2J6S | PD0910 - JenaLib

Title :   TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, O6-METHYLGUANINE MODIFIED DNA, AND DATP.

Authors :   A. Irimia, R. L. Eoff, F. P. Guengerich, M. Egli

Date :   04 Oct 06 (Deposition) - 22 Nov 06 (Release) - 05 Jul 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A,P,T

Keywords :   Transferase/Dna, Transferase-Dna Complex, Mutator Protein, Dna Replication, O6-Methylguanine, Transferase, Metal-Binding, Dna Polymerase, Translesion Dna Synthesis, Dna-Directed Dna Polymerase, Dpo4, Magnesium, Dna Repair, Dna Damage, Dna-Binding, Nucleotidyltransferase, Sulfolobus Solfataricus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. L. Eoff, A. Irimia, M. Egli, F. P. Guengerich
Sulfolobus Solfataricus Dna Polymerase Dpo4 Is Partially Inhibited By "Wobble" Pairing Between O6- Methylguanine And Cytosine, But Accurate Bypass Is Preferred.
J. Biol. Chem. V. 282 1456 2007
PubMed-ID: 17105728 | Reference-DOI: 10.1074/JBC.M609661200

Compounds

Molecule 1 - DNA POLYMERASE IV
	Chains	:	A
	EC Number	:	2.7.7.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B/DPO4-NHIS
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	SULFOLOBUS SOLFATARICUS
	Organism Taxid	:	2287
	Other Details	:	GENE DPO4
	Synonym	:	POL IV

*Molecule 2 - 5'-D(GPGPGPGPGPAPAPGPGPAP TPTPCPC)-3'*
	Chains	:	P
	Engineered	:	YES
	Other Details	:	5'GGGGGAAGGATTCC3'
	Synonym	:	14-MER PRIMER
	Synthetic	:	YES

*Molecule 3 - 5'-D(TPCPAPTPXPGPAPAPTPCP CPTPTPCPCPCPCPC)-3'*
	Chains	:	T
	Engineered	:	YES
	Other Details	:	5'TCAT G32 GAATCCTTCCCCC3'
	Synonym	:	18MER TEMPLATE
	Synthetic	:	YES

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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
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Chain A from PDB  Type:PROTEIN  Length:342
 aligned with DPO4_SULSO | Q97W02 from UniProtKB/Swiss-Prot  Length:352

    Alignment length:342
                                    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  
           DPO4_SULSO     1 MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFIE 342
               SCOP domains d2j6sa2 A:1-240 automated matches                                                                                                                                                                                                               d2j6sa1 A:241-342 automated matches                                                                    SCOP domains
               CATH domains -2j6sA01  -------------------------------------------------------------------2j6sA01 A:2-10,A:78-166  [code=3.30.70.270, no name defined]                             2j6sA03 A:167-233 5' to 3' exonuclease, C-terminal subdomain       ----------2j6sA04 A:244-336  [code=3.30.1490.100, no name defined]                                     ------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhh........eeeeee.......eeeeeehhhhhh.......hhhhhhhhh...eeee.hhhhhhhhhhhhhhhhh.....eeeee..eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh...eee.hhhhhhhhhhhh.hhhh...hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee...eeeeeeee.....hhhhhhhhhhhhhhhhhhhh...eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --UMUC  PDB: A:3-187 UniProt: 3-187                                                                                                                                                        ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2j6s A   1 MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFIE 342
                                    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

Chain P from PDB  Type:DNA  Length:14
                                              
                 2j6s P   1 GGGGGAAGGATTCC  14
                                    10

Chain T from PDB  Type:DNA  Length:16
                                                
                 2j6s T   3 ATgGAATCCTTCCCCC  18
                              |     12      
                              5-6OG

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 '\|'

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (3, 3)

Pfam Domains (0, 0)

Gene Ontology (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (DPO4_SULSO | Q97W02)

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:0003684	damaged DNA binding	Interacting selectively and non-covalently with damaged DNA.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	2j6s
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	2.7.7.7
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

1jx4	CRYSTAL STRUCTURE OF A Y-FAMILY DNA POLYMERASE IN A TERNARYCOMPLEX WITH DNA SUBSTRATES AND AN INCOMING NUCLEOTIDE
1jxl	CRYSTAL STRUCTURE OF A Y-FAMILY DNA POLYMERASE IN A TERNARYCOMPLEX WITH DNA SUBSTRATES AND AN INCOMING NUCLEOTIDE
1n48	Y-FAMILY DNA POLYMERASE DPO4 IN COMPLEX WITH DNA CONTAININGABASIC LESION
1n56	Y-FAMILY DNA POLYMERASE DPO4 IN COMPLEX WITH DNA CONTAININGABASIC LESION
1ryr	REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION
1rys	REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION
1s0m	CRYSTAL STRUCTURE OF A BENZO[A]PYRENE DIOL EPOXIDE ADDUCTIN A TERNARY COMPLEX WITH A DNA POLYMERASE
1s0n	SNAPSHOTS OF REPLICATION THROUGH AN ABASIC LESION:STRUCTURAL BASIS FOR BASE SUBSTITUTION AND FRAMESHIFT
1s0o	SNAPSHOTS OF REPLICATION THROUGH AN ABASIC LESION:STRUCTURAL BASIS FOR BASE SUBSTITUTION AND FRAMESHIFT
1s10	SNAPSHOTS OF REPLICATION THROUGH AN ABASIC LESION:STRUCTURAL BASIS FOR BASE SUBSTITUTION AND FRAMESHIFT
1s97	DPO4 WITH GT MISMATCH
1s9f	DPO WITH AT MATCHED
2ago	FIDELITY OF DPO4: EFFECT OF METAL IONS, NUCLEOTIDESELECTION AND PYROPHOSPHOROLYSIS
2agp	FIDELITY OF DPO4: EFFECT OF METAL IONS, NUCLEOTIDESELECTION AND PYROPHOSPHOROLYSIS
2agq	FIDELITY OF DPO4: EFFECT OF METAL IONS, NUCLEOTIDESELECTION AND PYROPHOSPHOROLYSIS
2asd	OXOG-MODIFIED INSERTION TERNARY COMPLEX
2asj	OXOG-MODIFIED PREINSERTION BINARY COMPLEX
2asl	OXOG-MODIFIED POSTINSERTION BINARY COMPLEX
2atl	UNMODIFIED INSERTION TERNARY COMPLEX
2au0	UNMODIFIED PREINSERTION BINARY COMPLEX
2bq3	DNA ADDUCT BYPASS POLYMERIZATION BY SULFOLOBUS SOLFATARICUS DPO4. ANALYSIS AND CRYSTAL STRUCTURES OF MULTIPLE BASE-PAIR SUBSTITUTION AND FRAMESHIFT PRODUCTS WITH THE ADDUCT 1 ,N2-ETHENOGUANINE
2bqr	DNA ADDUCT BYPASS POLYMERIZATION BY SULFOLOBUS SOLFATARICUS DPO4. ANALYSIS AND CRYSTAL STRUCTURES OF MULTIPLE BASE-PAIR SUBSTITUTION AND FRAMESHIFT PRODUCTS WITH THE ADDUCT 1 ,N2-ETHENOGUANINE
2bqu	DNA ADDUCT BYPASS POLYMERIZATION BY SULFOLOBUS SOLFATARICUS DPO4. ANALYSIS AND CRYSTAL STRUCTURES OF MULTIPLE BASE-PAIR SUBSTITUTION AND FRAMESHIFT PRODUCTS WITH THE ADDUCT 1 ,N2-ETHENOGUANINE
2br0	DNA ADDUCT BYPASS POLYMERIZATION BY SULFOLOBUS SOLFATARICUS DPO4. ANALYSIS AND CRYSTAL STRUCTURES OF MULTIPLE BASE-PAIR SUBSTITUTION AND FRAMESHIFT PRODUCTS WITH THE ADDUCT 1 ,N2-ETHENOGUANINE
2c22	EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8- DIHYDRO-8- OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE DPO4
2c28	EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8- DIHYDRO-8- OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE DPO4
2c2d	EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8- DIHYDRO-8- OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE DPO4
2c2e	EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8- DIHYDRO-8- OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE DPO4
2c2r	EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8- DIHYDRO-8- OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE DPO4
2j6t	TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, O6- METHYLGUANINE MODIFIED DNA, AND DATP.
2j6u	TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, O6- METHYLGUANINE MODIFIED DNA, AND DGTP.

Description