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Title :   CRYSTAL STRUCTURE OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS IN A CLOSED TERNARY COMPLEX WITH AMINOPENTINYL-7-DEAZA-2-DATP

Authors :   K. Bergen, A. Steck, S. Struett, A. Baccaro, W. Welte, K. Diederichs, A.

Date :   23 Jan 12 (Deposition) - 16 May 12 (Release) - 08 Aug 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,B,C

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

Reference :   K. Bergen, A. L. Steck, S. Strutt, A. Baccaro, W. Welte, K. Diederichs, A. Marx
Structures Of Klentaq Dna Polymerase Caught While Incorporating C5-Modified Pyrimidine And C7-Modified 7-Deazapurine Nucleoside Triphosphates.
J. Am. Chem. Soc. V. 134 11840 2012
PubMed-ID: 22475415 | Reference-DOI: 10.1021/JA3017889

Molecule 1 - DNA POLYMERASE I, THERMOSTABLE
	Chains	:	A
	EC Number	:	2.7.7.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21B
	Expression System Strain	:	BL21-DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PET SERIES
	Fragment	:	KLENOW FRAGMENT
	Gene	:	POL I, POL1, POLA
	Organism Scientific	:	THERMUS AQUATICUS
	Organism Taxid	:	271
	Synonym	:	TAQ POLYMERASE 1

*Molecule 2 - DNA (5'-D(GPAPCPCPAPCPGPGPCPGPCP(DOC))-3')*
	Chains	:	B
	Engineered	:	YES
	Fragment	:	DNA PRIMER
	Other Details	:	DNA SYNTHESIZER
	Synthetic	:	YES

*Molecule 3 - DNA (5'-D(APAPAPTPGPGPCPGPCPCPGPTPGPGPTPC)- 3')*
	Chains	:	C
	Engineered	:	YES
	Fragment	:	DNA TEMPLATE
	Other Details	:	DNA SYNTHESIZER
	Synthetic	:	YES

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 15)

No.	Name	Count	Type	Full Name
1	0L4	1	Ligand/Ion	5-(5-AMINOPENT-1-YN-1-YL)-7-{2-DEOXY-5-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO-PENTOFURANOSYL}-7H-PYRROLO[2,3-D]PYRIMIDIN-4-AMINE
2	CL	2	Ligand/Ion	CHLORIDE ION
3	DOC	1	Mod. Nucleotide	2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
4	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
5	FMT	4	Ligand/Ion	FORMIC ACID
6	MG	3	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:573 , ASP A:610 , TYR A:611 , SER A:612 , GLN A:613 , ILE A:614 , GLU A:615 , HIS A:639 , ARG A:659 , ARG A:660 , LYS A:663 , PHE A:667 , ASP A:785 , MG A:902 , MG A:903 , EDO A:907 , CL A:910 , HOH A:1001 , HOH A:1007 , HOH A:1019 , HOH A:1049 , HOH A:1106 , DOC B:112 , DT C:204 , DG C:205	BINDING SITE FOR RESIDUE 0L4 A 901
02	AC2	SOFTWARE	ASP A:610 , ASP A:785 , 0L4 A:901 , MG A:903 , HOH A:1002 , HOH A:1019	BINDING SITE FOR RESIDUE MG A 902
03	AC3	SOFTWARE	ASP A:610 , TYR A:611 , ASP A:785 , 0L4 A:901 , MG A:902	BINDING SITE FOR RESIDUE MG A 903
04	AC4	SOFTWARE	LYS A:354 , ASP A:355 , GLN A:566 , HOH A:1010	BINDING SITE FOR RESIDUE EDO A 904
05	AC5	SOFTWARE	LEU A:311 , ARG A:405 , HOH A:1096	BINDING SITE FOR RESIDUE FMT A 905
06	AC6	SOFTWARE	ARG A:313	BINDING SITE FOR RESIDUE CL A 906
07	AC7	SOFTWARE	ARG A:573 , GLU A:615 , GLN A:754 , ALA A:757 , ALA A:758 , HIS A:784 , 0L4 A:901 , HOH A:1079	BINDING SITE FOR RESIDUE EDO A 907
08	AC8	SOFTWARE	ARG A:704	BINDING SITE FOR RESIDUE FMT A 908
09	AC9	SOFTWARE	ASP A:488 , LYS A:511 , DC B:106 , DG B:107 , DG C:211 , DT C:212	BINDING SITE FOR RESIDUE EDO A 909
10	BC1	SOFTWARE	ARG A:660 , LYS A:663 , 0L4 A:901	BINDING SITE FOR RESIDUE CL A 910
11	BC2	SOFTWARE	HOH B:301 , HOH B:302 , HOH B:303 , HOH B:304 , HOH B:305 , HOH C:401	BINDING SITE FOR RESIDUE MG B 201
12	BC3	SOFTWARE	DG C:206 , FMT C:302	BINDING SITE FOR RESIDUE EDO C 301
13	BC4	SOFTWARE	DG C:205 , EDO C:301	BINDING SITE FOR RESIDUE FMT C 302
14	BC5	SOFTWARE	ARG A:728 , DG C:206 , DC C:207	BINDING SITE FOR RESIDUE FMT C 303

(no "SS Bond" information available for 4DF8)

Asymmetric/Biological Unit

No.	Residues
1	Trp A:299	-	Pro A:300
2	Asp A:578	-	Pro A:579

(no "SAP(SNP)/Variant" information available for 4DF8)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_POLYMERASE_A	PS00447	DNA polymerase family A signature.	DPO1_THEAQ	659-678	1	A:659-678

(no "Exon" information available for 4DF8)

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:539
 aligned with DPO1_THEAQ | P19821 from UniProtKB/Swiss-Prot  Length:832

    Alignment length:539
                                   303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823         
           DPO1_THEAQ   294 LEEAPWPPPEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALRDLKEARGLLAKDLSVLALREGLGLPPGDDPMLLAYLLDPSNTTPEGVARRYGGEWTEEAGERAALSERLFANLWGRLEGEERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPFNLNSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKILQYRELTKLKSTYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGRRRGYVETLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPRLEEMGARMLLQVHDELVLEAPKERAEAVARLAKEVMEGVYPLAVPLEVEVGIGEDWLSAKE 832
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee........eeeeee.........eeeeeeee..eeee..hhhhhhhhh......hhhhhhhhhhhh........hhhhhhhhhh....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh..................hhhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhh.........eee.........eee..........hhhhhhhhh.ee....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.....eee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee...eeeeeeehhhhhhhhhhhhhhhhh.........eeeeee.hhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYMERASE_A    ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4df8 A 294 LEEAPWPPPEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALRDLKEARGLLAKDLSVLALREGLGLPPGDDPMLLAYLLDPSNTTPEGVARRYGGEWTEEAGERAALSERLFANLWGRLEGEERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPFNLNSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKILQYRELTKLKSTYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGRRRGYVETLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPRLEEMGARMLLQVHDELVLEAPKERAEAVARLAKEVMEGVYPLAVPLEVEVGIGEDWLSAKE 832
                                   303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823

Chain B from PDB  Type:DNA  Length:12
                                            
                 4df8 B 101 GACCACGGCGCc 112
                                   110 |
                                     112-DOC

Chain C from PDB  Type:DNA  Length:16
                                                
                 4df8 C 201 AAATGGCGCCGTGGTC 216
                                   210

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 4DF8)

(no "CATH Domain" information available for 4DF8)

(no "Pfam Domain" information available for 4DF8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (DPO1_THEAQ | P19821)

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:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0001882	nucleoside binding	Interacting selectively and non-covalently with a nucleoside, a compound consisting of a purine or pyrimidine nitrogenous base linked either to ribose or deoxyribose.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
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.
	GO:0006261	DNA-dependent DNA replication	A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Asp A:578 - Pro A:579	[ RasMol ]
		Trp A:299 - Pro A:300	[ RasMol ]

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	4df8
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	DPO1_THEAQ \| P19821
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	2.7.7.7
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 15)

Sites (14, 14)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (12, 12)

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