3RRH - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   TERNARY STRUCTURE OF THE LARGE FRAGMENT OF TAQ DNA POLYMERASE BOUND TO AN ABASIC SITE AND A DDTTP

Authors :   A. Marx, K. Diederichs, S. Obeid

Date :   29 Apr 11 (Deposition) - 15 Feb 12 (Release) - 09 May 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Dna Polymerase, Abasic Site, Translesion Synthesis, A-Rule, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Obeid, W. Welte, K. Diederichs, A. Marx
Amino Acid Templating Mechanisms In Selection Of Nucleotide Opposite Abasic Sites By A Family A Dna Polymerase.
J. Biol. Chem. V. 287 14099 2012
PubMed-ID: 22318723 | Reference-DOI: 10.1074/JBC.M111.334904

Molecule 1 - DNA POLYMERASE I, THERMOSTABLE
	Chains	:	A
	EC Number	:	2.7.7.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-21B
	Expression System Strain	:	BL21 DE3
	Expression System Taxid	:	469008
	Fragment	:	KLENOW FRAGMENT
	Gene	:	POL I, POL1, POLA
	Organism Scientific	:	THERMUS AQUATICUS
	Organism Taxid	:	271
	Synonym	:	TAQ POLYMERASE 1

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

*Molecule 3 - (5'-D(APAPAP(3DR)PAPGPCPGPCPCPGPTPGPGPTPC)- 3')*
	Chains	:	C
	Engineered	:	YES
	Fragment	:	DNA TEMPLATE
	Synthetic	:	YES

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (7, 12)

No.	Name	Count	Type	Full Name
1	2DT	1	Mod. Nucleotide	3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE
2	3DR	1	Mod. Nucleotide	1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
3	ACT	1	Ligand/Ion	ACETATE ION
4	GOL	4	Ligand/Ion	GLYCEROL
5	MG	2	Ligand/Ion	MAGNESIUM ION
6	PGE	2	Ligand/Ion	TRIETHYLENE GLYCOL
7	TTP	1	Ligand/Ion	THYMIDINE-5'-TRIPHOSPHATE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HOH A:67 , HOH A:85 , HOH A:171 , GLN A:613 , HIS A:639 , ARG A:659 , LYS A:663 , PHE A:667 , TYR A:671 , ASP A:785 , MG A:833 , HOH A:854 , HOH A:875 , HOH A:876 , HOH A:888 , 2DT B:112	BINDING SITE FOR RESIDUE TTP A 1
02	AC2	SOFTWARE	TTP A:1 , HOH A:875 , HOH A:876	BINDING SITE FOR RESIDUE MG A 833
03	AC3	SOFTWARE	HOH A:149 , THR A:544 , TYR A:545 , PRO A:579 , ASN A:580 , ASN A:583 , DC C:209 , DC C:210	BINDING SITE FOR RESIDUE GOL A 834
04	AC4	SOFTWARE	ARG A:313	BINDING SITE FOR RESIDUE PGE A 835
05	AC5	SOFTWARE	HOH A:74 , HOH A:276 , ARG A:425 , TRP A:428	BINDING SITE FOR RESIDUE GOL A 836
06	AC6	SOFTWARE	SER A:644 , HOH A:893	BINDING SITE FOR RESIDUE ACT A 837
07	AC7	SOFTWARE	HOH B:20 , HOH B:43 , HOH B:176 , HOH C:144 , HOH C:290	BINDING SITE FOR RESIDUE MG B 1
08	AC8	SOFTWARE	HOH A:90 , HOH B:43 , HOH B:63 , DC B:106 , DG B:107	BINDING SITE FOR RESIDUE PGE B 113
09	AC9	SOFTWARE	DG C:213 , DG C:214 , DT C:215 , HOH C:365	BINDING SITE FOR RESIDUE GOL C 1
10	BC1	SOFTWARE	ALA A:570 , ARG A:728 , DG C:206 , DC C:207 , HOH C:287	BINDING SITE FOR RESIDUE GOL C 217

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

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 3RRH)

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 3RRH)

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:538
 aligned with DPO1_THEAQ | P19821 from UniProtKB/Swiss-Prot  Length:832

    Alignment length:538
                                   304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824        
           DPO1_THEAQ   295 EEAPWPPPEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALRDLKEARGLLAKDLSVLALREGLGLPPGDDPMLLAYLLDPSNTTPEGVARRYGGEWTEEAGERAALSERLFANLWGRLEGEERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPFNLNSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKILQYRELTKLKSTYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGRRRGYVETLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPRLEEMGARMLLQVHDELVLEAPKERAEAVARLAKEVMEGVYPLAVPLEVEVGIGEDWLSAKE 832
               SCOP domains d3rrha1 A:295-422 Exonuclease domain of prokaryotic DNA polymerase                                                              d3rrha2 A:423-832 DNA polymerase I (Klenow fragment)                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.......eeeeee.........eeeeeeee..eeee..hhhhhhh........hhhhhhhhhhhh........hhhhhhhhhh....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh..................hhhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhh.........eee.........eee..........hhhhhhhhh.ee....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh........hhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.....eee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee...eeeeeee..hhhhhhhhhhhhhhh.........eeeeee.hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYMERASE_A    ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rrh A 295 EEAPWPPPEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALRDLKEARGLLAKDLSVLALREGLGLPPGDDPMLLAYLLDPSNTTPEGVARRYGGEWTEEAGERAALSERLFANLWGRLEGEERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPFNLNSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKILQYRELTKLKSTYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGRRRGYVETLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPRLEEMGARMLLQVHDELVLEAPKERAEAVARLAKEVMEGVYPLAVPLEVEVGIGEDWLSAKE 832
                                   304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824

Chain B from PDB  Type:DNA  Length:12
                                            
                 3rrh B 101 GACCACGGCGCt 112
                                   110 |
                                     112-2DT

Chain C from PDB  Type:DNA  Length:14
                                              
                 3rrh C 203 AxAGCGCCGTGGTC 216
                             |     212    
                             |            
                           204-3DR

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 "CATH Domain" information available for 3RRH)

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

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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	3rrh
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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 (7, 12)

Sites (10, 10)

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

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SCOP Domains (2, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (12, 12)

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