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Title :   CRYSTAL STRUCTURE OF HUMAN ADP-RIBOSE PYROPHOSPHATASE NUDT5 IN COMPLEX WITH MAGNESIUM AND AMP

Authors :   M. Zha, C. Zhong, J. Ding

Date :   28 Jun 06 (Deposition) - 14 Nov 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Nudix Domain, Adpr, Adp-Ribose Pyrophosphatase, Nudt5, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Zha, C. Zhong, Y. Peng, H. Hu, J. Ding
Crystal Structures Of Human Nudt5 Reveal Insights Into The Structural Basis Of The Substrate Specificity
J. Mol. Biol. V. 364 1021 2006
PubMed-ID: 17052728 | Reference-DOI: 10.1016/J.JMB.2006.09.078
(for further references see the PDB file header)

Molecule 1 - ADP-SUGAR PYROPHOSPHATASE
	Chains	:	A, B
	EC Number	:	3.6.1.13, 3.6.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PGEX4T-1
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1-210
	Gene	:	NUDT5
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 5, NUDIX MOTIF 5, YSA1H

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 8)

No.	Name	Count	Type	Full Name
1	AMP	2	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	MG	6	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:82 , ARG A:84 , ALA A:96 , GLU A:116 , AMP A:401 , HOH A:417	BINDING SITE FOR RESIDUE MG A 301
2	AC2	SOFTWARE	GLU A:112 , GLU A:115 , GLU A:116 , GLU A:166 , AMP A:401	BINDING SITE FOR RESIDUE MG A 302
3	AC3	SOFTWARE	LEU A:98 , GLU A:112 , AMP A:401 , HOH A:431	BINDING SITE FOR RESIDUE MG A 303
4	AC4	SOFTWARE	ALA B:96 , GLU B:116 , GLU B:166 , AMP B:402 , HOH B:419 , HOH B:440	BINDING SITE FOR RESIDUE MG B 304
5	AC5	SOFTWARE	GLU B:112 , GLU B:116 , GLU B:166 , AMP B:402	BINDING SITE FOR RESIDUE MG B 305
6	AC6	SOFTWARE	GLU B:112 , AMP B:402	BINDING SITE FOR RESIDUE MG B 306
7	AC7	SOFTWARE	TRP A:28 , ALA A:96 , GLY A:97 , GLU A:112 , GLU A:116 , GLU A:166 , MG A:301 , MG A:302 , MG A:303 , HOH A:417 , TRP B:46 , GLU B:47	BINDING SITE FOR RESIDUE AMP A 401
8	AC8	SOFTWARE	THR A:45 , TRP A:46 , GLU A:47 , VAL B:29 , ARG B:51 , ALA B:96 , GLY B:97 , LEU B:98 , GLU B:112 , GLU B:116 , GLU B:166 , MG B:304 , MG B:305 , MG B:306 , HOH B:419 , HOH B:442	BINDING SITE FOR RESIDUE AMP B 402

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

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

Asymmetric/Biological Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_034159	I	123	T	NUDT5_HUMAN	Polymorphism	34863826	A/B	I	123	T

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

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	NUDT5_HUMAN	57-197	2	A:57-197 B:57-197
2	NUDIX_BOX	PS00893	Nudix box signature.	NUDT5_HUMAN	97-118	2	A:97-118 B:97-118

(no "Exon" information available for 2DSD)

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:195
 aligned with NUDT5_HUMAN | Q9UKK9 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:195
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203     
          NUDT5_HUMAN    14 KQYIISEELISEGKWVKLEKTTYMDPTGKTRTWESVKRTTRKEQTADGVAVIPVLQRTLHYECIVLVKQFRPPMGGYCIEFPAGLIDDGETPEAAALRELEEETGYKGDIAECSPAVCMDPGLSNCTIHIVTVTINGDDAENARPKPKPGDGEFVEVISLPKNDLLQRLDALVAEEHLTVDARVYSYALALKHAN 208
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee....eeeeeeeee.....eeeeeeeee.........eeeeeeeee......eeeeeeeeehhhheeeee..eee.....hhhhhhhhhhhhhhh...eeee...eee........eeeeeeeeee..hhhhh............eeeeee..hhhhhhhhhhhhh..eehhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------T------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------NUDIX  PDB: A:57-197 UniProt: 57-197                                                                                                         ----------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------NUDIX_BOX             ------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dsd A  14 KQYIISEELISEGKWVKLEKTTYMDPTGKTRTWESVKRTTRKEQTADGVAVIPVLQRTLHYECIVLVKQFRPPMGGYCIEFPAGLIDDGETPEAAALRELEEETGYKGDIAECSPAVCMDPGLSNCTIHIVTVTINGDDAENARPKPKPGDGEFVEVISLPKNDLLQRLDALVAEEHLTVDARVYSYALALKHAN 208
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203

Chain B from PDB  Type:PROTEIN  Length:195
 aligned with NUDT5_HUMAN | Q9UKK9 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:195
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203     
          NUDT5_HUMAN    14 KQYIISEELISEGKWVKLEKTTYMDPTGKTRTWESVKRTTRKEQTADGVAVIPVLQRTLHYECIVLVKQFRPPMGGYCIEFPAGLIDDGETPEAAALRELEEETGYKGDIAECSPAVCMDPGLSNCTIHIVTVTINGDDAENARPKPKPGDGEFVEVISLPKNDLLQRLDALVAEEHLTVDARVYSYALALKHAN 208
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee....eeeeeeeee.....eeeeeeeee.........eeeeeeeee......eeeeeeee......eeee..eee.....hhhhhhhhhhhhhh....eeee....ee........eeeeeeeeee..hhhhh............eeeeee..hhhhhhhhhhhhh..eehhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------T------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------NUDIX  PDB: B:57-197 UniProt: 57-197                                                                                                         ----------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------NUDIX_BOX             ------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dsd B  14 KQYIISEELISEGKWVKLEKTTYMDPTGKTRTWESVKRTTRKEQTADGVAVIPVLQRTLHYECIVLVKQFRPPMGGYCIEFPAGLIDDGETPEAAALRELEEETGYKGDIAECSPAVCMDPGLSNCTIHIVTVTINGDDAENARPKPKPGDGEFVEVISLPKNDLLQRLDALVAEEHLTVDARVYSYALALKHAN 208
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203

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 2DSD)

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (NUDT5_HUMAN | Q9UKK9)

molecular function
	GO:0047631	ADP-ribose diphosphatase activity	Catalysis of the reaction: ADP-ribose + H2O = AMP + D-ribose 5-phosphate.
	GO:0019144	ADP-sugar diphosphatase activity	Catalysis of the reaction: ADP-sugar + H2O = AMP + sugar 1-phosphate.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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:0050072	m7G(5')pppN diphosphatase activity	Catalysis of the reaction: 7-methylguanosine 5'-triphospho-5'-polynucleotide + H2O = 7-methylguanosine 5'-phosphate + polynucleotide.
	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:0017110	nucleoside-diphosphatase activity	Catalysis of the reaction: a nucleoside diphosphate + H2O = a nucleotide + phosphate.
	GO:0030515	snoRNA binding	Interacting selectively and non-covalently with small nucleolar RNA.
biological process
	GO:0019303	D-ribose catabolic process	The chemical reactions and pathways resulting in the breakdown of D-ribose (ribo-pentose).
	GO:0006139	nucleobase-containing compound metabolic process	Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
	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:0009191	ribonucleoside diphosphate catabolic process	The chemical reactions and pathways resulting in the breakdown of a ribonucleoside diphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with diphosphate on the sugar.
cellular component
	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:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2dsd)

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	NUDT5_HUMAN \| Q9UKK9	:	2dsb 2dsc 3ac9 3aca 3bm4 3l85

2dsb	THE SAME PROTEIN WITHOUT LIGANDS
2dsc	THE SAME PROTEIN IN COMPLEX WITH MAGNESIUM AND ADP-RIBOSE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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