3AUO - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   DNA POLYMERASE X FROM THERMUS THERMOPHILUS HB8 TERNARY COMPLEX WITH 1-NT GAPPED DNA AND DDGTP

Authors :   S. Nakane, N. Nakagawa, R. Masui, S. Kuramitsu

Date :   11 Feb 11 (Deposition) - 25 Jan 12 (Release) - 25 Dec 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Rsgi, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Polxc Domain, Php Domain, Dna Polymerase, Drp Lyase, Ap Endonuclease, 3'-5' Exonuclease, Dna Repair, Dna Binding, Nucleotide Binding, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Nakane, H. Ishikawa, N. Nakagawa, S. Kuramitsu, R. Masui
The Structural Basis Of The Kinetic Mechanism Of A Gap-Filling X-Family Dna Polymerase That Binds Mg(2+)-Dntp Before Binding To Dna.
J. Mol. Biol. V. 417 179 2012
PubMed-ID: 22306405 | Reference-DOI: 10.1016/J.JMB.2012.01.025

Molecule 1 - DNA POLYMERASE BETA FAMILY (X FAMILY)
	Chains	:	A, B
	EC Number	:	2.7.7.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-11A
	Expression System Strain	:	ROSETTA2/PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	POLX, TTHA1150
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	300852
	Strain	:	HB8

Molecule 2 - 1-NT GAPPED DNA
	Chains	:	D, E
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	B	D	E
Biological Unit 1 (1x)	:	A		D
Biological Unit 2 (1x)	:		B		E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 10)

No.	Name	Count	Type	Full Name
1	DDG	2	Mod. Nucleotide	2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE
2	DG3	2	Ligand/Ion	2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
3	MG	4	Ligand/Ion	MAGNESIUM ION
4	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	DDG	1	Mod. Nucleotide	2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE
2	DG3	1	Ligand/Ion	2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	DDG	1	Mod. Nucleotide	2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE
2	DG3	1	Ligand/Ion	2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:35 , ARG A:157 , GLY A:187 , SER A:188 , ARG A:191 , VAL A:196 , GLY A:197 , ASP A:198 , ASP A:200 , TYR A:258 , LEU A:259 , GLY A:261 , LYS A:263 , ARG A:270 , MG A:577 , MG A:578 , HOH A:581 , DC D:13 , DDG D:29	BINDING SITE FOR RESIDUE DG3 A 576
2	AC2	SOFTWARE	SER A:188 , ASP A:198 , ASP A:200 , DG3 A:576	BINDING SITE FOR RESIDUE MG A 577
3	AC3	SOFTWARE	ASP A:198 , ASP A:200 , ASP A:243 , DG3 A:576 , DDG D:29	BINDING SITE FOR RESIDUE MG A 578
4	AC4	SOFTWARE	GLU A:413 , HIS A:440 , HIS A:468	BINDING SITE FOR RESIDUE ZN A 579
5	AC5	SOFTWARE	ARG B:35 , ARG B:157 , GLY B:187 , SER B:188 , ARG B:191 , VAL B:196 , GLY B:197 , ASP B:198 , ASP B:200 , TYR B:258 , LEU B:259 , LYS B:263 , ARG B:270 , MG B:577 , MG B:578 , HOH B:590 , DC E:13 , DDG E:29	BINDING SITE FOR RESIDUE DG3 B 576
6	AC6	SOFTWARE	SER B:188 , ASP B:198 , ASP B:200 , DG3 B:576 , HOH B:619	BINDING SITE FOR RESIDUE MG B 577
7	AC7	SOFTWARE	ASP B:198 , ASP B:200 , ASP B:243 , DG3 B:576 , DDG E:29	BINDING SITE FOR RESIDUE MG B 578
8	AC8	SOFTWARE	GLU B:413 , HIS B:440 , HIS B:468 , HOH B:580	BINDING SITE FOR RESIDUE ZN B 579

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

Asymmetric Unit

No.	Residues
1	Gly A:261	-	Ser A:262
2	Gly A:383	-	Pro A:384
3	Pro A:405	-	Pro A:406
4	Asp A:508	-	Leu A:509
5	Gly B:261	-	Ser B:262
6	Gly B:383	-	Pro B:384
7	Pro B:405	-	Pro B:406
8	Asp B:508	-	Leu B:509

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

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

(no "Exon" information available for 3AUO)

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:572
 aligned with Q5SJ64_THET8 | Q5SJ64 from UniProtKB/TrEMBL  Length:575

    Alignment length:572
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570  
         Q5SJ64_THET8     1 MRNQELARIFEEIGLMSEFLGDNPFRVRAYHQAARTLYDLDTPIEEIAEKGKEALMELPGVGPDLAEKILEFLRTGKVRKHEELSRKVPRGVLEVMEVPGVGPKTARLLYEGLGIDSLEKLKAALDRGDLTRLKGFGPKRAERIREGLALAQAAGKRRPLGAVLSLARSLLEAIRALPGVERAELCGSARRYKDTVGDLDFLVASREGERAVEGFVRLPQVKEVYAKGKERATVFLKNGLQVDLRVVPPESYGAGLQYLTGSKAHSIRLRALAQEKGLKLSEYGVFRGEKRIAGETEEEVYAALGLPWIPPPLREDQGEVEAALEGRLPKLLELPQVKGDLQVHSTYSDGQNTLEELWEAAKTMGYRYLAVTDHSPAVRVAGGPSPEEALKRVGEIRRFNETHGPPYLLAGAEVDIHPDGTLDYPDWVLRELDLVLVSVHSRFNLPKADQTKRLLKALENPFVHVLAHPTARLLGRRAPIEADWEAVFQKAKEKGVAVEIDGYYDRMDLPDDLARMAYGMGLWISLSTDAHQTDHLRFMELAVGTAQRAWIGPERVLNTLDYEDLLSWLKAR 572
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhh.....eeeehhhhhh...ee..eeeeee..hhhhhhhhhhh...eeeeeee...eeeeee....eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee....eee..eeee..hhhhhhhhh.....hhhhh...hhhhhhhh.......hhhhh.eeeee.........hhhhhhhhhhhhh..eeeeeee.hhhh........hhhhhhhhhhhhhhhhh..eeeeeeeee.........hhhhhhh..eeeee.......hhhhhhhhhhhhhhh....ee................hhhhhhhhhhhh..eeeee........hhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3auo A   1 MRNQELARIFEEIGLMSEFLGDNPFRVRAYHQAARTLYDLDTPIEEIAEKGKEALMELPGVGPDLAEKILEFLRTGKVRKHEELSRKVPRGVLEVMEVPGVGPKTARLLYEGLGIDSLEKLKAALDRGDLTRLKGFGPKRAERIREGLALAQAAGKRRPLGAVLSLARSLLEAIRALPGVERAELCGSARRYKDTVGDLDFLVASREGERAVEGFVRLPQVKEVYAKGKERATVFLKNGLQVDLRVVPPESYGAGLQYLTGSKAHSIRLRALAQEKGLKLSEYGVFRGEKRIAGETEEEVYAALGLPWIPPPLREDQGEVEAALEGRLPKLLELPQVKGDLQVHSTYSDGQNTLEELWEAAKTMGYRYLAVTDHSPAVRVAGGPSPEEALKRVGEIRRFNETHGPPYLLAGAEVDIHPDGTLDYPDWVLRELDLVLVSVHSRFNLPKADQTKRLLKALENPFVHVLAHPTARLLGRRAPIEADWEAVFQKAKEKGVAVEIDGYYDRMDLPDDLARMAYGMGLWISLSTDAHQTDHLRFMELAVGTAQRAWIGPERVLNTLDYEDLLSWLKAR 572
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570

Chain B from PDB  Type:PROTEIN  Length:572
 aligned with Q5SJ64_THET8 | Q5SJ64 from UniProtKB/TrEMBL  Length:575

    Alignment length:572
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570  
         Q5SJ64_THET8     1 MRNQELARIFEEIGLMSEFLGDNPFRVRAYHQAARTLYDLDTPIEEIAEKGKEALMELPGVGPDLAEKILEFLRTGKVRKHEELSRKVPRGVLEVMEVPGVGPKTARLLYEGLGIDSLEKLKAALDRGDLTRLKGFGPKRAERIREGLALAQAAGKRRPLGAVLSLARSLLEAIRALPGVERAELCGSARRYKDTVGDLDFLVASREGERAVEGFVRLPQVKEVYAKGKERATVFLKNGLQVDLRVVPPESYGAGLQYLTGSKAHSIRLRALAQEKGLKLSEYGVFRGEKRIAGETEEEVYAALGLPWIPPPLREDQGEVEAALEGRLPKLLELPQVKGDLQVHSTYSDGQNTLEELWEAAKTMGYRYLAVTDHSPAVRVAGGPSPEEALKRVGEIRRFNETHGPPYLLAGAEVDIHPDGTLDYPDWVLRELDLVLVSVHSRFNLPKADQTKRLLKALENPFVHVLAHPTARLLGRRAPIEADWEAVFQKAKEKGVAVEIDGYYDRMDLPDDLARMAYGMGLWISLSTDAHQTDHLRFMELAVGTAQRAWIGPERVLNTLDYEDLLSWLKAR 572
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.......eehhhhhhhhhhhhhhhhhh....eeeehhhhhh...ee..eeeeee..hhhhhhhhhhh...eeeeeee...eeeeee....eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee..eeee..eeee..hhhhhhhh......hhhhh...hhhhhhhh.......hhhhh.eeeee.........hhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhhhhhhhhhh..eeeeeeeee.........hhhhhhhh.eeeee.......hhhhhhhhhhhhhh.....ee................hhhhhhhhhhhh..eeeee........hhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3auo B   1 MRNQELARIFEEIGLMSEFLGDNPFRVRAYHQAARTLYDLDTPIEEIAEKGKEALMELPGVGPDLAEKILEFLRTGKVRKHEELSRKVPRGVLEVMEVPGVGPKTARLLYEGLGIDSLEKLKAALDRGDLTRLKGFGPKRAERIREGLALAQAAGKRRPLGAVLSLARSLLEAIRALPGVERAELCGSARRYKDTVGDLDFLVASREGERAVEGFVRLPQVKEVYAKGKERATVFLKNGLQVDLRVVPPESYGAGLQYLTGSKAHSIRLRALAQEKGLKLSEYGVFRGEKRIAGETEEEVYAALGLPWIPPPLREDQGEVEAALEGRLPKLLELPQVKGDLQVHSTYSDGQNTLEELWEAAKTMGYRYLAVTDHSPAVRVAGGPSPEEALKRVGEIRRFNETHGPPYLLAGAEVDIHPDGTLDYPDWVLRELDLVLVSVHSRFNLPKADQTKRLLKALENPFVHVLAHPTARLLGRRAPIEADWEAVFQKAKEKGVAVEIDGYYDRMDLPDDLARMAYGMGLWISLSTDAHQTDHLRFMELAVGTAQRAWIGPERVLNTLDYEDLLSWLKAR 572
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570

Chain D from PDB  Type:DNA  Length:29
                                                             
                 3auo D   1 GCCGTTTTCGGCCCGACTGTTTTCAGTCg  29
                                    10        20        |
                                                       29-DDG

Chain E from PDB  Type:DNA  Length:29
                                                             
                 3auo E   1 GCCGTTTTCGGCCCGACTGTTTTCAGTCg  29
                                    10        20        |
                                                       29-DDG

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 '\|'

(no "SCOP Domain" information available for 3AUO)

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q5SJ64_THET8 | Q5SJ64)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003887	DNA-directed DNA polymerase activity	Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0071897	DNA biosynthetic process	The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
	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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Asp A:508 - Leu A:509	[ RasMol ]
		Asp B:508 - Leu B:509	[ RasMol ]
		Gly A:261 - Ser A:262	[ RasMol ]
		Gly A:383 - Pro A:384	[ RasMol ]
		Gly B:261 - Ser B:262	[ RasMol ]
		Gly B:383 - Pro B:384	[ RasMol ]
		Pro A:405 - Pro A:406	[ RasMol ]
		Pro B:405 - Pro B:406	[ RasMol ]

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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	3auo
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	2.7.7.7
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UniProtKB/TrEMBL
	Q5SJ64_THET8 \| Q5SJ64	:	3au2 3au6 3b0x 3b0y

3au2	THE SAME PROTEIN COMPLEXED WITH CA-DGTP
3au6	THE SAME PROTEIN COMPLEXED WITH PRIMER/TEMPLATE DNA AND DDGTP RELATED ID: TTK003000748.1 RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 10)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (7, 7)

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