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Title :   CRYSTAL STRUCTURE OF HUMAN NUDIX MOTIF 16 (NUDT16) IN COMPLEX WITH IMP AND MAGNESIUM

Authors :   L. Tresaugues, M. Welin, C. H. Arrowsmith, H. Berglund, C. Bountra, R. C A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, I. Jo T. Karlberg, S. Kol, T. Kotenyova, E. Kouznetsova, M. Moche, T. Nyman, C. Persson, H. Schuler, P. Schutz, M. I. Siponen, A. G. Thorsell, S. Van Der Berg, E. Wahlberg, J. Weigelt, P. Nordlund

Date :   29 Sep 10 (Deposition) - 17 Nov 10 (Release) - 15 Jul 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.72

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Hydrolase, Mrna Decapping, Mrna Turnover, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Tresaugues, T. Lundback, M. Welin, S. Flodin, T. Nyman, C. Silvander, S. Graslund, P. Nordlund
Structural Basis For The Specificity Of Human Nudt16 And Its Regulation By Inosine Monophosphate.
Plos One V. 10 31507 2015
PubMed-ID: 26121039 | Reference-DOI: 10.1371/JOURNAL.PONE.0131507

Molecule 1 - U8 SNORNA-DECAPPING ENZYME
	Chains	:	A
	EC Number	:	3.6.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC-BSA4
	Expression System Strain	:	BL21(DE3)R3 PRARE
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	MAMMALIAN GENE COLLECTION (MGC)
	Synonym	:	NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 16, U8 SNORNA-BINDING PROTEIN H29K, NUDIX MOTIF 16

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 4)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	IMP	1	Ligand/Ion	INOSINIC ACID
3	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	IMP	2	Ligand/Ion	INOSINIC ACID
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:22 , HIS A:24 , ARG A:50 , PHE A:57 , PHE A:61 , ILE A:164 , GLN A:170 , HOH A:2099 , HOH A:2227 , HOH A:2228 , HOH A:2231 , HOH A:2232 , HOH A:2233 , HOH A:2234 , HOH A:2235 , HOH A:2236	BINDING SITE FOR RESIDUE IMP A1183
2	AC2	SOFTWARE	GLY A:59 , GLU A:80 , HOH A:2100 , HOH A:2120 , HOH A:2127 , HOH A:2128	BINDING SITE FOR RESIDUE MG A1184
3	AC3	SOFTWARE	GLU A:76 , HOH A:2100 , HOH A:2118 , HOH A:2119 , HOH A:2120 , HOH A:2186 , HOH A:2194	BINDING SITE FOR RESIDUE MG A1185
4	AC4	SOFTWARE	ARG A:38 , ARG A:149	BINDING SITE FOR RESIDUE CL A1186

(no "SS Bond" information available for 2XSQ)

(no "Cis Peptide Bond" information available for 2XSQ)

(no "SAP(SNP)/Variant" information available for 2XSQ)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	NUD16_HUMAN	18-173	1	A:18-173

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	NUD16_HUMAN	18-173	2	A:18-173

(no "Exon" information available for 2XSQ)

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)
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Chain A from PDB  Type:PROTEIN  Length:179
 aligned with NUD16_HUMAN | Q96DE0 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:179
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173         
          NUD16_HUMAN     4 ARRLELGEALALGSGWRHACHALLYAPDPGMLFGRIPLRYAILMQMRFDGRLGFPGGFVDTQDRSLEDGLNRELREELGEAAAAFRVERTDYRSSHVGSGPRVVAHFYAKRLTLEELLAVEAGATRAKDHGLEVLGLVRVPLYTLRDGVGGLPTFLENSFIGSAREQLLEALQDLGLLQ 182
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------NUDIX-2xsqA01 A:19-148                                                                                                            ---------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhh.....eeeeeeeeeeeeeeeehhheeeeeeeeeeee....ee..eee......hhhhhhhhhhhhhhhhhhhhh..hhh.eeeeee.....eeeeeeeee.hhhhhhhhhhhhhhh......eeeeee...........hhhhhh......hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------NUDIX  PDB: A:18-173 UniProt: 18-173                                                                                                                        --------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xsq A   4 ARRLELGEALALGSGWRHVCHALLYAPDPGMLFGRIPLRYAILMQMRFDGRLGFPGGFVDTQDRSLEDGLNRELREELGEAAAAFRVERTDYRSSHVGSGPRVVAHFYAKRLTLEELLAVEAGATRAKDHGLEVLGLVRVPLYTLRDGVGGLPTFLENSFIGSAREQLLEALQDLGLLQ 182
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173

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 2XSQ)

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NUDIX (85)

Family: NUDIX (78)

Homo sapiens (Human) (12)

NUDIX-2xsqA01

A:19-148

Asymmetric Unit(hide GO term definitions)

Chain A (NUD16_HUMAN | Q96DE0)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:1901641	ITP binding	Interacting selectively and non-covalently with ITP.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:1901640	XTP binding	Interacting selectively and non-covalently with XTP.
	GO:0050897	cobalt ion binding	Interacting selectively and non-covalently with a cobalt (Co) ion.
	GO:0097383	dIDP diphosphatase activity	Catalysis of the reaction: dIDP + H2O = dIMP + phosphate.
	GO:0035870	dITP diphosphatase activity	Catalysis of the reaction: dITP + H2O = dIMP + diphosphate.
	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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0050072	m7G(5')pppN diphosphatase activity	Catalysis of the reaction: 7-methylguanosine 5'-triphospho-5'-polynucleotide + H2O = 7-methylguanosine 5'-phosphate + polynucleotide.
	GO:0003729	mRNA binding	Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008235	metalloexopeptidase activity	Catalysis of the hydrolysis of a peptide bond not more than three residues from the N- or C-terminus of a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	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:0098519	nucleotide phosphatase activity, acting on free nucleotides	Catalysis of the reaction: nucleotide + H2O = nucleotide + phosphate.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0030515	snoRNA binding	Interacting selectively and non-covalently with small nucleolar RNA.
biological process
	GO:0046709	IDP catabolic process	The chemical reactions and pathways resulting in the breakdown of IDP, inosine 5'-diphosphate.
	GO:1901639	XDP catabolic process	The chemical reactions and pathways resulting in the breakdown of XDP.
	GO:0006382	adenosine to inosine editing	The conversion of an adenosine residue to inosine in an RNA molecule by deamination.
	GO:0035863	dITP catabolic process	The chemical reactions and pathways resulting in the breakdown of dITP, a deoxyinosine phosphate compound having a triphosphate group at the 5'-position.
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	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:2000233	negative regulation of rRNA processing	Any process that stops, prevents, or reduces the frequency, rate or extent of rRNA processing.
	GO:0034656	nucleobase-containing small molecule catabolic process	The chemical reactions and pathways resulting in the breakdown of a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide.
	GO:0009117	nucleotide metabolic process	The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
	GO:0090068	positive regulation of cell cycle process	Any process that increases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:2000781	positive regulation of double-strand break repair	Any process that activates or increases the frequency, rate or extent of double-strand break repair.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0016077	snoRNA catabolic process	The chemical reactions and pathways resulting in the breakdown of snoRNA, small nucleolar RNA, any of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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.

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