1PU6 - JenaLib

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Title :   CRYSTAL STRUCTURE OF H.PYLORI 3-METHYLADENINE DNA GLYCOSYLASE (MAGIII)

Authors :   B. F. Eichman, E. J. O'Rourke, J. P. Radicella, T. Ellenberger

Date :   24 Jun 03 (Deposition) - 07 Oct 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.64

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

Keywords :   Helix-Hairpin-Helix, 3-Methyladenine, Base Excision Repair, Glycosylase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. F. Eichman, E. J. O'Rourke, J. P. Radicella, T. Ellenberger
Crystal Structures Of 3-Methyladenine Dna Glycosylase Magiii And The Recognition Of Alkylated Bases
Embo J. V. 22 4898 2003
PubMed-ID: 14517230 | Reference-DOI: 10.1093/EMBOJ/CDG505
(for further references see the PDB file header)

Molecule 1 - 3-METHYLADENINE DNA GLYCOSYLASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector	:	PGEX-6P-1
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	HELICOBACTER PYLORI
	Organism Taxid	:	210
	Strain	:	13-5

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 6)

No.	Name	Count	Type	Full Name
1	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
2	CL	1	Ligand/Ion	CHLORIDE ION
3	KCX	2	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
4	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	KCX	1	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
4	MPD	-1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	BME	-1	Ligand/Ion	BETA-MERCAPTOETHANOL
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	KCX	1	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
4	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:41 , ASN A:42 , ARG A:96	BINDING SITE FOR RESIDUE CL A 301
2	AC2	SOFTWARE	TRP A:24 , TRP A:25 , THR A:40 , PHE A:45 , HOH A:373 , HOH A:481	BINDING SITE FOR RESIDUE BME A 302
3	AC3	SOFTWARE	ALA A:187 , GLU A:190 , HOH B:468	BINDING SITE FOR RESIDUE MPD B 303
4	AC4	SOFTWARE	SER A:184 , ALA A:187 , PHE B:209 , GLN B:212	BINDING SITE FOR RESIDUE MPD B 304

(no "SS Bond" information available for 1PU6)

(no "Cis Peptide Bond" information available for 1PU6)

(no "SAP(SNP)/Variant" information available for 1PU6)

(no "PROSITE Motif" information available for 1PU6)

(no "Exon" information available for 1PU6)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:217
 aligned with O25323_HELPY | O25323 from UniProtKB/TrEMBL  Length:218

    Alignment length:217
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       
         O25323_HELPY     2 LDSFEILKALKSLDLLKNAPSWWWPNALKFEALLGAVLTQNTKFEAVLKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSKNILKDFQSFENFKQEVTREWLLNQKGVGKESADAILCYVCAKEVMVVDKYSYLFLKKIGIEIEDYDELQHFFEKGVQENLNSALALYENTIPLAQLYARFHGKIVEFSKQKLELKL 218
               SCOP domains d1pu6a_ A: 3-Methyladenine DNA glycosylase III (MagIII)                                                                                                                                                                   SCOP domains
               CATH domains 1pu6A01             1pu6A02 A:22-144 Hypothetical protein; domain 2                                                                            1pu6A01 A:2-21,A:145-218                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh................hhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pu6 A   2 LDSFEILKALKSLDLLKNAPAWWWPNALKFEALLGAVLTQNTKFEAVLKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSGNILKDFQSFENFKQEVTREWLLDQKGIGKESADAILCYACAKEVMVVDKYSYLFLKKLGIEIEDYDELQHFFEKGVQENLNSALALYENTISLAQLYARFHGkIVEFSKQKLELKL 218
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201   |   211       
                                                                                                                                                                                                                                     205-KCX

Chain B from PDB  Type:PROTEIN  Length:217
 aligned with O25323_HELPY | O25323 from UniProtKB/TrEMBL  Length:218

    Alignment length:217
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       
         O25323_HELPY     2 LDSFEILKALKSLDLLKNAPSWWWPNALKFEALLGAVLTQNTKFEAVLKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSKNILKDFQSFENFKQEVTREWLLNQKGVGKESADAILCYVCAKEVMVVDKYSYLFLKKIGIEIEDYDELQHFFEKGVQENLNSALALYENTIPLAQLYARFHGKIVEFSKQKLELKL 218
               SCOP domains d1pu6b_ B: 3-Methyladenine DNA glycosylase III (MagIII)                                                                                                                                                                   SCOP domains
               CATH domains 1pu6B01             1pu6B02 B:22-144 Hypothetical protein; domain 2                                                                            1pu6B01 B:2-21,B:145-218                                                   CATH domains
           Pfam domains (1) ---------------------------------HhH-GPD-1pu6B01 B:35-180                                                                                                                          -------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------HhH-GPD-1pu6B02 B:35-180                                                                                                                          -------------------------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhh................hhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pu6 B   2 LDSFEILKALKSLDLLKNAPAWWWPNALKFEALLGAVLTQNTKFEAVLKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSGNILKDFQSFENFKQEVTREWLLDQKGIGKESADAILCYACAKEVMVVDKYSYLFLKKLGIEIEDYDELQHFFEKGVQENLNSALALYENTISLAQLYARFHGkIVEFSKQKLELKL 218
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201   |   211       
                                                                                                                                                                                                                                     205-KCX

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	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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: DNA-glycosylase (77)

Superfamily: DNA-glycosylase (77)

Family: 3-Methyladenine DNA glycosylase III (MagIII) (3)

Protein domain: 3-Methyladenine DNA glycosylase III (MagIII) (3)

Helicobacter pylori [TaxId: 210] (3)

1a	d1pu6a_	A:
1b	d1pu6b_	B:

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HHH (112)

Family: HhH-GPD (47)

Helicobacter pylori (Campylobacter pylori) (3)

1a	HhH-GPD-1pu6B01	B:35-180
1b	HhH-GPD-1pu6B02	B:35-180

Asymmetric Unit(hide GO term definitions)

Chain A,B (O25323_HELPY | O25323)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
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:0006284	base-excision repair	In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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	O25323_HELPY \| O25323	:	1pu7 1pu8

1pu7	3,9-DIMETHYLADENINE BOUND TO MAGIII
1pu8	1,N6-ETHENOADENINE BOUND TO MAGIII

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