2I7D - JenaLib

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Title :   STRUCTURE OF HUMAN CYTOSOLIC DEOXYRIBONUCLEOTIDASE IN COMPLEX WITH DEOXYURIDINE, ALF4 AND MG2+

Authors :   A. Rinaldo-Matthis, K. Wallden, P. Nordlund

Date :   30 Aug 06 (Deposition) - 30 Oct 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.20

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

Keywords :   Deoxyribonucleotidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Wallden, A. Rinaldo-Matthis, B. Ruzzenente, C. Rampazzo, V. Bianchi, P. Nordlund
Structures Of Human And Murine Cytosolic Deoxyribonucleotidase: Insights Into Substrate Specificity And Catalysis
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - 5'(3')-DEOXYRIBONUCLEOTIDASE, CYTOSOLIC TYPE
	Chains	:	A, B
	EC Number	:	3.1.3.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 3-195
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CYTOSOLIC 5',3'-PYRIMIDINE NUCLEOTIDASE, DEOXY-5'- NUCLEOTIDASE 1, DNT-1

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	ALF	2	Ligand/Ion	TETRAFLUOROALUMINATE ION
2	DUR	2	Ligand/Ion	2'-DEOXYURIDINE
3	MG	2	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:10 , ASP A:12 , ASP A:145 , ALF A:400 , HOH A:729 , HOH A:731	BINDING SITE FOR RESIDUE MG A 728
2	AC2	SOFTWARE	ASP B:10 , ASP B:12 , ASP B:145 , ALF B:401 , HOH B:730 , HOH B:733	BINDING SITE FOR RESIDUE MG B 729
3	AC3	SOFTWARE	ASP A:10 , MET A:11 , ASP A:12 , THR A:99 , SER A:100 , LYS A:112 , LYS A:134 , DUR A:300 , MG A:728 , HOH A:729 , HOH A:731	BINDING SITE FOR RESIDUE ALF A 400
4	AC4	SOFTWARE	ASP B:10 , MET B:11 , ASP B:12 , THR B:99 , SER B:100 , LYS B:112 , LYS B:134 , DUR B:301 , MG B:729 , HOH B:730 , HOH B:733	BINDING SITE FOR RESIDUE ALF B 401
5	AC5	SOFTWARE	ASP A:12 , PHE A:18 , PHE A:44 , LEU A:45 , ALA A:46 , SER A:100 , PRO A:101 , LEU A:102 , ALF A:400 , HOH A:731 , HOH A:759 , HOH A:782 , HOH A:821 , HOH A:859	BINDING SITE FOR RESIDUE DUR A 300
6	AC6	SOFTWARE	ASP B:12 , PHE B:18 , PHE B:44 , LEU B:45 , ALA B:46 , SER B:100 , PRO B:101 , LEU B:102 , ALF B:401 , HOH B:733 , HOH B:737 , HOH B:771 , HOH B:821 , HOH B:878	BINDING SITE FOR RESIDUE DUR B 301

(no "SS Bond" information available for 2I7D)

(no "Cis Peptide Bond" information available for 2I7D)

Asymmetric/Biological Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_048102	P	68	L	NT5C_HUMAN	Polymorphism	11541956	A/B	P	68	L

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

(no "PROSITE Motif" information available for 2I7D)

Asymmetric/Biological Unit (5, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000245552	1	ENSE00001174732	chr17:73127877-73127629	249	NT5C_HUMAN	1-58	58	2	A:3-58 B:4-58	56 55
1.2	ENST00000245552	2	ENSE00000744347	chr17:73127376-73127276	101	NT5C_HUMAN	59-92	34	2	A:59-92 B:59-92	34 34
1.3	ENST00000245552	3	ENSE00000744348	chr17:73127200-73127140	61	NT5C_HUMAN	92-112	21	2	A:92-112 B:92-112	21 21
1.4	ENST00000245552	4	ENSE00000744349	chr17:73126962-73126848	115	NT5C_HUMAN	113-151	39	2	A:113-151 B:113-151	39 39
1.5	ENST00000245552	5	ENSE00001174725	chr17:73126737-73126324	414	NT5C_HUMAN	151-201	51	2	A:151-195 B:151-195	45 45

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:193
 aligned with NT5C_HUMAN | Q8TCD5 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:193
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192   
           NT5C_HUMAN     3 RSVRVLVDMDGVLADFEAGLLRGFRRRFPEEPHVPLEQRRGFLAREQYRALRPDLADKVASVYEAPGFFLDLEPIPGALDAVREMNDLPDTQVFICTSPLLKYHHCVGEKYRWVEQHLGPQFVERIILTRDKTVVLGDLLIDDKDTVRGQEETPSWEHILFTCCHNRHLVLPPTRRRLLSWSDNWREILDSKR 195
               SCOP domains d2i7da_ A: automated matches                                                                                                                                                                      SCOP domains
               CATH domains 2i7dA01        2i7dA02 A:18-72 Deoxyribonucleotidase; domain 2        2i7dA01 A:3-17,A:73-195  [code=3.40.50.1000, no name defined]                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.......hhhhhhhhhhhhhh......hhhhh...hhhhhhhhhh.hhhhhhhhhhh............hhhhhhhhhhh...eeeeeee........hhhhhhhhhhhhhhhhhhh.eee..hhhhh...eeee..............eeeee.hhhhh.........ee.....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------L------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:3-58 UniProt: 1-58 [INCOMPLETE]        Exon 1.2  PDB: A:59-92            --------------------Exon 1.4  PDB: A:113-151               -------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------Exon 1.3             --------------------------------------Exon 1.5  PDB: A:151-195 UniProt: 151-201     Transcript 1 (2)
                 2i7d A   3 RSVRVLVDMDGVLADFEAGLLRGFRRRFPEEPHVPLEQRRGFLAREQYRALRPDLADKVASVYEAPGFFLDLEPIPGALDAVREMNDLPDTQVFICTSPLLKYHHCVGEKYRWVEQHLGPQFVERIILTRDKTVVLGDLLIDDKDTVRGQEETPSWEHILFTCCHNRHLVLPPTRRRLLSWSDNWREILDSKR 195
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192

Chain B from PDB  Type:PROTEIN  Length:192
 aligned with NT5C_HUMAN | Q8TCD5 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:192
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193  
           NT5C_HUMAN     4 SVRVLVDMDGVLADFEAGLLRGFRRRFPEEPHVPLEQRRGFLAREQYRALRPDLADKVASVYEAPGFFLDLEPIPGALDAVREMNDLPDTQVFICTSPLLKYHHCVGEKYRWVEQHLGPQFVERIILTRDKTVVLGDLLIDDKDTVRGQEETPSWEHILFTCCHNRHLVLPPTRRRLLSWSDNWREILDSKR 195
               SCOP domains d2i7db_ B: automated matches                                                                                                                                                                     SCOP domains
               CATH domains 2i7dB01       2i7dB02 B:18-72 Deoxyribonucleotidase; domain 2        2i7dB01 B:4-17,B:73-195  [code=3.40.50.1000, no name defined]                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.......hhhhhhhhhhhhhh......hhhhh...hhhhhhhhhh.hhhhhhhhhhh............hhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhhhhhhhh.eeee.hhhhh...eeee..............eeeee.hhhhh.........ee.....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------L------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:4-58 UniProt: 1-58 [INCOMPLETE]       Exon 1.2  PDB: B:59-92            --------------------Exon 1.4  PDB: B:113-151               -------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------Exon 1.3             --------------------------------------Exon 1.5  PDB: B:151-195 UniProt: 151-201     Transcript 1 (2)
                 2i7d B   4 SVRVLVDMDGVLADFEAGLLRGFRRRFPEEPHVPLEQRRGFLAREQYRALRPDLADKVASVYEAPGFFLDLEPIPGALDAVREMNDLPDTQVFICTSPLLKYHHCVGEKYRWVEQHLGPQFVERIILTRDKTVVLGDLLIDDKDTVRGQEETPSWEHILFTCCHNRHLVLPPTRRRLLSWSDNWREILDSKR 195
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: HAD-like (349)

Superfamily: HAD-like (349)

Family: 5'(3')-deoxyribonucleotidase (dNT-2) (18)

Protein domain: automated matches (14)

Human (Homo sapiens) [TaxId: 9606] (12)

1a	d2i7da_	A:
1b	d2i7db_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1000, no name defined] (211)

Human (Homo sapiens) (42)

1a	2i7dA01	A:3-17,A:73-195
1b	2i7dB01	B:4-17,B:73-195

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Ribonucleotide Reductase Protein R1; domain 1 (62)

Homologous Superfamily: Deoxyribonucleotidase; domain 2 (16)

Human (Homo sapiens) (13)

2a	2i7dA02	A:18-72
2b	2i7dB02	B:18-72

(no "Pfam Domain" information available for 2I7D)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (NT5C_HUMAN | Q8TCD5)

molecular function
	GO:0008253	5'-nucleotidase activity	Catalysis of the reaction: a 5'-ribonucleotide + H2O = a ribonucleoside + phosphate.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008252	nucleotidase activity	Catalysis of the reaction: a nucleotide + H2O = a nucleoside + phosphate.
	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:0016791	phosphatase activity	Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
	GO:0019103	pyrimidine nucleotide binding	Interacting selectively and non-covalently with pyrimidine nucleotide, any compound consisting of a pyrimidine nucleoside esterified with (ortho)phosphate.
biological process
	GO:0009264	deoxyribonucleotide catabolic process	The chemical reactions and pathways resulting in the breakdown of a deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	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:0006195	purine nucleotide catabolic process	The chemical reactions and pathways resulting in the breakdown of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
	GO:0009223	pyrimidine deoxyribonucleotide catabolic process	The chemical reactions and pathways resulting in the breakdown of a pyrimidine deoxyribonucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
	GO:0046135	pyrimidine nucleoside catabolic process	The chemical reactions and pathways resulting in the breakdown of one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
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: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:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	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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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (5, 10)

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