1Z4L - JenaLib

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Title :   STRUCTURE OF THE D41N VARIANT OF THE HUMAN MITOCHONDRIAL DEOXYRIBONUCLEOTIDASE IN COMPLEX WITH THYMIDINE 5'-MONOPHOSPHATE

Authors :   K. Wallden, B. Ruzzenente, A. Rinaldo-Matthis, V. Bianchi, P. Nordlund

Date :   16 Mar 05 (Deposition) - 26 Jul 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Alfa Beta Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Wallden, B. Ruzzenente, A. Rinaldo-Matthis, V. Bianchi, P. Nordlund
Structural Basis For Substrate Specificity Of The Human Mitochondrial Deoxyribonucleotidase
Structure V. 13 1081 2005
PubMed-ID: 16004879 | Reference-DOI: 10.1016/J.STR.2005.04.023
(for further references see the PDB file header)

Molecule 1 - 5'(3')-DEOXYRIBONUCLEOTIDASE
	Chains	:	A
	EC Number	:	3.1.3.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PLYSS
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MITOCHONDRIAL DEOXYRIBONUCLEOTIDASE, 5',3'- NUCLEOTIDASE, MITOCHONDRIAL, DEOXY-5'-NUCLEOTIDASE 2, DNT- 2

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION
2	TMP	1	Ligand/Ion	THYMIDINE-5'-PHOSPHATE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	TMP	2	Ligand/Ion	THYMIDINE-5'-PHOSPHATE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:41 , ASP A:43 , ASP A:176 , TMP A:1001 , HOH A:2037 , HOH A:2163	BINDING SITE FOR RESIDUE MG A 2001
2	AC2	SOFTWARE	ALA A:119 , LEU A:121 , THR A:124 , HOH A:2107 , HOH A:2116 , HOH A:2134	BINDING SITE FOR RESIDUE MG A 2002
3	AC3	SOFTWARE	ASN A:41 , ASP A:43 , PHE A:49 , PHE A:75 , TRP A:76 , VAL A:77 , SER A:78 , TRP A:96 , PHE A:102 , SER A:131 , PRO A:132 , ILE A:133 , LYS A:165 , MG A:2001 , HOH A:2037 , HOH A:2042 , HOH A:2163 , HOH A:2168 , HOH A:2169 , HOH A:2170 , HOH A:2181	BINDING SITE FOR RESIDUE TMP A 1001

(no "SS Bond" information available for 1Z4L)

Asymmetric Unit

No.	Residues
1	Pro A:206	-	Pro A:207

(no "SAP(SNP)/Variant" information available for 1Z4L)

(no "PROSITE Motif" information available for 1Z4L)

Asymmetric Unit (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000389022	1b	ENSE00001547211	chr17:17206680-17207131	452	NT5M_HUMAN	1-89	89	1	A:34-89	56
1.3	ENST00000389022	3	ENSE00001481533	chr17:17209857-17209957	101	NT5M_HUMAN	90-123	34	1	A:90-123	34
1.4	ENST00000389022	4	ENSE00001481531	chr17:17226499-17226559	61	NT5M_HUMAN	123-143	21	1	A:123-143	21
1.5a	ENST00000389022	5a	ENSE00001504694	chr17:17248108-17248222	115	NT5M_HUMAN	144-182	39	1	A:144-182	39
1.7c	ENST00000389022	7c	ENSE00001504693	chr17:17250119-17250975	857	NT5M_HUMAN	182-228	47	1	A:182-227	46

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)
	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:194
 aligned with NT5M_HUMAN | Q9NPB1 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:194
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223    
           NT5M_HUMAN    34 RALRVLVDMDGVLADFEGGFLRKFRARFPDQPFIALEDRRGFWVSEQYGRLRPGLSEKAISIWESKNFFFELEPLPGAVEAVKEMASLQNTDVFICTSPIKMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPDITGAEPTPSWEHVLFTACHNQHLQLQPPRRRLHSWADDWKAILDSKRP 227
               SCOP domains d1z4la_ A: automated matches                                                                                                                                                                       SCOP domains
               CATH domains 1z4lA01        1z4lA02 A:49-103 Deoxyribonucleotidase; domain 2       1z4lA01 A:34-48,A:104-227  [code=3.40.50.1000, no name defined]                                                              CATH domains
               Pfam domains NT5C-1z4lA01 A:34-227                                                                                                                                                                              Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhhh......hhhhh...hhhhhhhhhh.hhhhhhhhhhh............hhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhhhhhhh.eee..hhhhh...eeee..............eeeee.hhhhh........eee.....hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1b  PDB: A:34-89 UniProt: 1-89 [INCOMPLETE]      Exon 1.3  PDB: A:90-123           --------------------Exon 1.5a  PDB: A:144-182              --------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------Exon 1.4             --------------------------------------Exon 1.7c  PDB: A:182-227 UniProt: 182-228     Transcript 1 (2)
                 1z4l A  34 RALRVLVNMDGVLADFEGGFLRKFRARFPDQPFIALEDRRGFWVSEQYGRLRPGLSEKAISIWESKNFFFELEPLPGAVEAVKEMASLQNTDVFICTSPIKMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPDITGAEPTPSWEHVLFTACHNQHLQLQPPRRRLHSWADDWKAILDSKRP 227
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223

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 Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

)

Organisms( (-)

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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)

d1z4la_

Asymmetric Unit

Classes(

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Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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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)

1z4lA01

A:34-48,A:104-227

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)

1z4lA02

A:49-103

Asymmetric Unit

Clans(

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Families(

)

Organisms( (-)

)

Clan: HAD (186)

Family: NT5C (10)

Homo sapiens (Human) (10)

NT5C-1z4lA01

A:34-227

Asymmetric Unit(hide GO term definitions)

Chain A (NT5M_HUMAN | Q9NPB1)

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.
biological process
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0046079	dUMP catabolic process	The chemical reactions and pathways resulting in the breakdown of dUMP, deoxyuridine (5'-)monophosphate.
	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: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:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
	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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Pro A:206 - Pro A:207	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	1z4l
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1z4i	THE SAME PROTEIN COMPLEXED WITH DEOXYRIBOURIDINE 5'- MONOPHOSPHATE
1z4j	THE SAME PROTEIN COMPLEXED WITH URIDINE 2'-MONOPHOSPHATE
1z4k	THE SAME PROTEIN COMPLEXED WITH THYMIDINE 3'-MONOPHOSPHATE
1z4m	THE SAME PROTEIN COMPLEXED WITH URIDINE 5'-MONOPHOSPHATE
1z4p	THE SAME PROTEIN COMPLEXED WITH DEOXYRIBOGUANOSINE 5'- MONOPHOSPHATE
1z4q	THE SAME PROTEIN COMPLEXED WITH 3'-DEOXY 2'3'- DIDEHYDROTHYMIDINE 5'-MONOPHOSPHATE (D4T-MP)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (5, 5)

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SCOP Domains (1, 1)

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Pfam Domains (1, 1)

Gene Ontology (14, 14)

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