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(-) Description

Title :  TUNGSTATE DERIVATIVE OF STREPTOMYCES ANTIBIOTICUS PNPASE/ GPSI ENZYME
 
Authors :  M. F. Symmons, G. H. Jones, B. F. Luisi
Date :  20 Jun 00  (Deposition) - 03 Nov 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Polyribonucleotide Transferase, Atp-Gtp Diphosphotransferase Rna Processing, Rna Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. F. Symmons, G. H. Jones, B. F. Luisi
A Duplicated Fold Is The Structural Basis For Polynucleotide Phosphorylase Catalytic Activity, Processivity, And Regulation
Structure V. 8 1215 2000
PubMed-ID: 11080643  |  Reference-DOI: 10.1016/S0969-2126(00)00521-9

(-) Compounds

Molecule 1 - GUANOSINE PENTAPHOSPHATE SYNTHETASE
    Cellular LocationCYTOPLASM
    ChainsA
    EC Number2.7.7.8, 2.7.6.5
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Cellular LocationCYTOPLASM
    Expression System Taxid562
    GeneGPSI
    Organism ScientificSTREPTOMYCES ANTIBIOTICUS
    Organism Taxid1890
    Other DetailsBIFUNCTIONAL ENZYME POLYRIBONUCLEOTIDE NUCLEOTIDYL TRANSFERASE, ATP-GTP DIPHOSPHOTRANSFERASE
    Other Details - SourceBIFUNCTIONAL ENZYME ISOLATED
    StrainIMRU3720
    SynonymPOLYNUCLEOTIDE PHOSPHORYLASE, GUANOSINE PENTAPHOSPHATE SYNTHETASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (3x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1SO410Ligand/IonSULFATE ION
2WO41Ligand/IonTUNGSTATE(VI)ION
Biological Unit 1 (2, 33)
No.NameCountTypeFull Name
1SO430Ligand/IonSULFATE ION
2WO43Ligand/IonTUNGSTATE(VI)ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:84 , ARG A:86 , GLN A:388 , HOH A:2081BINDING SITE FOR RESIDUE SO4 A 901
02AC2SOFTWAREILE A:569 , ASP A:570 , THR A:571BINDING SITE FOR RESIDUE SO4 A 902
03AC3SOFTWARELYS A:421 , ARG A:422 , HOH A:2297BINDING SITE FOR RESIDUE SO4 A 903
04AC4SOFTWAREGLY A:415 , ARG A:416BINDING SITE FOR RESIDUE SO4 A 904
05AC5SOFTWARESER A:54 , LYS A:55 , ASN A:56 , LYS A:58 , HOH A:2052BINDING SITE FOR RESIDUE SO4 A 905
06AC6SOFTWAREPHE A:64 , LYS A:112 , GLY A:113 , ARG A:115 , HOH A:2299BINDING SITE FOR RESIDUE SO4 A 906
07AC7SOFTWAREARG A:160 , ASP A:183 , VAL A:185 , GLU A:202 , GLU A:204 , HOH A:2301BINDING SITE FOR RESIDUE SO4 A 907
08AC8SOFTWAREGLU A:207 , ARG A:397 , ARG A:399 , ARG A:442 , HOH A:2236 , HOH A:2302BINDING SITE FOR RESIDUE SO4 A 908
09AC9SOFTWAREHIS A:131 , LEU A:132 , TYR A:133 , LEU A:392 , SER A:393 , HOH A:2112 , HOH A:2303BINDING SITE FOR RESIDUE SO4 A 909
10BC1SOFTWAREARG A:360BINDING SITE FOR RESIDUE SO4 A 910
11BC2SOFTWAREHIS A:427 , SER A:461 , THR A:462 , SER A:463 , LYS A:522 , HOH A:2305BINDING SITE FOR RESIDUE WO4 A 911

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1E3P)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:154 -Pro A:155
2Leu A:307 -Pro A:308

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1E3P)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KH_TYPE_1PS50084 Type-1 KH domain profile.PNP_STRAT580-639  1A:580-634
2S1PS50126 S1 domain profile.PNP_STRAT651-723  1A:656-717
Biological Unit 1 (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KH_TYPE_1PS50084 Type-1 KH domain profile.PNP_STRAT580-639  3A:580-634
2S1PS50126 S1 domain profile.PNP_STRAT651-723  3A:656-717

(-) Exons   (0, 0)

(no "Exon" information available for 1E3P)

(-) 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:645
 aligned with PNP_STRAT | Q53597 from UniProtKB/Swiss-Prot  Length:740

    Alignment length:715
                                    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       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712     
            PNP_STRAT     3 NETHYAEAVIDNGAFGTRTIRFETGRLAKQAAGSAVAYLDDDTMVLSATTASKNPKDQLDFFPLTVDVEERMYAAGKIPGSFFRREGRPSEDAILTCRLIDRPLRPSFKKGLRNEIQVVATIMALNPDHLYDVVAINAASASTQLAGLPFSGPYGGVRVALIRGQWVAFPTHTELEDAVFDMVVAGRVLEDGDVAIMMVEAEATEKTVQLVKDGAEAPTEEVVAAGLDAAKPFIKVLCKAQADLAAKAAKPTGEFPVPSSTTRTTSEALSAAVRPELSAALTIAGKQDREAELDRVKALAAEKLLPEFEGREKEISAAYRPWPSSSSAERVIKEKKRIDGRGVTDIRTLAAEVEAIPRVHGSALFERGETQILGVTTLNMLRMEQQLDTLSPVTRKPYMHNYNFPPISVGETGRVGSPKRREIGHGALAERAIVPVLPTREEFPYAIRQVSEALGSNGSTSMGSVCASTMSLLNAGVPLKAPVAGIAMGLISQEINGETHYVALTDILGAEDAFGDMDFKVAGTKEFVTALQLDTKLDGIPASVLAAALKQARDARLHILDVMMEAIDTPDEMSPNAPRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIEDDGTIYIGAADGPAAEAARATINGIANPTSPEVGERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSRGK 717
               SCOP domains d1e3pa3 A:3-151 Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4                                        d1e3pa6 A:152-262 Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5d1e3pa1 A:263-345                                                                  d1e3pa4 A:346-482 Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4                          d1e3pa7 A:483-578                                                                               d1e3pa5                   A:579-634                                          d1e3pa 2 A:656-7   17                                          SCOP domains
               CATH domains 1e3pA01 A:3-252 GHMP Kinase, N-terminal domain                                                                                                                                                                                                            ----------1e3pA02 A:263-345  [code=1.10.10.400, no name defined]                             ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.hhh.eeeeeeee........eeeeeee...eeeeeeeee............eeeeeee.hhhhh.............hhhhhhhhhhhhhhhh..........eeeeeeeee......hhhhhhhhhhhhhhhh........eeeeeeee..eeee..hhhhhh...eeeeeeeee.....eeeeeeeeee..hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh..............eeeee.......eeeeeee..eeeeeeeeeee.hhh.............eeeeee.hhhhhh........hhhhhhhhhhhhhhhhhhh.......eeeeeeeeeee...hhhhhhhhhhhhhhhhhh.......eeeeeeeeeee....eeeeee...hhhhhhhh.eeeeeee....eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh................------------------..hhhhhhh..--------.....hhhhhh.---------------------......-.........---.....-------------------................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KH_TYPE_1  PDB: A:580-634 UniProt: 580-639                  -----------S1  PDB: A:656-717 UniProt: 651-723                                 PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e3p A   3 NETHYAEAVIDNGAFGTRTIRFETGRLARQAAGSAVAYLDDDTMVLSATTASKNPKDQLDFFPLTVDVEERMYAAGKIPGSFFRREGRPSEDAILTCRLIDRPLRPSFKKGLRNEIQVVATIMALNPDHLYDVVAINAASASTQLAGLPFSGPIGGVRVALIRGQWVAFPTHTELEDAVFDMVVAGRVLEDGDVAIMMVEAEATEKTIQLVKDGAEAPTEEVVAAGLDAAKPFIKVLCKAQADLAAKAAKPTGEFPVFLDYQDDVLEALSAAVRPELSAALTIAGKQDREAELDRVKALAAEKLLPEFEGREKEISAAYRALTKSLVRERVIAEKKRIDGRGVTDIRTLAAEVEAIPRVHGSALFERGETQILGVTTLNMLRMEQQLDTLSPVTRKRYMHNYNFPPYSVGETGRVGSPKRREIGHGALAERAIVPVLPTREEFPYAIRQVSEALGSNGSTSMGSVCASTMSLLNAGVPLKAPVAGIAMGLISQEINGETHYVALTDILGAEDAFGDMDFKVAGTKEFVTALQLDTKLDGIPASVLAAALKQARDARLHILDVMMEAIDTPDEMSPNAPRIITV------------------NQIQEDTGAEI--------YIGAADGPAAEA---------------------GSVVKT-TFGAFVSLL---DGLLH-------------------LGVGQKVQVEIAEIDSRGK 717
                                    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       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582  |      -         - |     612 |       -|      632 |       -         -   |    |-|       |-  |   |  -         -      |702       712     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                585                604       614      623        634                   656  661 |     671 675 679                 699                  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              663                                                      

   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  (5, 7)

Asymmetric Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1E3P)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (PNP_STRAT | Q53597)
molecular function
    GO:0000175    3'-5'-exoribonuclease activity    Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0004654    polyribonucleotide nucleotidyltransferase activity    Catalysis of the reaction: RNA(n+1) + phosphate <=> RNA(n) + a nucleoside diphosphate.
    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:0090503    RNA phosphodiester bond hydrolysis, exonucleolytic    The chemical reactions and pathways involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:0006402    mRNA catabolic process    The chemical reactions and pathways resulting in the breakdown of mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes.
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
        PNP_STRAT | Q535971e3h

(-) Related Entries Specified in the PDB File

1e3h SEMET DERIVATIVE OF STREPTOMYCES ANTIBIOTICUS PNPASE/GPSI ENZYME