Definition Dechloromonas aromatica RCB, complete genome.
Accession NC_007298
Length 4,501,104

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The map label for this gene is pnp

Identifier: 71908066

GI number: 71908066

Start: 2647811

End: 2649958

Strand: Reverse

Name: pnp

Synonym: Daro_2448

Alternate gene names: 71908066

Gene position: 2649958-2647811 (Counterclockwise)

Preceding gene: 71908067

Following gene: 71908051

Centisome position: 58.87

GC content: 58.66

Gene sequence:

>2148_bases
ATGTTTAACGTCGTTAAAAAGACCTTCGCCTATGGGGACCATCAGGTCACCATCGAAACCGGTGAAGTTGCCCGCCAGGC
TGGCGGTGCTGTTCTCGTTTCCATGGAAGAAACCGTGGTTCTGGTTACCGTCGTGGCTGCCAAGAATGCCAAGCCGGGTC
AGGATTTCTTCCCGCTGACCGTTGATTACCAGGAAAAGACCTACGCTGCCGGCCGTATCCCCGGTGGCTTCTTCAAGCGC
GAAGGCCGTCCTTCCGAAAAGGAAACGCTGACCTGCCGCCTGATCGACCGTCCGATCCGTCCGCTGTTCCCGGATGGTTT
CTACAACGAAGTCCAGGTCATCGCCACGGTGATGTCCCTGAACCCGGAAATCGATTCTGACATTCCCGCCTTGATTGGCG
CTTCCGCCGCACTGGCTATTTCCGGCGTGCCGTTCAACGGCCCGATCGGCGCCGCTCGCGTTGGTTATATCGATGGTCAG
TACGTCCTGTGCCCGACCCTGAGCCAACTCAAGGGTAGCCAGCTCGACCTCGTCGTCGCCGGTACCGAAGCTGCTGTGCT
GATGGTTGAGTCCGAAGCCGACCAGCTGTCCGAAGAGGTCATGCTCGGCGCCGTCGTTTTTGGCCACACCGAAATGCAGA
AGGCGATCAACGCCATCAACGAACTGGTTGAAGAAGCCGGCAAGCCGGAATGGGAATGGGAGGCTGCGCCGAAAGACGAA
GCGTTGGTTGCCAGCCTGTCCGCTCTGGTTAGCGCCAAGCTCGAAGAAGCCTACAACATCACCGTCAAGCAAACGCGCAG
CCAGGCCGTCAAGGCCATCCGTGCTGAAGCTGTTGCCGCCCTTTGTACCGGTGCCGAAGGCGCCCCGGACGAAAACACCG
TCGGCAACCTGTTCCATGAAATCGAAGCCTCGATCGTTCGTGGCCGCATCCTGAGCGGTGCCCCGCGTATCGACGGTCGC
GACACGCGCACTGTGCGTCCGATCACCATGCGTTCTGGCGTTCTGCCGCGTACCCATGGTTCCGCCCTGTTTACCCGTGG
CGAAACCCAGGCGCTGGCAGTTGCCACGCTCGGTACCAACCGCGACGAGCAGATCATCGATGCCCTGGCTGGTGAGTATC
GTGATCGCTTCATGCTGCACTACAACATGCCCCCGTACGCCACCGGCGAATGCGGTCGTGTCGGTACGCCGAAGCGTCGT
GAAATCGGTCACGGCCGTCTGGCCAAGCGTGCACTGCTTGCTGTGCTACCAAAGCCGGAAGACTTCTCCTACTCGATGCG
TCTGGTTTCGGAAATCACTGAATCCAACGGTTCGTCCTCGATGGCTTCCGTCTGTGGCGGCTGCCTCGCCCTGCTCGACG
CCGGTGTGCCGCTCAAGGCCCACGTCGCCGGTATCGCCATGGGGCTGATCAAGGATGGCAATCGTTTTGCCGTTCTGACC
GACATTCTCGGCGACGAAGATCACCTCGGTGACATGGACTTCAAGGTGGCCGGTTCGACAACCGGTATTACTGCGCTGCA
GATGGACATCAAGATCCAGGGTATCACCAAGGAAATCATGCAGGTTGCACTGGCCCAGGCCAAGGAGGCACGCATCCACA
TCCTGAACCTGATGCAGGAATCGGCTGCCGGTCCGCGTGAAGAGATGTCTGCTTACGCTCCGCGTCTGTATACCTTCAAG
ATCAATCCGGAAAAGATCCGTGACGTCATTGGCAAGGGCGGTGCTGTTATCCGCGCCCTGACCGAAGAGACCGGCACGAC
GATCGATATTCAGGATGATGGCACGATTACCATTGCTGCCACCAGTGGCGAAGCTGCTGCTGCGGCTCGTTCGCGTATTG
ATGCGATTACCGCTGAAGTCGAGATTGGCAAGATCTATGAAGGAACTGTGCTGAAGATTCTTGACTTCGGTGCAATCGTC
TCCGTGTTGCCGGGCAAGGATGGTTTGCTGCACATCTCCCAGATCGCTCAAGAGCGAGTCAATAAGGTCGAAGATTACGT
CAAGGAAGGCCAGATTGTTCGCGTCAAGGTTCTGGAAACCGATGACCGTGGTCGCGTCAAGCTGTCGATGAAGGCTGCTG
CAGCGGACGAGGGTACGGTAGCTCAGCCGGTCGCTGCACCAGAGGCCGCTGTCCAACAACAGCAGTAA

Upstream 100 bases:

>100_bases
ATCTCCCGGCCGCTTTTTTGTTTTTGTTGCTTCGTTGTTTTTTGTTGATATCGTAAGTTGTTGTTATTGTTGTTAATTGT
GATGAGAGAGAAAGGAAGCT

Downstream 100 bases:

>100_bases
TTCAGCATCGTCTGAACGCAAAAAGGGCGCCGAAAGGCGCCCTTTTTTTGTGCTGCCGATTGAGATATAGGCAGCGGAAA
AACGTGGCGAGTTACTTCGC

Product: polynucleotide phosphorylase/polyadenylase

Products: NA

Alternate protein names: Polynucleotide phosphorylase; PNPase

Number of amino acids: Translated: 715; Mature: 715

Protein sequence:

>715_residues
MFNVVKKTFAYGDHQVTIETGEVARQAGGAVLVSMEETVVLVTVVAAKNAKPGQDFFPLTVDYQEKTYAAGRIPGGFFKR
EGRPSEKETLTCRLIDRPIRPLFPDGFYNEVQVIATVMSLNPEIDSDIPALIGASAALAISGVPFNGPIGAARVGYIDGQ
YVLCPTLSQLKGSQLDLVVAGTEAAVLMVESEADQLSEEVMLGAVVFGHTEMQKAINAINELVEEAGKPEWEWEAAPKDE
ALVASLSALVSAKLEEAYNITVKQTRSQAVKAIRAEAVAALCTGAEGAPDENTVGNLFHEIEASIVRGRILSGAPRIDGR
DTRTVRPITMRSGVLPRTHGSALFTRGETQALAVATLGTNRDEQIIDALAGEYRDRFMLHYNMPPYATGECGRVGTPKRR
EIGHGRLAKRALLAVLPKPEDFSYSMRLVSEITESNGSSSMASVCGGCLALLDAGVPLKAHVAGIAMGLIKDGNRFAVLT
DILGDEDHLGDMDFKVAGSTTGITALQMDIKIQGITKEIMQVALAQAKEARIHILNLMQESAAGPREEMSAYAPRLYTFK
INPEKIRDVIGKGGAVIRALTEETGTTIDIQDDGTITIAATSGEAAAAARSRIDAITAEVEIGKIYEGTVLKILDFGAIV
SVLPGKDGLLHISQIAQERVNKVEDYVKEGQIVRVKVLETDDRGRVKLSMKAAAADEGTVAQPVAAPEAAVQQQQ

Sequences:

>Translated_715_residues
MFNVVKKTFAYGDHQVTIETGEVARQAGGAVLVSMEETVVLVTVVAAKNAKPGQDFFPLTVDYQEKTYAAGRIPGGFFKR
EGRPSEKETLTCRLIDRPIRPLFPDGFYNEVQVIATVMSLNPEIDSDIPALIGASAALAISGVPFNGPIGAARVGYIDGQ
YVLCPTLSQLKGSQLDLVVAGTEAAVLMVESEADQLSEEVMLGAVVFGHTEMQKAINAINELVEEAGKPEWEWEAAPKDE
ALVASLSALVSAKLEEAYNITVKQTRSQAVKAIRAEAVAALCTGAEGAPDENTVGNLFHEIEASIVRGRILSGAPRIDGR
DTRTVRPITMRSGVLPRTHGSALFTRGETQALAVATLGTNRDEQIIDALAGEYRDRFMLHYNMPPYATGECGRVGTPKRR
EIGHGRLAKRALLAVLPKPEDFSYSMRLVSEITESNGSSSMASVCGGCLALLDAGVPLKAHVAGIAMGLIKDGNRFAVLT
DILGDEDHLGDMDFKVAGSTTGITALQMDIKIQGITKEIMQVALAQAKEARIHILNLMQESAAGPREEMSAYAPRLYTFK
INPEKIRDVIGKGGAVIRALTEETGTTIDIQDDGTITIAATSGEAAAAARSRIDAITAEVEIGKIYEGTVLKILDFGAIV
SVLPGKDGLLHISQIAQERVNKVEDYVKEGQIVRVKVLETDDRGRVKLSMKAAAADEGTVAQPVAAPEAAVQQQQ
>Mature_715_residues
MFNVVKKTFAYGDHQVTIETGEVARQAGGAVLVSMEETVVLVTVVAAKNAKPGQDFFPLTVDYQEKTYAAGRIPGGFFKR
EGRPSEKETLTCRLIDRPIRPLFPDGFYNEVQVIATVMSLNPEIDSDIPALIGASAALAISGVPFNGPIGAARVGYIDGQ
YVLCPTLSQLKGSQLDLVVAGTEAAVLMVESEADQLSEEVMLGAVVFGHTEMQKAINAINELVEEAGKPEWEWEAAPKDE
ALVASLSALVSAKLEEAYNITVKQTRSQAVKAIRAEAVAALCTGAEGAPDENTVGNLFHEIEASIVRGRILSGAPRIDGR
DTRTVRPITMRSGVLPRTHGSALFTRGETQALAVATLGTNRDEQIIDALAGEYRDRFMLHYNMPPYATGECGRVGTPKRR
EIGHGRLAKRALLAVLPKPEDFSYSMRLVSEITESNGSSSMASVCGGCLALLDAGVPLKAHVAGIAMGLIKDGNRFAVLT
DILGDEDHLGDMDFKVAGSTTGITALQMDIKIQGITKEIMQVALAQAKEARIHILNLMQESAAGPREEMSAYAPRLYTFK
INPEKIRDVIGKGGAVIRALTEETGTTIDIQDDGTITIAATSGEAAAAARSRIDAITAEVEIGKIYEGTVLKILDFGAIV
SVLPGKDGLLHISQIAQERVNKVEDYVKEGQIVRVKVLETDDRGRVKLSMKAAAADEGTVAQPVAAPEAAVQQQQ

Specific function: Involved in mRNA degradation. Hydrolyzes single-stranded polyribonucleotides processively in the 3'- to 5'-direction

COG id: COG1185

COG function: function code J; Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase)

Gene ontology:

Cell location: Cytoplasm

Metaboloic importance: Non_Essential [C]

Operon status: Not Known

Operon components: None

Similarity: Contains 1 S1 motif domain

Homologues:

Organism=Homo sapiens, GI188528628, Length=722, Percent_Identity=37.2576177285319, Blast_Score=439, Evalue=1e-123,
Organism=Escherichia coli, GI145693187, Length=693, Percent_Identity=66.3780663780664, Blast_Score=949, Evalue=0.0,
Organism=Caenorhabditis elegans, GI115534063, Length=668, Percent_Identity=33.2335329341317, Blast_Score=327, Evalue=1e-89,
Organism=Drosophila melanogaster, GI281362905, Length=714, Percent_Identity=37.8151260504202, Blast_Score=442, Evalue=1e-124,
Organism=Drosophila melanogaster, GI24651641, Length=714, Percent_Identity=37.8151260504202, Blast_Score=442, Evalue=1e-124,
Organism=Drosophila melanogaster, GI24651643, Length=714, Percent_Identity=37.8151260504202, Blast_Score=442, Evalue=1e-124,
Organism=Drosophila melanogaster, GI161079377, Length=652, Percent_Identity=37.4233128834356, Blast_Score=399, Evalue=1e-111,

Paralogues:

None

Copy number: 200 Molecules/Cell In: Growth Phase, Minimal Media (Based on E. coli). 1000 Molecules/Cell In: Growth-Phase, Minimal-Media (Based on E. coli). 3328 Molecules/Cell In: Growth Phase, Glucose-minimal MOPS Media. 3,000 Molecules/Cell In: Glucose minimal media

Swissprot (AC and ID): PNP_DECAR (Q47D98)

Other databases:

- EMBL:   CP000089
- RefSeq:   YP_285653.1
- HSSP:   Q9UXC2
- ProteinModelPortal:   Q47D98
- SMR:   Q47D98
- STRING:   Q47D98
- GeneID:   3568221
- GenomeReviews:   CP000089_GR
- KEGG:   dar:Daro_2448
- NMPDR:   fig|159087.4.peg.2423
- eggNOG:   COG1185
- HOGENOM:   HBG382411
- OMA:   YGETVVL
- ProtClustDB:   PRK11824
- BioCyc:   DARO159087:DARO_2448-MONOMER
- GO:   GO:0005739
- HAMAP:   MF_01595
- InterPro:   IPR001247
- InterPro:   IPR015847
- InterPro:   IPR004087
- InterPro:   IPR004088
- InterPro:   IPR018111
- InterPro:   IPR012340
- InterPro:   IPR016027
- InterPro:   IPR012162
- InterPro:   IPR015848
- InterPro:   IPR003029
- InterPro:   IPR020568
- InterPro:   IPR022967
- Gene3D:   G3DSA:2.40.50.140
- Gene3D:   G3DSA:1.10.10.400
- PANTHER:   PTHR11252
- PIRSF:   PIRSF005499
- SMART:   SM00322
- SMART:   SM00316
- TIGRFAMs:   TIGR03591

Pfam domain/function: PF00013 KH_1; PF03726 PNPase; PF01138 RNase_PH; PF03725 RNase_PH_C; PF00575 S1; SSF46915 3_ExoRNase; SSF55666 3_ExoRNase; SSF50249 Nucleic_acid_OB; SSF54211 Ribosomal_S5_D2-typ_fold

EC number: =2.7.7.8

Molecular weight: Translated: 76402; Mature: 76402

Theoretical pI: Translated: 4.94; Mature: 4.94

Prosite motif: PS50084 KH_TYPE_1; PS50126 S1

Important sites: NA

Signals:

None

Transmembrane regions:

None

Cys/Met content:

0.8 %Cys     (Translated Protein)
2.5 %Met     (Translated Protein)
3.4 %Cys+Met (Translated Protein)
0.8 %Cys     (Mature Protein)
2.5 %Met     (Mature Protein)
3.4 %Cys+Met (Mature Protein)

Secondary structure: 

>Translated Secondary Structure
MFNVVKKTFAYGDHQVTIETGEVARQAGGAVLVSMEETVVLVTVVAAKNAKPGQDFFPLT
CCCHHHHHHCCCCEEEEEEHHHHHHHCCCEEEEEECCEEEEEEEEEECCCCCCCCCCCEE
VDYQEKTYAAGRIPGGFFKREGRPSEKETLTCRLIDRPIRPLFPDGFYNEVQVIATVMSL
EECCCCEEECCCCCCHHHCCCCCCCCHHEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHC
NPEIDSDIPALIGASAALAISGVPFNGPIGAARVGYIDGQYVLCPTLSQLKGSQLDLVVA
CCCCCCCCHHHHCCCCEEEEECCCCCCCCCCCEEEEECCCEEECCCHHHCCCCCEEEEEE
GTEAAVLMVESEADQLSEEVMLGAVVFGHTEMQKAINAINELVEEAGKPEWEWEAAPKDE
CCCEEEEEEECCHHHHHHHHHHHHHEECHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCH
ALVASLSALVSAKLEEAYNITVKQTRSQAVKAIRAEAVAALCTGAEGAPDENTVGNLFHE
HHHHHHHHHHHHHHHHHHEEEEHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHH
IEASIVRGRILSGAPRIDGRDTRTVRPITMRSGVLPRTHGSALFTRGETQALAVATLGTN
HHHHHHHHHHHCCCCCCCCCCCCEECEEECCCCCCCCCCCCEEEECCCCCEEEEEEECCC
RDEQIIDALAGEYRDRFMLHYNMPPYATGECGRVGTPKRREIGHGRLAKRALLAVLPKPE
CHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCCCCCCHHHCCCCHHHHHHHHHCCCCCC
DFSYSMRLVSEITESNGSSSMASVCGGCLALLDAGVPLKAHVAGIAMGLIKDGNRFAVLT
CCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHEEECCCEEEEEE
DILGDEDHLGDMDFKVAGSTTGITALQMDIKIQGITKEIMQVALAQAKEARIHILNLMQE
ECCCCCCCCCCCCEEEECCCCCEEEEEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHH
SAAGPREEMSAYAPRLYTFKINPEKIRDVIGKGGAVIRALTEETGTTIDIQDDGTITIAA
HCCCCHHHHHHHCCEEEEEEECHHHHHHHHCCCCCEEEEEECCCCCEEEEECCCEEEEEE
TSGEAAAAARSRIDAITAEVEIGKIYEGTVLKILDFGAIVSVLPGKDGLLHISQIAQERV
CCCCHHHHHHHHHHHEEEEEEECCEECCCEEEHHHHHHHHEECCCCCCCCHHHHHHHHHH
NKVEDYVKEGQIVRVKVLETDDRGRVKLSMKAAAADEGTVAQPVAAPEAAVQQQQ
HHHHHHHHCCCEEEEEEEECCCCCEEEEEEEECCCCCCCCCCCCCCCHHHHCCCC
>Mature Secondary Structure
MFNVVKKTFAYGDHQVTIETGEVARQAGGAVLVSMEETVVLVTVVAAKNAKPGQDFFPLT
CCCHHHHHHCCCCEEEEEEHHHHHHHCCCEEEEEECCEEEEEEEEEECCCCCCCCCCCEE
VDYQEKTYAAGRIPGGFFKREGRPSEKETLTCRLIDRPIRPLFPDGFYNEVQVIATVMSL
EECCCCEEECCCCCCHHHCCCCCCCCHHEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHC
NPEIDSDIPALIGASAALAISGVPFNGPIGAARVGYIDGQYVLCPTLSQLKGSQLDLVVA
CCCCCCCCHHHHCCCCEEEEECCCCCCCCCCCEEEEECCCEEECCCHHHCCCCCEEEEEE
GTEAAVLMVESEADQLSEEVMLGAVVFGHTEMQKAINAINELVEEAGKPEWEWEAAPKDE
CCCEEEEEEECCHHHHHHHHHHHHHEECHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCH
ALVASLSALVSAKLEEAYNITVKQTRSQAVKAIRAEAVAALCTGAEGAPDENTVGNLFHE
HHHHHHHHHHHHHHHHHHEEEEHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHH
IEASIVRGRILSGAPRIDGRDTRTVRPITMRSGVLPRTHGSALFTRGETQALAVATLGTN
HHHHHHHHHHHCCCCCCCCCCCCEECEEECCCCCCCCCCCCEEEECCCCCEEEEEEECCC
RDEQIIDALAGEYRDRFMLHYNMPPYATGECGRVGTPKRREIGHGRLAKRALLAVLPKPE
CHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCCCCCCHHHCCCCHHHHHHHHHCCCCCC
DFSYSMRLVSEITESNGSSSMASVCGGCLALLDAGVPLKAHVAGIAMGLIKDGNRFAVLT
CCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHEEECCCEEEEEE
DILGDEDHLGDMDFKVAGSTTGITALQMDIKIQGITKEIMQVALAQAKEARIHILNLMQE
ECCCCCCCCCCCCEEEECCCCCEEEEEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHH
SAAGPREEMSAYAPRLYTFKINPEKIRDVIGKGGAVIRALTEETGTTIDIQDDGTITIAA
HCCCCHHHHHHHCCEEEEEEECHHHHHHHHCCCCCEEEEEECCCCCEEEEECCCEEEEEE
TSGEAAAAARSRIDAITAEVEIGKIYEGTVLKILDFGAIVSVLPGKDGLLHISQIAQERV
CCCCHHHHHHHHHHHEEEEEEECCEECCCEEEHHHHHHHHEECCCCCCCCHHHHHHHHHH
NKVEDYVKEGQIVRVKVLETDDRGRVKLSMKAAAADEGTVAQPVAAPEAAVQQQQ
HHHHHHHHCCCEEEEEEEECCCCCEEEEEEEECCCCCCCCCCCCCCCHHHHCCCC

PDB accession: NA

Resolution: NA

Structure class: Alpha Beta

Cofactors: NA

Metal ions: NA

Kcat value (1/min): NA

Specific activity: NA

Km value (mM): NA

Substrates: NA

Specific reaction: NA

General reaction: NA

Inhibitor: NA

Structure determination priority: 9.0

TargetDB status: NA

Availability: NA

References: NA