PNP_STRAT
ID PNP_STRAT Reviewed; 740 AA.
AC Q53597;
DT 29-APR-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 109.
DE RecName: Full=Polyribonucleotide nucleotidyltransferase {ECO:0000255|HAMAP-Rule:MF_01595};
DE EC=2.7.7.8 {ECO:0000255|HAMAP-Rule:MF_01595};
DE AltName: Full=Polynucleotide phosphorylase {ECO:0000255|HAMAP-Rule:MF_01595};
DE Short=PNPase {ECO:0000255|HAMAP-Rule:MF_01595};
GN Name=pnp {ECO:0000255|HAMAP-Rule:MF_01595};
OS Streptomyces antibioticus.
OC Bacteria; Actinobacteria; Streptomycetales; Streptomycetaceae;
OC Streptomyces.
OX NCBI_TaxID=1890;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=DSM 41481 / IMRU 3720;
RX PubMed=8763958; DOI=10.1128/jb.178.14.4281-4288.1996;
RA Jones G.H., Bibb M.J.;
RT "Guanosine pentaphosphate synthetase from Streptomyces antibioticus is also
RT a polynucleotide phosphorylase.";
RL J. Bacteriol. 178:4281-4288(1996).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS), AND SUBUNIT.
RX PubMed=11080643; DOI=10.1016/s0969-2126(00)00521-9;
RA Symmons M.F., Jones G.H., Luisi B.F.;
RT "A duplicated fold is the structural basis for polynucleotide phosphorylase
RT catalytic activity, processivity, and regulation.";
RL Structure 8:1215-1226(2000).
CC -!- FUNCTION: Involved in mRNA degradation. Catalyzes the phosphorolysis of
CC single-stranded polyribonucleotides processively in the 3'- to 5'-
CC direction. {ECO:0000255|HAMAP-Rule:MF_01595}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=phosphate + RNA(n+1) = a ribonucleoside 5'-diphosphate +
CC RNA(n); Xref=Rhea:RHEA:22096, Rhea:RHEA-COMP:14527, Rhea:RHEA-
CC COMP:17342, ChEBI:CHEBI:43474, ChEBI:CHEBI:57930, ChEBI:CHEBI:140395;
CC EC=2.7.7.8; Evidence={ECO:0000255|HAMAP-Rule:MF_01595};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01595};
CC -!- SUBUNIT: Homotrimer. {ECO:0000269|PubMed:11080643}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01595}.
CC -!- SIMILARITY: Belongs to the polyribonucleotide nucleotidyltransferase
CC family. {ECO:0000255|HAMAP-Rule:MF_01595}.
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DR EMBL; U19858; AAB17498.1; -; Genomic_DNA.
DR PDB; 1E3H; X-ray; 2.60 A; A=1-740.
DR PDB; 1E3P; X-ray; 2.50 A; A=1-740.
DR PDBsum; 1E3H; -.
DR PDBsum; 1E3P; -.
DR AlphaFoldDB; Q53597; -.
DR SMR; Q53597; -.
DR STRING; 1890.AFM16_28085; -.
DR BRENDA; 2.7.6.5; 5974.
DR BRENDA; 2.7.7.8; 5974.
DR EvolutionaryTrace; Q53597; -.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004654; F:polyribonucleotide nucleotidyltransferase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0006402; P:mRNA catabolic process; IEA:UniProtKB-UniRule.
DR GO; GO:0006396; P:RNA processing; IEA:InterPro.
DR Gene3D; 2.40.50.140; -; 1.
DR Gene3D; 3.30.1370.10; -; 1.
DR Gene3D; 3.30.230.70; -; 2.
DR HAMAP; MF_01595; PNPase; 1.
DR InterPro; IPR001247; ExoRNase_PH_dom1.
DR InterPro; IPR036345; ExoRNase_PH_dom2_sf.
DR InterPro; IPR014069; GPSI/PNP.
DR InterPro; IPR004087; KH_dom.
DR InterPro; IPR004088; KH_dom_type_1.
DR InterPro; IPR036612; KH_dom_type_1_sf.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR012162; PNPase.
DR InterPro; IPR027408; PNPase/RNase_PH_dom_sf.
DR InterPro; IPR015848; PNPase_PH_RNA-bd_bac/org-type.
DR InterPro; IPR036456; PNPase_PH_RNA-bd_sf.
DR InterPro; IPR020568; Ribosomal_S5_D2-typ_fold.
DR InterPro; IPR022967; S1_dom.
DR InterPro; IPR003029; S1_domain.
DR PANTHER; PTHR11252; PTHR11252; 1.
DR Pfam; PF00013; KH_1; 1.
DR Pfam; PF03726; PNPase; 1.
DR Pfam; PF01138; RNase_PH; 2.
DR Pfam; PF00575; S1; 1.
DR PIRSF; PIRSF005499; PNPase; 1.
DR SMART; SM00322; KH; 1.
DR SMART; SM00316; S1; 1.
DR SUPFAM; SSF46915; SSF46915; 1.
DR SUPFAM; SSF54211; SSF54211; 2.
DR SUPFAM; SSF54791; SSF54791; 1.
DR SUPFAM; SSF55666; SSF55666; 2.
DR TIGRFAMs; TIGR03591; polynuc_phos; 1.
DR TIGRFAMs; TIGR02696; pppGpp_PNP; 1.
DR PROSITE; PS50084; KH_TYPE_1; 1.
DR PROSITE; PS50126; S1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Magnesium; Metal-binding; Nucleotidyltransferase;
KW RNA-binding; Transferase.
FT CHAIN 1..740
FT /note="Polyribonucleotide nucleotidyltransferase"
FT /id="PRO_0000329887"
FT DOMAIN 580..639
FT /note="KH"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01595"
FT DOMAIN 651..723
FT /note="S1 motif"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01595"
FT BINDING 514
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01595"
FT BINDING 520
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01595"
FT STRAND 6..13
FT /evidence="ECO:0007829|PDB:1E3P"
FT HELIX 15..17
FT /evidence="ECO:0007829|PDB:1E3P"
FT STRAND 19..29
FT /evidence="ECO:0007829|PDB:1E3P"
FT STRAND 33..41
FT /evidence="ECO:0007829|PDB:1E3P"
FT TURN 42..44
FT /evidence="ECO:0007829|PDB:1E3P"
FT STRAND 45..57
FT /evidence="ECO:0007829|PDB:1E3P"
FT STRAND 66..72
FT /evidence="ECO:0007829|PDB:1E3P"
FT HELIX 74..77
FT /evidence="ECO:0007829|PDB:1E3P"
FT HELIX 93..106
FT /evidence="ECO:0007829|PDB:1E3P"
FT HELIX 107..109
FT /evidence="ECO:0007829|PDB:1E3P"
FT STRAND 116..126
FT /evidence="ECO:0007829|PDB:1E3P"
FT HELIX 134..147
FT /evidence="ECO:0007829|PDB:1E3P"
FT STRAND 150..152
FT /evidence="ECO:0007829|PDB:1E3P"
FT STRAND 157..164
FT /evidence="ECO:0007829|PDB:1E3P"
FT STRAND 167..171
FT /evidence="ECO:0007829|PDB:1E3P"
FT HELIX 174..177
FT /evidence="ECO:0007829|PDB:1E3P"
FT STRAND 180..190
FT /evidence="ECO:0007829|PDB:1E3P"
FT STRAND 196..205
FT /evidence="ECO:0007829|PDB:1E3P"
FT HELIX 209..214
FT /evidence="ECO:0007829|PDB:1E3P"
FT HELIX 222..250
FT /evidence="ECO:0007829|PDB:1E3P"
FT HELIX 265..282
FT /evidence="ECO:0007829|PDB:1E3P"
FT HELIX 288..303
FT /evidence="ECO:0007829|PDB:1E3P"
FT TURN 307..310
FT /evidence="ECO:0007829|PDB:1E3P"
FT HELIX 314..335
FT /evidence="ECO:0007829|PDB:1E3P"
FT STRAND 351..355
FT /evidence="ECO:0007829|PDB:1E3P"
FT STRAND 358..369
FT /evidence="ECO:0007829|PDB:1E3P"
FT STRAND 372..382
FT /evidence="ECO:0007829|PDB:1E3P"
FT HELIX 383..385
FT /evidence="ECO:0007829|PDB:1E3P"
FT STRAND 386..388
FT /evidence="ECO:0007829|PDB:1E3P"
FT STRAND 391..394
FT /evidence="ECO:0007829|PDB:1E3P"
FT STRAND 397..405
FT /evidence="ECO:0007829|PDB:1E3P"
FT HELIX 408..411
FT /evidence="ECO:0007829|PDB:1E3P"
FT HELIX 422..435
FT /evidence="ECO:0007829|PDB:1E3P"
FT HELIX 436..438
FT /evidence="ECO:0007829|PDB:1E3P"
FT TURN 442..444
FT /evidence="ECO:0007829|PDB:1E3P"
FT STRAND 447..457
FT /evidence="ECO:0007829|PDB:1E3P"
FT HELIX 462..477
FT /evidence="ECO:0007829|PDB:1E3P"
FT STRAND 486..499
FT /evidence="ECO:0007829|PDB:1E3P"
FT STRAND 501..508
FT /evidence="ECO:0007829|PDB:1E3P"
FT HELIX 511..516
FT /evidence="ECO:0007829|PDB:1E3P"
FT STRAND 518..525
FT /evidence="ECO:0007829|PDB:1E3P"
FT STRAND 527..537
FT /evidence="ECO:0007829|PDB:1E3P"
FT HELIX 544..568
FT /evidence="ECO:0007829|PDB:1E3P"
FT HELIX 607..611
FT /evidence="ECO:0007829|PDB:1E3P"
FT STRAND 626..628
FT /evidence="ECO:0007829|PDB:1E3P"
FT HELIX 629..632
FT /evidence="ECO:0007829|PDB:1E3P"
FT STRAND 657..660
FT /evidence="ECO:0007829|PDB:1E3P"
SQ SEQUENCE 740 AA; 79160 MW; F07224C64018BA54 CRC64;
MENETHYAEA VIDNGAFGTR TIRFETGRLA KQAAGSAVAY LDDDTMVLSA TTASKNPKDQ
LDFFPLTVDV EERMYAAGKI PGSFFRREGR PSEDAILTCR LIDRPLRPSF KKGLRNEIQV
VATIMALNPD HLYDVVAINA ASASTQLAGL PFSGPYGGVR VALIRGQWVA FPTHTELEDA
VFDMVVAGRV LEDGDVAIMM VEAEATEKTV QLVKDGAEAP TEEVVAAGLD AAKPFIKVLC
KAQADLAAKA AKPTGEFPVP SSTTRTTSEA LSAAVRPELS AALTIAGKQD REAELDRVKA
LAAEKLLPEF EGREKEISAA YRPWPSSSSA ERVIKEKKRI DGRGVTDIRT LAAEVEAIPR
VHGSALFERG ETQILGVTTL NMLRMEQQLD TLSPVTRKPY MHNYNFPPIS VGETGRVGSP
KRREIGHGAL AERAIVPVLP TREEFPYAIR QVSEALGSNG STSMGSVCAS TMSLLNAGVP
LKAPVAGIAM GLISQEINGE THYVALTDIL GAEDAFGDMD FKVAGTKEFV TALQLDTKLD
GIPASVLAAA LKQARDARLH ILDVMMEAID TPDEMSPNAP RIITVKIPVD KIGEVIGPKR
QMINQIQEDT GAEITIEDDG TIYIGAADGP AAEAARATIN GIANPTSPEV GERILGSVVK
TTTFGAFVSL LPGKDGLLHI SQIRKLAGGK RVENVEDVLG VGQKVQVEIA EIDSRGKLSL
IPVIEGEEAA SDEKKDDAEQ
