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(-) Description

Title :  TRNA PROCESSING ENZYME COMPLEX 3
 
Authors :  S. Yamashita, D. Takeshita, K. Tomita
Date :  23 Jul 13  (Deposition) - 01 Jan 14  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.31
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Terminal Nucleotide Transferase, Transferase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Yamashita, D. Takeshita, K. Tomita
Translocation And Rotation Of Trna During Template-Independent Rna Polymerization By Trna Nucleotidyltransferase
Structure V. 22 315 2014
PubMed-ID: 24389024  |  Reference-DOI: 10.1016/J.STR.2013.12.002

(-) Compounds

Molecule 1 - RNA (74-MER)
    Chains: A, B
    Engineered: YES
    Organism Scientific: THERMOTOGA MARITIMA MSB8
    Organism Taxid: 243274
    Synthetic: YES
 
Molecule 2 - POLY A POLYMERASE
    Chains: C, D
    EC Number: 2.7.7.72
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PCNB2
    Organism Scientific: SYNTHETIC CONSTRUCT, AQUIFEX AEOLICUS (STRAIN VF5)
    Organism Taxid: 32630, 224324
    Strain: VF5

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 70)

Asymmetric Unit (2, 70)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
2UNK66Mod. Amino Acid
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2UNK-1Mod. Amino Acid
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2UNK-1Mod. Amino Acid

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREC A:74 , GLY C:42 , ARG C:45 , ASP C:58 , ARG C:188BINDING SITE FOR RESIDUE SO4 C 1001
2AC2SOFTWAREGLY C:54 , TYR C:55 , ASN C:56BINDING SITE FOR RESIDUE SO4 C 1002
3AC3SOFTWAREC B:74 , GLY D:42 , ARG D:45 , ASP D:58 , ARG D:188 , ARG D:191BINDING SITE FOR RESIDUE SO4 D 1001
4AC4SOFTWAREGLY D:54 , TYR D:55 , ASN D:56BINDING SITE FOR RESIDUE SO4 D 1002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ile D:92 -Lys D:93
2Lys D:93 -Arg D:94

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3WFS)

(-) 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:RNA  Length:74
                                                                                                          
                 3wfs A   1 GGCCAGGUAGCUCAGUUGGUAGAGCACUGGACUGAAAAUCCAGGUGUCGGCGGUUCGAUUCCGCCCCUGGCCAC  74
                                    10        20        30        40        50        60        70    


Chain B from PDB  Type:RNA  Length:74
                                                                                                          
                 3wfs B   1 GGCCAGGUAGCUCAGUUGGUAGAGCACUGGACUGAAAAUCCAGGUGUCGGCGGUUCGAUUCCGCCCCUGGCCAC  74
                                    10        20        30        40        50        60        70    


Chain C from PDB  Type:PROTEIN  Length:436
 aligned with O67911_AQUAE | O67911 from UniProtKB/TrEMBL  Length:512

    Alignment length:500
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504
         O67911_AQUAE     5 EIVSSGKHTLHGLNFYLSYFDDVAKVLPREHYCFIVGGWVRDRILGEPVGYNIDVDFLTTADPVELAKNFAKRIGGHFFVFEKRGFLIKRPTIASVVLHLPPYRYRFDFSPLKGKDLEKALIEDLKERDFTANAIAVNLDDVLSIGAKQTIVYDPTGGIKDLEQGLLRPVSIENLKRDPVRVLRGFRIAIEKNLQLTEDFYEFVKEDPRIVLKSAVERITHELFKIMKEKTAHKVIRELYEYGVLEAIIPEIGRLREVKDQGEHHIYPLDEHTLKTLEYLEQVIEDRAKYLSAELLENFGKKRVLGEFTDVELLKWGALFHDIGKPQTFAVREGKVTFYEHDKVGAQIVREIGERLRWGDEATEFVAKLVRHHLRPFFLREAFKKGELKRRGMANFWRECGDIAPHLFLLSIADAMASGDEEEDIKALMETIAELESFNRNEMKEEIQKPLLNGDEIMEILGIKPGKIVGILKKALLEAQIDGKVETKEEAIEFIKRSTK 504
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ...---------....................eeeeeeeeeeeeeeeeehhhhhhhhh-..hhhhhhhhhhhhhh.eeeee.--------..eeeeeee....eeeeeeee....hhhhhhhhhhh.........eee.....------..ee...hhhhhhhh.-----hhhhhhhh-hhhhhhhhhhhhh----hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....-------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee...eehhhhhhhhhhh........--------...hhhhhhhhhhhhhhhhh.................hhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...------------------------hhhhhhhhhhhhhhhh--.hhhhhhhhhhhhh Sec.struct. author (1)
     Sec.struct. author (2) ---------------------------------------------------eeeeeeee----------------------------------------------------------------------------------------------------------eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wfs C   5 xxx---------LNFYLSYFDDVAKVLPREHYCFIVGGWVRDRILGEPVGYNIDVDFLTTADPVELAKNFAKRIGGHFFVFE--------PTIASVVLHLPPYRYRFDFSPLKGKDLEKALIEDLKERDFTANAIAVNLDDVL------TIVYDPTGGIKDLEQGLLRPVSIENLKRDPVRVLRGFRIAIEKNLQLTEDFYEFVKEDPRIVLKSAVERITHELFKIMKEKTAHKVIRELYEYGVLEAIIPEIGRLREVKD-------PLDEHTLKTLEYLEQVIEDRAKYLSAELLENFGKKRVLGEFTDVELLKWGALFHDIGKPQT--------TFYEHDKVGAQIVREIGERLRWGDEATEFVAKLVRHHLRPFFLREAFKKGELKRRGMANFWRECGDIAPHLFLLSIADAMASGDEEEDIKALMETIAELESFNRNEMK------------------------xxxxxxxxxxxxxxxx--xxxxxxxxxxxxxx 504
                            |||      -  |     24        34        44        54        64        74        84 |       -|      104       114       124       134       144  |    154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       | -      |344       354       364       374       384       394       404       414       424       434       444   |     -         -       474|||||||484||||  |494|||||||504
                            |||        17                                                                   86       95                                                 147    154                                                                                                           264     272                                                         332      341                                                                                                        448                      473-UNK||482-UNK||  493-UNK||502-UNK
                            5-UNK                                                                                                                                                                                                                                                                                                                                                                                                                                                                              474-UNK||483-UNK|  |494-UNK||503-UNK
                             6-UNK                                                                                                                                                                                                                                                                                                                                                                                                                                                                              475-UNK||484-UNK  ||495-UNK||504-UNK
                              7-UNK                                                                                                                                                                                                                                                                                                                                                                                                                                                                              476-UNK| 485-UNK || 496-UNK|   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  477-UNK  486-UNK||  497-UNK   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   478-UNK  487-UNK|   498-UNK  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    479-UNK  488-UNK    499-UNK 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     480-UNK    491-UNK  500-UNK
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      481-UNK    492-UNK  501-UNK


Chain D from PDB  Type:PROTEIN  Length:445
 aligned with O67911_AQUAE | O67911 from UniProtKB/TrEMBL  Length:512

    Alignment length:500
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504
         O67911_AQUAE     5 EIVSSGKHTLHGLNFYLSYFDDVAKVLPREHYCFIVGGWVRDRILGEPVGYNIDVDFLTTADPVELAKNFAKRIGGHFFVFEKRGFLIKRPTIASVVLHLPPYRYRFDFSPLKGKDLEKALIEDLKERDFTANAIAVNLDDVLSIGAKQTIVYDPTGGIKDLEQGLLRPVSIENLKRDPVRVLRGFRIAIEKNLQLTEDFYEFVKEDPRIVLKSAVERITHELFKIMKEKTAHKVIRELYEYGVLEAIIPEIGRLREVKDQGEHHIYPLDEHTLKTLEYLEQVIEDRAKYLSAELLENFGKKRVLGEFTDVELLKWGALFHDIGKPQTFAVREGKVTFYEHDKVGAQIVREIGERLRWGDEATEFVAKLVRHHLRPFFLREAFKKGELKRRGMANFWRECGDIAPHLFLLSIADAMASGDEEEDIKALMETIAELESFNRNEMKEEIQKPLLNGDEIMEILGIKPGKIVGILKKALLEAQIDGKVETKEEAIEFIKRSTK 504
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ...---------....................eeeeeeeeeeeeeeeee..eeeeeeee..hhhhhhhhhhhhhh.eeeeee.........eeeeeeee....eeeeeeee........................eeehhhhh------hhhhhhhhhhhhhhh.ee...hhhhhhhh.hhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....-------..................hhhhhhhhhhhhh..........hhhhhhhhhhhh..........-------..hhhhhhhhhhhhhhhhh................................hhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...------------------------hhhhhhhhhhhhhhh.--.hhhhhhhhhhhhh Sec.struct. author (1)
     Sec.struct. author (2) -------------------------------------------------------------------------------------------------------------------------------------------------------ee----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wfs D   5 xxx---------LNFYLSYFDDVAKVLPREHYCFIVGGWVRDRILGEPVGYNIDVDFLTTADPVELAKNFAKRIGGHFFVFEKRGFLIKRPTIASVVLHLPPYRYRFDFSPLKGKDLEKALIEDLKERDFTANAIAVNLDDVL------TIVYDPTGGIKDLEQGLLRPVSIENLKRDPVRVLRGFRIAIEKNLQLTEDFYEFVKEDPRIVLKSAVERITHELFKIMKEKTAHKVIRELYEYGVLEAIIPEIGRLREVKD-------PLDEHTLKTLEYLEQVIEDRAKYLSAELLENFGKKRVLGEFTDVELLKWGALFHDIGKPQTFA-------FYEHDKVGAQIVREIGERLRWGDEATEFVAKLVRHHLRPFFLREAFKKGELKRRGMANFWRECGDIAPHLFLLSIADAMASGDEEEDIKALMETIAELESFNRNEMK------------------------xxxxxxxxxxxxxxxx--xxxxxxxxxxxxxx 504
                            |||      -  |     24        34        44        54        64        74        84        94       104       114       124       134       144  |    154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444   |     -         -       474|||||||484||||  |494|||||||504
                            |||        17                                                                                                                               147    154                                                                                                           264     272                                                           334     342                                                                                                       448                      473-UNK||482-UNK||  493-UNK||502-UNK
                            5-UNK                                                                                                                                                                                                                                                                                                                                                                                                                                                                              474-UNK||483-UNK|  |494-UNK||503-UNK
                             6-UNK                                                                                                                                                                                                                                                                                                                                                                                                                                                                              475-UNK||484-UNK  ||495-UNK||504-UNK
                              7-UNK                                                                                                                                                                                                                                                                                                                                                                                                                                                                              476-UNK| 485-UNK || 496-UNK|   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  477-UNK  486-UNK||  497-UNK   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   478-UNK  487-UNK|   498-UNK  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    479-UNK  488-UNK    499-UNK 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     480-UNK    491-UNK  500-UNK
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      481-UNK    492-UNK  501-UNK
   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 3WFS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain C,D   (O67911_AQUAE | O67911)
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: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.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
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.

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  3wfs
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  2.7.7.72
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 Related Entries

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

UniProtKB/TrEMBL
        O67911_AQUAE | O67911: 3wfo 3wfp 3wfq 3wfr

(-) Related Entries Specified in the PDB File

3wfo 3wfp 3wfq 3wfr