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Title :   CRYSTAL STRUCTURE OF C. CRESCENTUS PNPASE BOUND TO RNASE E RECOGNITION PEPTIDE

Authors :   S. W. Hardwick, T. Gubbey, I. Hug, U. Jenal, B. F. Luisi

Date :   10 Feb 12 (Deposition) - 18 Apr 12 (Release) - 05 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.30

Chains :   Asym. Unit : A,C
Biol. Unit 1: A,C  (3x)

Keywords :   Transferase-Peptide Complex, Kh Domain, S1 Domain, Gww Peptide (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

Molecule 1 - POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE
	Atcc	:	19089
	Chains	:	A
	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 - RIBONUCLEASE, RNE/RNG FAMILY PROTEIN
	Atcc	:	19089
	Chains	:	C
	Fragment	:	PNPASE BINDING PEPTIDE - GWW, RESIDUES 885-898
	Organism Common	:	CAULOBACTER CRESCENTUS
	Organism Scientific	:	CAULOBACTER VIBRIOIDES
	Organism Taxid	:	155892
	Strain	:	CB15
	Synonym	:	RNASE E
	Synthetic	:	YES

		1	2
Asymmetric Unit	:	A	C
Biological Unit 1 (3x)	:	A	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	PO4	3	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:401 , HIS A:405 , SER A:436 , GLY A:438	BINDING SITE FOR RESIDUE PO4 A1697

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

Asymmetric Unit

No.	Residues
1	Asp A:3	-	Ile A:4
2	Ser A:283	-	Asp A:284
3	Asp A:284	-	Glu A:285
4	Glu A:285	-	Asn A:286
5	Thr A:288	-	Gly A:289
6	Phe A:553	-	Ala A:554
7	Lys A:556	-	Ile A:557
8	Asp A:590	-	Ile A:591
9	Ala A:621	-	Glu A:622
10	Glu A:622	-	Ile A:623
11	Gly A:624	-	Lys A:625
12	Asp A:683	-	Arg A:684
13	Val A:693	-	Val A:694
14	Val A:694	-	Asp A:695
15	Arg C:893	-	Gly C:894
16	Trp C:896	-	Arg C:897

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

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	KH_TYPE_1	PS50084	Type-1 KH domain profile.	PNP_CAUCR	555-614	1	A:555-614
2	S1	PS50126	S1 domain profile.	PNP_CAUCR	624-692	1	A:624-692

Biological Unit 1 (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	KH_TYPE_1	PS50084	Type-1 KH domain profile.	PNP_CAUCR	555-614	3	A:555-614
2	S1	PS50126	S1 domain profile.	PNP_CAUCR	624-692	3	A:624-692

(no "Exon" information available for 4AIM)

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:698
 aligned with PNP_CAUCR | Q9AC32 from UniProtKB/Swiss-Prot  Length:712

    Alignment length:698
                              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       628       638       648       658       668       678       688        
            PNP_CAUCR     - --MFDIKRKTIEWGGKTLVLETGRIARQADGAVLATMGETVVLATAVFAKSQKPGQDFFPLTVNYQEKTFAAGKIPGGFFKREGRPSEKETLVSRLIDRPIRPLFVKGFKNEVQVVVTVLQHDLENDPDILGMVAASAALCLSGAPFMGPIGAARVGWVDGAYVLNPTLDEMKESKMDLVVAGTADAVMMVESEIQELSEEIVLGGVNFAHQQMQAVIDAIIDLAEHAAKEPFAFEPEDTDAIKAKMKDLVGADIAAAYKIQKKQDRYEAVGAAKKKAIAALGLSDENPTGYDPLKLGAIFKELEADVVRRGILDTGLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDEQFIDALEGTYKESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPMLPTKEDFPYTIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAVLSDILGDEDHLGDMDFKVAGTSEGLTSLQMDIKIAGITPAIMEQALAQAKEGRAHILGEMNKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDDGVVKVSASDGAKIKAAIDWIKSITDEAEVGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFDDRGKTKLSMKVVDQ 696
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........ee..eeeeee.........eeeeeee..eeeeeeeee............eeeeeee.hhhhh.............hhhhhhhhhhhhhhhh..........eeeeeeeee.....hhhhhhhhhhhhhhhhhh.......eeeeeeee..eeee..hhhhhhh..eeeeeee....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhh...............ee..........eee..ee....eeeee........eee......eee....eee.hhhhhh........hhhhhhhhhhhhh..................eeee.....hhhhhhhhhhhhhhhhhh.......eeeeee.ee....ee.....hhhhhh...eeeeeeee..eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh..............eeeeee.hhhhhhhhhh..hhhhhhhhhhhh.eee.....eeeeee.hhhhhhhhhhhhhhhhh.......eeeeeeeee..eeeee......eeee....................eeeeeeee.......eee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KH_TYPE_1  PDB: A:555-614 UniProt: 555-614                  ---------S1  PDB: A:624-692 UniProt: 624-692                                  ---- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aim A  -1 SPMFDIKRKTIEWGGKTLVLETGRIARQADGAVLATMGETVVLATAVFAKSQKPGQDFFPLTVNYQEKTFAAGKIPGGFFKREGRPSEKETLVSRLIDRPIRPLFVKGFKNEVQVVVTVLQHDLENDPDILGMVAASAALCLSGAPFMGPIGAARVGWVDGAYVLNPTLDEMKESKMDLVVAGTADAVMMVESEIQELSEEIVLGGVNFAHQQMQAVIDAIIDLAEHAAKEPFAFEPEDTDAIKAKMKDLVGADIAAAYKIQKKQDRYEAVGAAKKKAIAALGLSDENPTGYDPLKLGAIFKELEADVVRRGILDTGLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDEQFIDALEGTYKESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPMLPTKEDFPYTIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAVLSDILGDEDHLGDMDFKVAGTSEGLTSLQMDIKIAGITPAIMEQALAQAKEGRAHILGEMNKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDDGVVKVSASDGAKIKAAIDWIKSITDEAEIGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFDDRGKTKLSMKVVDQ 696
                                     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       628       638       648       658       668       678       688

Chain C from PDB  Type:PROTEIN  Length:8
 aligned with Q9A749_CAUCR | Q9A749 from UniProtKB/TrEMBL  Length:898

    Alignment length:8
         Q9A749_CAUCR   890 KPRRGWWR 897
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 4aim C 890 KPRRGWWR 897

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 '\|'

(no "SCOP Domain" information available for 4AIM)

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

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

Asymmetric Unit(hide GO term definitions)

Chain A (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.

Chain C (Q9A749_CAUCR | Q9A749)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0004521	endoribonuclease activity	Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	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:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0008995	ribonuclease E activity	Catalysis of the cleavage of single-stranded RNA that is monophosphorylated at its 5'-end; cleavage occurs predominantly at 5 nucleotides from the 5'-end and in A + U-rich regions, and is blocked by the presence of a 5'-triphosphate group.
	GO:0004540	ribonuclease activity	Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0090501	RNA phosphodiester bond hydrolysis	The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
	GO:0090502	RNA phosphodiester bond hydrolysis, endonucleolytic	The chemical reactions and pathways involving the hydrolysis of internal 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.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
	GO:0006364	rRNA processing	Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
	GO:0008033	tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0009898	cytoplasmic side of plasma membrane	The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		PO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala A:621 - Glu A:622	[ RasMol ]
		Arg C:893 - Gly C:894	[ RasMol ]
		Asp A:284 - Glu A:285	[ RasMol ]
		Asp A:3 - Ile A:4	[ RasMol ]
		Asp A:590 - Ile A:591	[ RasMol ]
		Asp A:683 - Arg A:684	[ RasMol ]
		Glu A:285 - Asn A:286	[ RasMol ]
		Glu A:622 - Ile A:623	[ RasMol ]
		Gly A:624 - Lys A:625	[ RasMol ]
		Lys A:556 - Ile A:557	[ RasMol ]
		Phe A:553 - Ala A:554	[ RasMol ]
		Ser A:283 - Asp A:284	[ RasMol ]
		Thr A:288 - Gly A:289	[ RasMol ]
		Trp C:896 - Arg C:897	[ RasMol ]
		Val A:693 - Val A:694	[ RasMol ]
		Val A:694 - Asp A:695	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	4aim
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	2.7.7.8
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	PNP_CAUCR \| Q9AC32	:	4aid 4am3
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	Q9A749_CAUCR \| Q9A749	:	4aid 4oxp

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (16, 16)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (27, 33)

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