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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   MTH0212 (WT) IN COMPLEX WITH A 6BP DSDNA CONTAINING A SINGLE ONE NUCLEOTIDE LONG 3'-OVERHANG

Authors :   K. Lakomek, A. Dickmanns, R. Ficner

Date :   02 Feb 09 (Deposition) - 09 Mar 10 (Release) - 12 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.04

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

Keywords :   Protein-Dna Complex, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Lakomek, A. Dickmanns, E. Ciirdaeva, L. Schomacher, R. Ficner
Crystal Structure Analysis Of Dna Uridine Endonuclease Mth212 Bound To Dna
J. Mol. Biol. V. 399 604 2010
PubMed-ID: 20434457 | Reference-DOI: 10.1016/J.JMB.2010.04.044
(for further references see the PDB file header)

Molecule 1 - EXODEOXYRIBONUCLEASE
	Chains	:	A, B
	EC Number	:	3.1.11.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET_B_001-MTH212 (WT)
	Expression System Strain	:	BL21-CODONPLUS(DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MTH0212, MTH212, MTH_212
	Mutation	:	YES
	Organism Scientific	:	METHANOTHERMOBACTER THERMAUTOTROPHICUS
	Organism Taxid	:	187420
	Strain	:	DELTA H (DSM 1053)
	Synonym	:	MTH0212

*Molecule 2 - 5'-D(CPGPTPAPCPTPAPCPG)-3'**
	Chains	:	H
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 3 - 5'-D(CPGPTPAP(UPS)PTPAPCPG)-3'**
	Chains	:	I
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	H	I

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 6)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION
2	MRD	1	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL
3	PO4	2	Ligand/Ion	PHOSPHATE ION
4	UPS	1	Mod. Nucleotide	2'-DEOXY-5'-O-THIOPHOSPHONOURIDINE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU B:38 , TYR B:111 , ASP B:151 , ASN B:153 , HIS B:248 , MG B:267 , DA H:7	BINDING SITE FOR RESIDUE PO4 B 266
2	AC2	SOFTWARE	GLU A:38 , TYR A:111 , ASP A:151 , ASN A:153 , HIS A:248 , MG A:267 , HOH A:271 , DG I:9	BINDING SITE FOR RESIDUE PO4 A 266
3	AC3	SOFTWARE	ASN B:10 , ASN B:12 , GLU B:38 , ASP B:247 , PO4 B:266 , DA H:7	BINDING SITE FOR RESIDUE MG B 267
4	AC4	SOFTWARE	ASN A:12 , GLU A:38 , ASP A:247 , PO4 A:266 , DG I:9	BINDING SITE FOR RESIDUE MG A 267
5	AC5	SOFTWARE	ARG A:157	BINDING SITE FOR RESIDUE MRD A 268

(no "SS Bond" information available for 3G3C)

(no "Cis Peptide Bond" information available for 3G3C)

(no "SAP(SNP)/Variant" information available for 3G3C)

(no "PROSITE Motif" information available for 3G3C)

(no "Exon" information available for 3G3C)

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:255
 aligned with O26314_METTH | O26314 from UniProtKB/TrEMBL  Length:257

    Alignment length:255
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251     
         O26314_METTH     2 TVLKIISWNVNGLRAVHRKGFLKWFMEEKPDILCLQEIKAAPEQLPRKLRHVEGYRSFFTPAERKGYSGVAMYTKVPPSSLREGFGVERFDTEGRIQIADFDDFLLYNIYFPNGKMSEERLKYKLEFYDAFLEDVNRERDSGRNVIICGDFNTAHREIDLARPKENSNVSGFLPVERAWIDKFIENGYVDTFRMFNSDPGQYTWWSYRTRARERNVGWRLDYFFVNEEFKGKVKRSWILSDVMGSDHCPIGLEIE 256
               SCOP domains d3g3ca_ A: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..hhhhhhh.hhhhhhhhhh..eeeee....hhhhhhhhhhh....eeeee.........eeeee.....eee....hhhhhh...eeeee....eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.....hhhhh.hhhhhh.....hhhhhhhhhhhhhh.eee.hhhh..............hhhhhh.....eeeeee..hhh.eeeeee...........eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g3c A   2 AVLKIISWNVNGLRAVHRKGFLKWFMEEKPDILCLQEIKAAPEQLPRKLRHVEGYRSFFTPAERKGYSGVAMYTKVPPSSLREGFGVERFDTEGRIQIADFDDFLLYNIYFPNGKMSEERLKYKLEFYDAFLEDVNRERDSGRNVIICGDFNTAHREIDLARPKENSNVSGFLPVERAWIDKFIENGYVDTFRMFNSDPGQYTWWSYRTRARERNVGWRLDYFFVNEEFKGKVKRSWILSDVMGSDHCPIGLEIE 256
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251

Chain B from PDB  Type:PROTEIN  Length:257
 aligned with O26314_METTH | O26314 from UniProtKB/TrEMBL  Length:257

    Alignment length:257
                                                                                                                                                                                                                                                                                         257 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251     | 
         O26314_METTH     2 TVLKIISWNVNGLRAVHRKGFLKWFMEEKPDILCLQEIKAAPEQLPRKLRHVEGYRSFFTPAERKGYSGVAMYTKVPPSSLREGFGVERFDTEGRIQIADFDDFLLYNIYFPNGKMSEERLKYKLEFYDAFLEDVNRERDSGRNVIICGDFNTAHREIDLARPKENSNVSGFLPVERAWIDKFIENGYVDTFRMFNSDPGQYTWWSYRTRARERNVGWRLDYFFVNEEFKGKVKRSWILSDVMGSDHCPIGLEIEL-   -
               SCOP domains d3g3cb_ B: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..hhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh....eeeee.........eeeee.....eee....hhhhhh...eeeee....eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.....hhhhh.hhhhhh.....hhhhhhhhhhhhhh.eee.hhhh..............hhhhhh.....eeeeee..hhh.eeeeee...........eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g3c B   2 AVLKIISWNVNGLRAVHRKGFLKWFMEEKPDILCLQEIKAAPEQLPRKLRHVEGYRSFFTPAERKGYSGVAMYTKVPPSSLREGFGVERFDTEGRIQIADFDDFLLYNIYFPNGKMSEERLKYKLEFYDAFLEDVNRERDSGRNVIICGDFNTAHREIDLARPKENSNVSGFLPVERAWIDKFIENGYVDTFRMFNSDPGQYTWWSYRTRARERNVGWRLDYFFVNEEFKGKVKRSWILSDVMGSDHCPIGLEIELL 258
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251

Chain H from PDB  Type:DNA  Length:7
                                       
                 3g3c H   1 CGTACTA   7

Chain I from PDB  Type:DNA  Length:7
                                       
                 3g3c I   3 TAxTACG   9
                              |    
                              5-UPS

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) (23004)

Fold: DNase I-like (70)

Superfamily: DNase I-like (70)

Family: automated matches (26)

Protein domain: automated matches (26)

Methanothermobacter thermautotrophicus [TaxId: 187420] (15)

1a	d3g3ca_	A:
1b	d3g3cb_	B:

(no "CATH Domain" information available for 3G3C)

(no "Pfam Domain" information available for 3G3C)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (O26314_METTH | O26314)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
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:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3g3c)

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	3.1.11.2
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3fzi	1.9 ANGSTROM STRUCTURE OF THE THERMOPHILIC EXONUCLEASE III HOMOLOGUE MTH0212
3g00	MTH0212 IN COMPLEX WITH A 9BP BLUNT END DSDNA AT 1.7 ANGSTROM
3g0a	MTH0212 WITH TWO BOUND MANGANESE IONS
3g0r	COMPLEX OF MTH0212 AND AN 8BP DSDNA WITH DISTORTED ENDS
3g1k	MTH0212 (WT) CRYSTALLIZED IN A MONOCLINIC SPACE GROUP
3g2c	MTH0212 IN COMPLEX WITH A SHORT SSDNA (CGTA)
3g2d	COMPLEX OF MTH0212 AND A 4 BP DSDNA WITH 3'-OVERHANG
3g38	THE CATALYTICALLY INACTIVE MUTANT MTH0212 (D151N) IN COMPLEX WITH AN 8 BP DSDNA
3g3y	MTH0212 IN COMPLEX WITH SSDNA IN SPACE GROUP P32
3g4t	MTH0212 (WT) IN COMPLEX WITH A 7BP DSDNA
3g8v	THE RATIONALLY DESIGNED CATALYTICALLY INACTIVE MUTANT MTH0212(D151N)
3g91	1.2 ANGSTROM STRUCTURE OF THE EXONUCLEASE III HOMOLOGUE MTH0212
3ga6	MTH0212 IN COMPLEX WITH TWO DNA HELICES

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 6)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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