3A6T - JenaLib

Title :   CRYSTAL STRUCTURE OF MUTT-8-OXO-DGMP COMPLEX

Authors :   T. Nakamura, Y. Yamagata

Date :   09 Sep 09 (Deposition) - 27 Oct 09 (Release) - 05 Jan 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.96

Chains :   Asym./Biol. Unit : A

Keywords :   Alpha-Beta-Alpha Sandwich, Dna Damage, Dna Repair, Dna Replication, Hydrolase, Mutator Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Nakamura, S. Meshitsuka, S. Kitagawa, N. Abe, J. Yamada, T. Ishino, H. Nakano, T. Tsuzuki, T. Doi, Y. Kobayashi, S. Fujii, M. Sekiguchi, Y. Yamagata
Structural And Dynamic Features Of The Mutt Protein In The Recognition Of Nucleotides With The Mutagenic 8-Oxoguanine Base
J. Biol. Chem. V. 285 444 2010
PubMed-ID: 19864691 | Reference-DOI: 10.1074/JBC.M109.066373
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 5)

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:47 , HIS A:64 , PHE A:65 , SER A:66 , TRP A:95 , GLY A:99 , ASN A:111 , ASP A:113 , LYS A:127 , SO4 A:132 , HOH A:140 , HOH A:173 , HOH A:180 , HOH A:209 , HOH A:214 , HOH A:228 , HOH A:255 , HOH A:256 , HOH A:262 , HOH A:265 , HOH A:269	BINDING SITE FOR RESIDUE SUC A 130
2	AC2	SOFTWARE	GLU A:53 , HOH A:145 , HOH A:233 , HOH A:252 , HOH A:267	BINDING SITE FOR RESIDUE NA A 131
3	AC3	SOFTWARE	GLN A:63 , HIS A:64 , PHE A:65 , LYS A:127 , SUC A:130 , HOH A:164 , HOH A:212 , HOH A:241 , HOH A:255 , HOH A:270	BINDING SITE FOR RESIDUE SO4 A 132
4	AC4	SOFTWARE	HIS A:64 , ARG A:89 , GLU A:120 , HOH A:244 , HOH A:257	BINDING SITE FOR RESIDUE SO4 A 133
5	AC5	SOFTWARE	ILE A:6 , VAL A:8 , ARG A:23 , HIS A:28 , GLU A:34 , PHE A:35 , GLY A:37 , PHE A:75 , ILE A:80 , LEU A:82 , PRO A:116 , ASN A:119 , HOH A:145 , HOH A:150 , HOH A:165 , HOH A:169 , HOH A:250	BINDING SITE FOR RESIDUE 8OG A 134

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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
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Chain A from PDB  Type:PROTEIN  Length:127
 aligned with MUTT_ECOLI | P08337 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:127
                                    12        22        32        42        52        62        72        82        92       102       112       122       
           MUTT_ECOLI     3 KLQIAVGIIRNENNEIFITRRAADAHMANKLEFPGGKIEMGETPEQAVVRELQEEVGITPQHFSLFEKLEYEFPDRHITLWFWLVERWEGEPWGKEGQPGEWMSLVGLNADDFPPANEPVIAKLKRL 129
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3a6tA00 A:3-129 Nucleoside Triphosphate Pyrophosphohydrolase                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....eeeeee..........ee..eee.....hhhhhhhhhhhhhhh.eee..eeeeeeeeee..eeeeeeeeee.eee..........eeeee....hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------NUDIX_BOX  PDB: A:38-5---------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a6t A   3 KLQIAVGIIRNENNEIFITRRAADAHMANKLEFPGGKIEMGETPEQAVVRELQEEVGITPQHFSLFEKLEYEFPDRHITLWFWLVERWEGEPWGKEGQPGEWMSLVGLNADDFPPANEPVIAKLKRL 129
                                    12        22        32        42        52        62        72        82        92       102       112       122

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (MUTT_ECOLI | P08337)

molecular function
	GO:0035539	8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity	Catalysis of the reaction: 8-oxo-7,8-dihydrodeoxyguanosine-triphosphate + H2O = 8-oxo-7,8-dihydrodeoxyguanosine phosphate + diphosphate. 8-oxo-7,8-dihydrodeoxyguanosine-triphosphate, or 8-oxo-dGTP, is the oxidised form of the free guanine nucleotide and can act as a potent mutagenic substrate for DNA synthesis causing transversion mutations. 8-oxo-dGTPase hydrolyses 8-oxo-dGTP to its monophosphate form to prevent the misincorporation of 8-oxo-dGTP into cellular DNA.
	GO:0008413	8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity	Catalysis of the reaction: 8-oxo-7,8-dihydroguanosine triphosphate = 8-oxo-7,8-dihydroguanosine phosphate + diphosphate. 8-oxo-7,8-dihydroguanosine triphosphate (8-oxo-GTP) is the oxidised form of the free guanine nucleotide and can act as a potent mutagenic substrate for transcription.
	GO:0044716	8-oxo-GDP phosphatase activity	Catalysis of the reaction 8-oxo-GDP + H2O = 8-oxo-GMP + phosphate.
	GO:0044715	8-oxo-dGDP phosphatase activity	Catalysis of the reaction 8-oxo-dGDP + H2O = 8-oxo-dGMP + phosphate.
	GO:0047693	ATP diphosphatase activity	Catalysis of the reaction: ATP + H2O = AMP + 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: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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0006281	DNA repair	The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	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:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.

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