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(-) Description

Title :  CRYSTAL STRUCTURE OF C. CRESCENTUS PNPASE BOUND TO RNA
 
Authors :  S. W. Hardwick, T. Gubbey, I. Hug, U. Jenal, B. F. Luisi
Date :  07 Mar 12  (Deposition) - 18 Apr 12  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B,C,D,E,H,I
Keywords :  Transferase-Rna Complex, Kh Domain, Rnase E (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. W. Hardwick, T. Gubbey, I. Hug, U. Jenal, B. F. Luisi
Crystal Structure Of Caulobacter Crescentus Polynucleotide Phosphorylase Reveals A Mechanism Of Rna Substrate Channelling And Rna Degradosome Assembly.
Open Biol. V. 2 20028 2012
PubMed-ID: 22724061  |  Reference-DOI: 10.1098/RSOB.120028

(-) Compounds

Molecule 1 - POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE
    Atcc: 19089
    Chains: A, B, C
    EC Number: 2.7.7.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: CAULOBACTER VIBRIOIDES
    Organism Taxid: 190650
    Strain: CB15
    Synonym: POLYNUCLEOTIDE PHOSPHORYLASE, PNPASE
 
Molecule 2 - RNA, 5'-R(*UP*AP*AP*CP*UP*UP*UP*GP*GP)-3'
    Chains: D, E, H, I
    Fragment: CO-PURIFIED RNA FROM E. COLI EXPRESSION STRAIN
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 469008
    Strain: BL21(DE3)

 Structural Features

(-) Chains, Units

  1234567
Asymmetric/Biological Unit : ABCDEHI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1PO46Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:401 , HIS A:405 , SER A:439 , SER A:440 , SER A:441 , LYS A:496 , PO4 A:1622 , HOH A:2018BINDING SITE FOR RESIDUE PO4 A1621
2AC2SOFTWARESER A:436 , GLY A:438 , PO4 A:1621 , HOH A:2019BINDING SITE FOR RESIDUE PO4 A1622
3AC3SOFTWAREARG B:401 , HIS B:405 , GLY B:438 , SER B:439 , SER B:440 , SER B:441 , LYS B:496 , PO4 B:1621BINDING SITE FOR RESIDUE PO4 B1620
4AC4SOFTWAREARG C:401 , HIS C:405 , SER C:439 , SER C:440 , SER C:441 , LYS C:496 , PO4 C:1621 , HOH C:2017BINDING SITE FOR RESIDUE PO4 C1620
5AC5SOFTWARESER B:436 , GLY B:438 , GLY B:485 , PO4 B:1620BINDING SITE FOR RESIDUE PO4 B1621
6AC6SOFTWAREARG C:401 , SER C:436 , GLY C:438 , PO4 C:1620 , HOH C:2022BINDING SITE FOR RESIDUE PO4 C1621

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AM3)

(-) Cis Peptide Bonds  (26, 26)

Asymmetric/Biological Unit
No.Residues
1Asp A:3 -Ile A:4
2Gly A:147 -Pro A:148
3Gln A:260 -Lys A:261
4Lys A:262 -Gln A:263
5Gln A:263 -Asp A:264
6Asp A:264 -Arg A:265
7Ser A:283 -Asp A:284
8Asp A:284 -Glu A:285
9Thr A:288 -Gly A:289
10Ala A:554 -Pro A:555
11Asp B:3 -Ile B:4
12Tyr B:257 -Lys B:258
13Ile B:259 -Gln B:260
14Lys B:261 -Lys B:262
15Asp B:284 -Glu B:285
16Glu B:285 -Asn B:286
17Asn B:286 -Pro B:287
18Thr B:288 -Gly B:289
19Thr B:314 -Gly B:315
20Asn B:592 -Asp B:593
21Asp C:3 -Ile C:4
22Pro C:235 -Glu C:236
23Ser C:283 -Asp C:284
24Asp C:284 -Glu C:285
25Thr C:288 -Gly C:289
26Asn C:592 -Asp C:593

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AM3)

(-) PROSITE Motifs  (1, 3)

Asymmetric/Biological Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KH_TYPE_1PS50084 Type-1 KH domain profile.PNP_CAUCR555-614
 
 		  3A:555-614
B:555-614
C:555-614

(-) Exons   (0, 0)

(no "Exon" information available for 4AM3)

(-) 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:622
 aligned with PNP_CAUCR | Q9AC32 from UniProtKB/Swiss-Prot  Length:712

    Alignment length:622
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618  
            PNP_CAUCR     - --MFDIKRKTIEWGGKTLVLETGRIARQADGAVLATMGETVVLATAVFAKSQKPGQDFFPLTVNYQEKTFAAGKIPGGFFKREGRPSEKETLVSRLIDRPIRPLFVKGFKNEVQVVVTVLQHDLENDPDILGMVAASAALCLSGAPFMGPIGAARVGWVDGAYVLNPTLDEMKESKMDLVVAGTADAVMMVESEIQELSEEIVLGGVNFAHQQMQAVIDAIIDLAEHAAKEPFAFEPEDTDAIKAKMKDLVGADIAAAYKIQKKQDRYEAVGAAKKKAIAALGLSDENPTGYDPLKLGAIFKELEADVVRRGILDTGLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDEQFIDALEGTYKESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPMLPTKEDFPYTIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAVLSDILGDEDHLGDMDFKVAGTSEGLTSLQMDIKIAGITPAIMEQALAQAKEGRAHILGEMNKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDDGVVKVSASDGAKIKAAIDWIKSITDE 620
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........ee..eeeeee.........eeeeeee..eeeeeeeee............eeeeeee.hhhhh.............hhhhhhhhhhhhhhhh..........eeeeeeeee.....hhhhhhhhhhhhhhh..........eeeeeeee..eeee..hhhhhh...eeeeeee....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh...............eeeee.......eeeeeee..eeeeeeeeeehhhhheeeee..eeeee.eeeeee.hhhhhh........hhhhhhhhhhhhhhhhhhh........eeeeeeeeee...hhhhhhhhhhhhhhhhhh.......eeeeeeeee....eeeee...hhhhhhh.eeeeeeee..eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhh...............eeeeee.hhhhhhhhhh..hhhhhhhhhhhh.eeee....eeeeee.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KH_TYPE_1  PDB: A:555-614 UniProt: 555-614                  ------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4am3 A  -1 GSMFDIKRKTIEWGGKTLVLETGRIARQADGAVLATMGETVVLATAVFAKSQKPGQDFFPLTVNYQEKTFAAGKIPGGFFKREGRPSEKETLVSRLIDRPIRPLFVKGFKNEVQVVVTVLQHDLENDPDILGMVAASAALCLSGAPFMGPIGAARVGWVDGAYVLNPTLDEMKESKMDLVVAGTADAVMMVESEIQELSEEIVLGGVNFAHQQMQAVIDAIIDLAEHAAKEPFAFEPEDTDAIKAKMKDLVGADIAAAYKIQKKQDRYEAVGAAKKKAIAALGLSDENPTGYDPLKLGAIFKELEADVVRRGILDTGLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDEQFIDALEGTYKESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPMLPTKEDFPYTIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAVLSDILGDEDHLGDMDFKVAGTSEGLTSLQMDIKIAGITPAIMEQALAQAKEGRAHILGEMNKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDDGVVKVSASDGAKIKAAIDWIKSITDE 620
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618  


Chain B from PDB  Type:PROTEIN  Length:621
 aligned with PNP_CAUCR | Q9AC32 from UniProtKB/Swiss-Prot  Length:712

    Alignment length:621
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618 
            PNP_CAUCR     - --MFDIKRKTIEWGGKTLVLETGRIARQADGAVLATMGETVVLATAVFAKSQKPGQDFFPLTVNYQEKTFAAGKIPGGFFKREGRPSEKETLVSRLIDRPIRPLFVKGFKNEVQVVVTVLQHDLENDPDILGMVAASAALCLSGAPFMGPIGAARVGWVDGAYVLNPTLDEMKESKMDLVVAGTADAVMMVESEIQELSEEIVLGGVNFAHQQMQAVIDAIIDLAEHAAKEPFAFEPEDTDAIKAKMKDLVGADIAAAYKIQKKQDRYEAVGAAKKKAIAALGLSDENPTGYDPLKLGAIFKELEADVVRRGILDTGLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDEQFIDALEGTYKESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPMLPTKEDFPYTIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAVLSDILGDEDHLGDMDFKVAGTSEGLTSLQMDIKIAGITPAIMEQALAQAKEGRAHILGEMNKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDDGVVKVSASDGAKIKAAIDWIKSITD 619
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........ee..eeeeee.........eeeeeee..eeeeeeeee............eeeeeee.hhhhh.............hhhhhhhhhhhhhhhh..........eeeeeeeee.....hhhhhhhhhhhhhhh..........eeeeeeee..eeee..hhhhhh...eeeeeee....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh...............eeeee.......eeeeeee..eeeeeeeeeehhhhheee......eee.eeeeee.hhhhhh........hhhhhhhhhhhhhhhhhhh.hhhhh..eeeeeeeeee...hhhhhhhhhhhhhhhhhh.......eeeeeeeeee..eeeee............eeeeeeee..eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh..............eeeeee.hhhhhhhhhh..hhhhhhhhhhhh.eeee....eeeeee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KH_TYPE_1  PDB: B:555-614 UniProt: 555-614                  ----- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4am3 B  -1 GSMFDIKRKTIEWGGKTLVLETGRIARQADGAVLATMGETVVLATAVFAKSQKPGQDFFPLTVNYQEKTFAAGKIPGGFFKREGRPSEKETLVSRLIDRPIRPLFVKGFKNEVQVVVTVLQHDLENDPDILGMVAASAALCLSGAPFMGPIGAARVGWVDGAYVLNPTLDEMKESKMDLVVAGTADAVMMVESEIQELSEEIVLGGVNFAHQQMQAVIDAIIDLAEHAAKEPFAFEPEDTDAIKAKMKDLVGADIAAAYKIQKKQDRYEAVGAAKKKAIAALGLSDENPTGYDPLKLGAIFKELEADVVRRGILDTGLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDEQFIDALEGTYKESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPMLPTKEDFPYTIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAVLSDILGDEDHLGDMDFKVAGTSEGLTSLQMDIKIAGITPAIMEQALAQAKEGRAHILGEMNKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDDGVVKVSASDGAKIKAAIDWIKSITD 619
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618 


Chain C from PDB  Type:PROTEIN  Length:621
 aligned with PNP_CAUCR | Q9AC32 from UniProtKB/Swiss-Prot  Length:712

    Alignment length:621
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618 
            PNP_CAUCR     - --MFDIKRKTIEWGGKTLVLETGRIARQADGAVLATMGETVVLATAVFAKSQKPGQDFFPLTVNYQEKTFAAGKIPGGFFKREGRPSEKETLVSRLIDRPIRPLFVKGFKNEVQVVVTVLQHDLENDPDILGMVAASAALCLSGAPFMGPIGAARVGWVDGAYVLNPTLDEMKESKMDLVVAGTADAVMMVESEIQELSEEIVLGGVNFAHQQMQAVIDAIIDLAEHAAKEPFAFEPEDTDAIKAKMKDLVGADIAAAYKIQKKQDRYEAVGAAKKKAIAALGLSDENPTGYDPLKLGAIFKELEADVVRRGILDTGLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDEQFIDALEGTYKESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPMLPTKEDFPYTIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAVLSDILGDEDHLGDMDFKVAGTSEGLTSLQMDIKIAGITPAIMEQALAQAKEGRAHILGEMNKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDDGVVKVSASDGAKIKAAIDWIKSITD 619
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee..eeeeee.........eeeeeee..eeeeeeeee............eeeeeee.hhhhh.............hhhhhhhhhhhhhhhh..........eeeeeeeee.....hhhhhhhhhhhhhhh..........eeeeeeee..eeee....hhhhh..eeeeeee....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhh.hhhhhhhh.........hhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhh...............eeeee.......eeeeeee..eeeeeeeeeehhhhheeeee..eeeee.eeeeee.hhhhhh........hhhhhhhhhhhhhhhhhhh........eeeeeeeeee...hhhhhhhhhhhhhhhhhh.......eeeeeeeeee..eeeee....hhhhhhh.eeeeeeee..eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh..............eeeeee.hhhhhhhhhh..hhhhhhhhhhhh.eeee....eeeeee.hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KH_TYPE_1  PDB: C:555-614 UniProt: 555-614                  ----- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4am3 C  -1 GSMFDIKRKTIEWGGKTLVLETGRIARQADGAVLATMGETVVLATAVFAKSQKPGQDFFPLTVNYQEKTFAAGKIPGGFFKREGRPSEKETLVSRLIDRPIRPLFVKGFKNEVQVVVTVLQHDLENDPDILGMVAASAALCLSGAPFMGPIGAARVGWVDGAYVLNPTLDEMKESKMDLVVAGTADAVMMVESEIQELSEEIVLGGVNFAHQQMQAVIDAIIDLAEHAAKEPFAFEPEDTDAIKAKMKDLVGADIAAAYKIQKKQDRYEAVGAAKKKAIAALGLSDENPTGYDPLKLGAIFKELEADVVRRGILDTGLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDEQFIDALEGTYKESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPMLPTKEDFPYTIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAVLSDILGDEDHLGDMDFKVAGTSEGLTSLQMDIKIAGITPAIMEQALAQAKEGRAHILGEMNKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDDGVVKVSASDGAKIKAAIDWIKSITD 619
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618 


Chain D from PDB  Type:DNA  Length:1
                          -      
                 4am3 D  -1 U   1


Chain E from PDB  Type:RNA  Length:9
                                         
                 4am3 E   1 UAACUUUGG   9


Chain H from PDB  Type:DNA  Length:1
                                 
                 4am3 H   1 A   2


Chain I from PDB  Type:DNA  Length:1
                                 
                 4am3 I   1 U   1
   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 4AM3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AM3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AM3)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (PNP_CAUCR | Q9AC32)
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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    Asn B:286 - Pro B:287   [ RasMol ]  
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    Asn C:592 - Asp C:593   [ RasMol ]  
    Asp A:264 - Arg A:265   [ RasMol ]  
    Asp A:284 - Glu A:285   [ RasMol ]  
    Asp A:3 - Ile A:4   [ RasMol ]  
    Asp B:284 - Glu B:285   [ RasMol ]  
    Asp B:3 - Ile B:4   [ RasMol ]  
    Asp C:284 - Glu C:285   [ RasMol ]  
    Asp C:3 - Ile C:4   [ RasMol ]  
    Gln A:260 - Lys A:261   [ RasMol ]  
    Gln A:263 - Asp A:264   [ RasMol ]  
    Glu B:285 - Asn B:286   [ RasMol ]  
    Gly A:147 - Pro A:148   [ RasMol ]  
    Ile B:259 - Gln B:260   [ RasMol ]  
    Lys A:262 - Gln A:263   [ RasMol ]  
    Lys B:261 - Lys B:262   [ RasMol ]  
    Pro C:235 - Glu C:236   [ RasMol ]  
    Ser A:283 - Asp A:284   [ RasMol ]  
    Ser C:283 - Asp C:284   [ RasMol ]  
    Thr A:288 - Gly A:289   [ RasMol ]  
    Thr B:288 - Gly B:289   [ RasMol ]  
    Thr B:314 - Gly B:315   [ RasMol ]  
    Thr C:288 - Gly C:289   [ RasMol ]  
    Tyr B:257 - Lys B:258   [ RasMol ]  
 

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  4am3
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  PNP_CAUCR | Q9AC32
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  2.7.7.8
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  PNP_CAUCR | Q9AC32
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 Related Entries

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

UniProtKB/Swiss-Prot
        PNP_CAUCR | Q9AC32: 4aid 4aim

(-) Related Entries Specified in the PDB File

4aid CRYSTAL STRUCTURE OF C. CRESCENTUS PNPASE BOUND TO RNASE E RECOGNITION PEPTIDE
4aim CRYSTAL STRUCTURE OF C. CRESCENTUS PNPASE BOUND TO RNASE E RECOGNITION PEPTIDE