A:18 , ARG A:21 , ARG A:40 , ARG A:43 , GLN A:104 , SER A:129 , ALA A:130 , PRO A:131 , PHE A:251 , TYR A:284 , ASP A:287 , GLN A:288 , ASN A:309 , HOH A:341 , HOH A:380 , HOH A:386 , HOH A:430 , HOH A:567 , HOH A:589 , MN A:601 , HOH A:603 , HOH A:634BINDING SITE FOR RESIDUE ATP A 501
2AC2SOFTWAREGLU A:14 , HOH A:392 , HOH A:418 , ATP A:501BINDING SITE FOR RESIDUE MN A 601
3AC3SOFTWARELYS A:45 , ARG A:50 , SER A:95 , HOH A:414BINDING SITE FOR RESIDUE SO4 A 340
4AC4SOFTWARETHR A:35 , THR A:37 , ARG A:76 , ASP A:88 , PRO A:116 , SER A:117 , ARG A:118BINDING SITE FOR RESIDUE GOL A 502
5AC5SOFTWAREGLN A:104 , ILE A:136 , LEU A:140 , GLN A:288 , HOH A:445 , HOH A:625BINDING SITE FOR RESIDUE EDO A 503
6AC6SOFTWAREARG A:137 , ARG A:138 , HOH A:647BINDING SITE FOR RESIDUE EDO A 504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:161 -Pro A:162
2Gly A:232 -Pro A:233

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RTCPS01287 RNA 3'-terminal phosphate cyclase signature.RTCA_ECOLI157-167  1A:158-168

(-) Exons   (0, 0)

(no "Exon" information available for 3TUX)

(-) 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:336
 aligned with RTCA_ECOLI | P46849 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:336
                                    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      
           RTCA_ECOLI     3 RMIALDGAQGEGGGQILRSALSLSMITGQPFTITSIRAGRAKPGLLRQHLTAVKAATEICGATVEGAELGSQRLLFRPGTVRGGDYRFAIGSAGSCTLVLQTVLPALWFADGPSRVEVSGGTDNPSAPPADFIRRVLEPLLAKIGIHQQTTLLRHGFYPAGGGVVATEVSPVASFNTLQLGERGNIVQMRGEVLLAGVPRHVAEREIATLAGSFSLHEQNIHNLPRDQGPGNTVSLEVESENITERFFVVGEKRVSAEVVAAQLVKEVKRYLASTAAVGEYLADQLVLPMALAGAGEFTVAHPSCHLLTNIAVVERFLPVRFSLIETDGVTRVSIE 338
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee.......hhhhhhhhhhhhhhh..eeee...........hhhhhhhhhhhhhhhh.eee........eeee.......eeeee.....hhhhhhhhhhhhhh.....eeeeeee........hhhhhhhhhhhhhhhhh.eeeeeeee........eeeeeeee...............eeeeeeeeeee..hhhhhhhhhhhhhhhh...eeeeeeehhhhh.eeeeeeeeee...eeeeeee.....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh...eeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------RTC        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3tux A   4 RMIALDGAQGEGGGQILRSALSLSMITGQPFTITSIRAGRAKPGLLRQHLTAVKAATEICGATVEGAELGSQRLLFRPGTVRGGDYRFAIGSAGSCTLVLQTVLPALWFADGPSRVEVSGGTDNPSAPPADFIRRVLEPLLAKIGIHQQTTLLRHGFYPAGGGVVATEVSPVASFNTLQLGERGNIVQMRGEVLLAGVPRHVAEREIATLAGSFSLHEQNIHNLPRDQGPGNTVSLEVESENITERFFVVGEKRVSAEVVAAQLVKEVKRYLASTAAVGEYLADQLVLPMALAGAGEFTVAHPSSNLLTNIAVVERFLPVRFSLIETDGVTRVSIE 339
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333      

   Legend:   → Mismatch (orange background)
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  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 3TUX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TUX)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RTCA_ECOLI | P46849)
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:0003963    RNA-3'-phosphate cyclase activity    Catalysis of the reaction: ATP + RNA 3'-terminal-phosphate = AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RTCA_ECOLI | P468491qmh 1qmi 3kgd 3tut 3tv1 3tw3

(-) Related Entries Specified in the PDB File

1qmh 1qmi 3kgd 3tut 3tv1 3tw3