3A6S - JenaLib

Title :   CRYSTAL STRUCTURE OF THE MUTT PROTEIN

Authors :   T. Nakamura, Y. Yamagata

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

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

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 (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	MUTT_ECOLI	1-129	2	A:1-129 B:1-129
2	NUDIX_BOX	PS00893	Nudix box signature.	MUTT_ECOLI	38-59	2	A:38-59 B:38-59

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	MUTT_ECOLI	1-129	1	A:1-129 -
2	NUDIX_BOX	PS00893	Nudix box signature.	MUTT_ECOLI	38-59	1	A:38-59 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	MUTT_ECOLI	1-129	1	- B:1-129
2	NUDIX_BOX	PS00893	Nudix box signature.	MUTT_ECOLI	38-59	1	- B:38-59

Biological Unit 3 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	MUTT_ECOLI	1-129	2	A:1-129 B:1-129
2	NUDIX_BOX	PS00893	Nudix box signature.	MUTT_ECOLI	38-59	2	A:38-59 B:38-59

Exons (0, 0)

Sequences/Alignments

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:125
 aligned with MUTT_ECOLI | P08337 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:129
                                    10        20        30        40        50        60        70        80        90       100       110       120         
           MUTT_ECOLI     1 MKKLQIAVGIIRNENNEIFITRRAADAHMANKLEFPGGKIEMGETPEQAVVRELQEEVGITPQHFSLFEKLEYEFPDRHITLWFWLVERWEGEPWGKEGQPGEWMSLVGLNADDFPPANEPVIAKLKRL 129
               SCOP domains d3a6sa_ A: Nucleoside tr    iphosphate pyrophosphorylase (MutT)                                                                   SCOP domains
               CATH domains 3a6sA00 A:1-129 Nucleosi    de Triphosphate Pyrophosphohydrolase                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee.....eeeeee..----....ee..eee.....hhhhhhhhhhhhhh.eeeeeeeeeeeeeeee..eeeeeeeeeeeeeee..........eeee....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) NUDIX  PDB: A:1-129 UniProt: 1-129                                                                                                PROSITE (1)
                PROSITE (2) -------------------------------------NUDIX_BOX  PDB: A:38-5---------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a6s A   1 MKKLQIAVGIIRNENNEIFITRRA----MANKLEFPGGKIEMGETPEQAVVRELQEEVGITPQHFSLFEKLEYEFPDRHITLWFWLVERWEGEPWGKEGQPGEWMSLVGLNADDFPPANEPVIAKLKRL 129
                                    10        20   |    30        40        50        60        70        80        90       100       110       120         
                                                  24   29

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with MUTT_ECOLI | P08337 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:129
                                    10        20        30        40        50        60        70        80        90       100       110       120         
           MUTT_ECOLI     1 MKKLQIAVGIIRNENNEIFITRRAADAHMANKLEFPGGKIEMGETPEQAVVRELQEEVGITPQHFSLFEKLEYEFPDRHITLWFWLVERWEGEPWGKEGQPGEWMSLVGLNADDFPPANEPVIAKLKRL 129
               SCOP domains d3a6sb_ B: Nucleoside         triphosphate pyrophosphorylase (MutT)                                                               SCOP domains
               CATH domains 3a6sB00 B:1-129 Nucleo        side Triphosphate Pyrophosphohydrolase                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee.....eeeee.--------......eee.....hhhhhhhhhhhhhh.eeeeeeeeeeeeeeee..eeeeeeeeeeeeeee.........eeeee....hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) NUDIX  PDB: B:1-129 UniProt: 1-129                                                                                                PROSITE (1)
                PROSITE (2) -------------------------------------NUDIX_BOX  PDB: B:38-5---------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a6s B   1 MKKLQIAVGIIRNENNEIFITR--------NKLEFPGGKIEMGETPEQAVVRELQEEVGITPQHFSLFEKLEYEFPDRHITLWFWLVERWEGEPWGKEGQPGEWMSLVGLNADDFPPANEPVIAKLKRL 129
                                    10        20 |       -|       40        50        60        70        80        90       100       110       120         
                                                22       31

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 (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (13, 13)

Asymmetric Unit(hide GO term definitions)

Chain A,B (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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