3ACA - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN NUDT5 COMPLEXED WITH 8-OXO-DADP AND MANGANESE

Authors :   T. Arimori, Y. Yamagata

Date :   30 Dec 09 (Deposition) - 12 Jan 11 (Release) - 05 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

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

Keywords :   Nudix Motif, Magnesium, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Arimori, H. Tamaoki, T. Nakamura, H. Kamiya, S. Ikemizu, Y. Takagi, T. Ishibashi, H. Harashima, M. Sekiguchi, Y. Yamagata
Diverse Substrate Recognition And Hydrolysis Mechanisms Of Human Nudt5
Nucleic Acids Res. V. 39 8972 2011
PubMed-ID: 21768126 | Reference-DOI: 10.1093/NAR/GKR575

Molecule 1 - ADP-SUGAR PYROPHOSPHATASE
	Chains	:	A, B
	EC Number	:	3.6.1.13
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B(+)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 13-208
	Gene	:	NUDT5, HSPC115
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	NUDT5, 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, 7)

No.	Name	Count	Type	Full Name
1	8DD	2	Ligand/Ion	8-OXO-7,8-DIHYDRO-2'-DEOXY-ADENOSINE-5'-DIPHOSPHATE
2	MN	5	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	8DD A:2 , MN A:4 , ALA A:96 , GLU A:116 , HOH A:387 , HOH A:388	BINDING SITE FOR RESIDUE MN A 3
2	AC2	SOFTWARE	8DD A:2 , MN A:3 , GLU A:112 , GLU A:116 , HOH A:326 , HOH A:340	BINDING SITE FOR RESIDUE MN A 4
3	AC3	SOFTWARE	8DD A:2 , GLU A:112 , HOH A:307	BINDING SITE FOR RESIDUE MN A 5
4	AC4	SOFTWARE	MN A:3 , MN A:4 , MN A:5 , TRP A:28 , ARG A:51 , ARG A:84 , ALA A:96 , GLY A:97 , LEU A:98 , GLU A:112 , HOH A:340 , HOH A:407 , TRP B:46 , GLU B:47	BINDING SITE FOR RESIDUE 8DD A 2
5	AC5	SOFTWARE	MN B:2 , ALA B:96 , GLU B:116 , 8DD B:209 , HOH B:518 , HOH B:519	BINDING SITE FOR RESIDUE MN B 1
6	AC6	SOFTWARE	MN B:1 , ALA B:96 , GLU B:112 , GLU B:116 , GLU B:166 , 8DD B:209 , HOH B:452 , HOH B:491	BINDING SITE FOR RESIDUE MN B 2
7	AC7	SOFTWARE	THR A:45 , TRP A:46 , GLU A:47 , MN B:1 , MN B:2 , TRP B:28 , ARG B:51 , ARG B:84 , ALA B:96 , LEU B:98 , GLU B:166 , HOH B:491	BINDING SITE FOR RESIDUE 8DD B 209

(no "SS Bond" information available for 3ACA)

(no "Cis Peptide Bond" information available for 3ACA)

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 3ACA)

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:196
 aligned with NUDT5_HUMAN | Q9UKK9 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:196
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202      
          NUDT5_HUMAN    13 GKQYIISEELISEGKWVKLEKTTYMDPTGKTRTWESVKRTTRKEQTADGVAVIPVLQRTLHYECIVLVKQFRPPMGGYCIEFPAGLIDDGETPEAAALRELEEETGYKGDIAECSPAVCMDPGLSNCTIHIVTVTINGDDAENARPKPKPGDGEFVEVISLPKNDLLQRLDALVAEEHLTVDARVYSYALALKHAN 208
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee...eeeeeeeee.....eeeeeeeee.........eeeeeeeee......eeeeeeeee....eeeee..eee.....hhhhhhhhhhhhhhh...eeeeeeeeee........eeeeeeeeee..hhhhhh...........eeeeee..hhhhhhhhhhhhhh.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
                 3aca A  13 GKQYIISEELISEGKWVKLEKTTYMDPTGKTRTWESVKRTTRKEQTADGVAVIPVLQRTLHYECIVLVKQFRPPMGGYCIEFPAGLIDDGETPEAAALRELEEETGYKGDIAECSPAVCMDPGLSNCTIHIVTVTINGDDAENARPKPKPGDGEFVEVISLPKNDLLQRLDALVAEEHLTVDARVYSYALALKHAN 208
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202

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 ..eeeeeeeeee...eeeeeeeee.....eeeeeeeee.........eeeeeeeee......eeeeeeee......eeee..eee.....hhhhhhhhhhhhhhh...eeeeeeeeee........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
                 3aca 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 3ACA)

(no "CATH Domain" information available for 3ACA)

(no "Pfam Domain" information available for 3ACA)

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 3aca)

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Access by PDB/NDB ID
	3aca
		Family and Domain Information	:	ProDom \| SYSTERS
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	NUDT5_HUMAN \| Q9UKK9
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	3.6.1.13
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	NUDT5_HUMAN \| Q9UKK9
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UniProtKB/Swiss-Prot
	NUDT5_HUMAN \| Q9UKK9	:	2dsb 2dsc 2dsd 3ac9 3bm4 3l85

3ac9	THE SAME PROTEIN IN COMPLEX WITH 8-OXO-DGDP AND MANGANESE
3l85	THE SAME PROTEIN IN COMPLEX WITH 8-OXO-DGMP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (18, 18)

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Related Entries

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Related Entries Specified in the PDB File