2A1R | PR0166 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PARN NUCLEASE DOMAIN

Authors :   M. Wu, H. Song

Date :   21 Jun 05 (Deposition) - 20 Dec 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Parn, Dedd, Nuclease Domain, Hydrolase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Wu, M. Reuter, H. Lilie, Y. Liu, E. Wahle, H. Song
Structural Insight Into Poly(A) Binding And Catalytic Mechanism Of Human Parn
Embo J. V. 24 4082 2005
PubMed-ID: 16281054 | Reference-DOI: 10.1038/SJ.EMBOJ.7600869

*Molecule 1 - 5'-R(APAPA)-3'**
	Chains	:	C, D
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - POLY(A)-SPECIFIC RIBONUCLEASE PARN
	Chains	:	A, B
	EC Number	:	3.1.13.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P-1
	Expression System Strain	:	BL-21 STAR
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	PARN(1-430)
	Gene	:	PARN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	POLYADENYLATE-SPECIFIC RIBONUCLEASE, DEADENYLATING NUCLEASE, DEADENYLATION NUCLEASE, PARN

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2A1R)

(no "Site" information available for 2A1R)

Asymmetric/Biological Unit

No.	Residues
1	A:108	-	B:108

Asymmetric/Biological Unit

No.	Residues
1	Gln A:332	-	Pro A:333
2	Thr A:353	-	Pro A:354
3	Ser A:402	-	Pro A:403
4	Gln B:332	-	Pro B:333
5	Thr B:353	-	Pro B:354
6	Ser B:402	-	Pro B:403

Asymmetric/Biological Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_073782	A	383	V	PARN_HUMAN	Disease (DKCB6)	786200999	A/B	A	383	V
2	UniProt	VAR_073783	K	421	R	PARN_HUMAN	Disease (PFBMFT4)	777090017	A/B	K	421	R

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 2A1R)

(no "Exon" information available for 2A1R)

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:300
 aligned with PARN_HUMAN | O95453 from UniProtKB/Swiss-Prot  Length:639

    Alignment length:423
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420   
           PARN_HUMAN     1 MEIIRSNFKSNLHKVYQAIEEADFFAIDGEFSGISDGPSVSALTNGFDTPEERYQKLKKHSMDFLLFQFGLCTFKYDYTDSKYITKSFNFYVFPKPFNRSSPDVKFVCQSSSIDFLASQGFDFNKVFRNGIPYLNQEEERQLREQYDEKRSQANGAGALSYVSPNTSKCPVTIPEDQKKFIDQVVEKIEDLLQSEENKNLDLEPCTGFQRKLIYQTLSWKYPKGIHVETLETEKKERYIVISKVDEEERKRREQQKHAKEQEELNDAVGFSRVIHAIANSGKLVIGHNMLLDVMHTVHQFYCPLPADLSEFKEMTTCVFPRLLDTKLMASTQPFKDIINNTSLAELEKRLKETPFNPPKVESAEGFPSYDTASEQLHEAGYDAYITGLCFISMANYLGSFLSPPKIHVSARSKLIEPFFNKLF 423
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhhhhhhhhhhh.eeeeeeee.........-----...hhhhhhhhhhhhh....eeeeeeeeeeee....eeeeeeeeee.............eeeeehhhhhhhhhh..hhhhhhh......hhhhhhhh.-----------------------------------------------------------------------------------------------------------------..hhhhhhhh...hhhhhhhhhhhh.eeee..hhhhhhhhhhhhh.....hhhhhhhhhhhhh..eeehhhhhh...........hhhhhhhhh.........eee.......-----...hhhhhhhhhhhhhhhhhhhhhhhh.............hhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V-------------------------------------R-- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a1r A   1 MEIIRSNFKSNLHKVYQAIEEADFFAIDGEFSGISDGPSV-----GFDTPEERYQKLKKHSMDFLLFQFGLCTFKYDYTDSKYITKSFNFYVFPKPFNRSSPDVKFVCQSSSIDFLASQGFDFNKVFRNGIPYLNQEEERQLR-----------------------------------------------------------------------------------------------------------------HAKEQEELNDAVGFSRVIHAIANSGKLVIGHNMLLDVMHTVHQFYCPLPADLSEFKEMTTCVFPRLLDTKLMASTQPFKDIINNTSLAELEKRLKETPFNPPKVESAEGFPSY-----QLHEAGYDAYITGLCFISMANYLGSFLSPPKIHVSARSKLIEPFFNKLF 423
                                    10        20        30        40     |  50        60        70        80        90       100       110       120       130       140  |      -         -         -         -         -         -         -         -         -         -         -      |260       270       280       290       300       310       320       330       340       350       360        |-    |  380       390       400       410       420   
                                                                  40    46                                                                                              143                                                                                                               257                                                                                                             369   375

Chain B from PDB  Type:PROTEIN  Length:292
 aligned with PARN_HUMAN | O95453 from UniProtKB/Swiss-Prot  Length:639

    Alignment length:423
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420   
           PARN_HUMAN     1 MEIIRSNFKSNLHKVYQAIEEADFFAIDGEFSGISDGPSVSALTNGFDTPEERYQKLKKHSMDFLLFQFGLCTFKYDYTDSKYITKSFNFYVFPKPFNRSSPDVKFVCQSSSIDFLASQGFDFNKVFRNGIPYLNQEEERQLREQYDEKRSQANGAGALSYVSPNTSKCPVTIPEDQKKFIDQVVEKIEDLLQSEENKNLDLEPCTGFQRKLIYQTLSWKYPKGIHVETLETEKKERYIVISKVDEEERKRREQQKHAKEQEELNDAVGFSRVIHAIANSGKLVIGHNMLLDVMHTVHQFYCPLPADLSEFKEMTTCVFPRLLDTKLMASTQPFKDIINNTSLAELEKRLKETPFNPPKVESAEGFPSYDTASEQLHEAGYDAYITGLCFISMANYLGSFLSPPKIHVSARSKLIEPFFNKLF 423
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhhhhhhhhhh..eeeeeeee.........---------..hhhhhhhhhh....eeeeeeeeeeee....eeeeeeeeee.............eeeeehhhhhhhhhh...hhhhhh......hhhhhhhh.---------------------------------------------------------------------------------------------------------------------hhhhhh...hhhhhhhhhhh..eeee..hhhhhhhhhhhhh.....hhhhhhhhhhhhh..eeehhhhhh...........hhhhhhhhh.........eee.......-----...hhhhhhhhhhhhhhhhhhhhhhhh.............hhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V-------------------------------------R-- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a1r B   1 MEIIRSNFKSNLHKVYQAIEEADFFAIDGEFSGISDGPSV---------PEERYQKLKKHSMDFLLFQFGLCTFKYDYTDSKYITKSFNFYVFPKPFNRSSPDVKFVCQSSSIDFLASQGFDFNKVFRNGIPYLNQEEERQLR---------------------------------------------------------------------------------------------------------------------QEELNDAVGFSRVIHAIANSGKLVIGHNMLLDVMHTVHQFYCPLPADLSEFKEMTTCVFPRLLDTKLMASTQPFKDIINNTSLAELEKRLKETPFNPPKVESAEGFPSY-----QLHEAGYDAYITGLCFISMANYLGSFLSPPKIHVSARSKLIEPFFNKLF 423
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140  |      -         -         -         -         -         -         -         -         -         -         -         -|      270       280       290       300       310       320       330       340       350       360        |-    |  380       390       400       410       420   
                                                                  40        50                                                                                          143                                                                                                                   261                                                                                                         369   375

Chain C from PDB  Type:RNA  Length:3
                                   
                 2a1r C 501 AAA 503

Chain D from PDB  Type:RNA  Length:3
                                   
                 2a1r D 601 AAA 603

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 2A1R)

(no "CATH Domain" information available for 2A1R)

(no "Pfam Domain" information available for 2A1R)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PARN_HUMAN | O95453)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0004527	exonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
	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:0003730	mRNA 3'-UTR binding	Interacting selectively and non-covalently with the 3' untranslated region of an mRNA molecule.
	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:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0004535	poly(A)-specific ribonuclease activity	Catalysis of the exonucleolytic cleavage of poly(A) to 5'-AMP.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
biological process
	GO:0009451	RNA modification	The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically.
	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:0007292	female gamete generation	Generation of the female gamete; specialised haploid cells produced by meiosis and along with a male gamete takes part in sexual reproduction.
	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:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.
	GO:0000289	nuclear-transcribed mRNA poly(A) tail shortening	Shortening of the poly(A) tail of a nuclear-transcribed mRNA from full length to an oligo(A) length.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
	GO:0043488	regulation of mRNA stability	Any process that modulates the propensity of mRNA molecules to degradation. Includes processes that both stabilize and destabilize mRNAs.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2a1r)

	Sites
(no "Sites" information available for 2a1r)

	Cis Peptide Bonds
		Gln A:332 - Pro A:333	[ RasMol ]
		Gln B:332 - Pro B:333	[ RasMol ]
		Ser A:402 - Pro A:403	[ RasMol ]
		Ser B:402 - Pro B:403	[ RasMol ]
		Thr A:353 - Pro A:354	[ RasMol ]
		Thr B:353 - Pro B:354	[ RasMol ]

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	2a1r
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Access by UniProt ID/Accession number
	PARN_HUMAN \| O95453
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	3.1.13.4
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	616353
		Disease Information	:	OMIM
	616371
		Disease Information	:	OMIM

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	PARN_HUMAN \| O95453	:	2a1s 3ctr

2a1s	NATIVE PARN NUCLEASE DOMAIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (1, 1)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 4)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (23, 23)

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