3V6H - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   REPLICATION OF N2,3-ETHENOGUANINE BY DNA POLYMERASES

Authors :   L. Zhao

Date :   19 Dec 11 (Deposition) - 25 Apr 12 (Release) - 06 Jun 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B,C,D,P,T
Biol. Unit 1: B,P,T  (1x)
Biol. Unit 2: A,C,D  (1x)

Keywords :   Sulfolobus Solfataricus Dna Polymerase Iv, Dpo4, Ethenoguanine, Dna Adduct, Dna Lesion, Dna Polymerase, Dna Replication, Lesion Bypass, 2'-Fluoro Arabinose, N2, 3-Ethenoguanine, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Zhao, P. P. Christov, I. D. Kozekov, M. G. Pence, P. S. Pallan, C. J. Rizzo, M. Egli, F. P. Guengerich
Replication Of N(2) , 3-Ethenoguanine By Dna Polymerases.
Angew. Chem. Int. Ed. Engl. V. 51 5466 2012
PubMed-ID: 22488769 | Reference-DOI: 10.1002/ANIE.201109004

*Molecule 1 - DNA (5'-D(TPCPAPCP(EFG) PGPAPAPTPCPCPTPTPCPCPCPCPC)-3')*
	Chains	:	T, C
	Engineered	:	YES
	Other Details	:	TEMPLATE
	Other Details - Source	:	BASED ON PREVIOUSLY CRYSTALLIZATION SEQUENCE.
	Synthetic	:	YES

*Molecule 2 - DNA (5'-D(GPGGPGPGPAPAPGPGPAPTPTP(DOC))-3')**
	Chains	:	P, D
	Engineered	:	YES
	Other Details	:	PRIMER
	Other Details - Source	:	BASED ON PREVIOUSLY CRYSTALLIZATION SEQUENCE.
	Synthetic	:	YES

Molecule 3 - DNA POLYMERASE IV
	Chains	:	A, B
	EC Number	:	2.7.7.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21 GOLD (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DBH, DPO4, SSO2448
	Organism Scientific	:	SULFOLOBUS SOLFATARICUS P2
	Organism Taxid	:	273057
	Strain	:	ATCC 35092 / DSM 1617 / JCM 11322 / P2
	Synonym	:	POL IV

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	P	T
Biological Unit 1 (1x)	:		B			P	T
Biological Unit 2 (1x)	:	A		C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 13)

No.	Name	Count	Type	Full Name
1	CA	3	Ligand/Ion	CALCIUM ION
2	DCP	2	Ligand/Ion	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
3	DOC	2	Mod. Nucleotide	2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
4	EFG	2	Mod. Nucleotide	1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1H-IMIDAZO[2,1-B]PURIN-4(5H)-ONE
5	MG	4	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	DCP	1	Ligand/Ion	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
3	DOC	1	Mod. Nucleotide	2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
4	EFG	1	Mod. Nucleotide	1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1H-IMIDAZO[2,1-B]PURIN-4(5H)-ONE
5	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	DCP	1	Ligand/Ion	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
3	DOC	1	Mod. Nucleotide	2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
4	EFG	1	Mod. Nucleotide	1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1H-IMIDAZO[2,1-B]PURIN-4(5H)-ONE
5	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:104 , HOH A:536 , DOC D:13	BINDING SITE FOR RESIDUE CA D 101
2	AC2	SOFTWARE	ASP A:7 , PHE A:8 , ASP A:9 , TYR A:10 , PHE A:11 , TYR A:12 , ALA A:44 , THR A:45 , TYR A:48 , ARG A:51 , ASP A:105 , LYS A:159 , MG A:402 , MG A:403 , HOH A:529 , HOH A:554 , HOH A:556 , EFG C:5 , DOC D:13	BINDING SITE FOR RESIDUE DCP A 401
3	AC3	SOFTWARE	ASP A:7 , PHE A:8 , ASP A:105 , DCP A:401 , MG A:403	BINDING SITE FOR RESIDUE MG A 402
4	AC4	SOFTWARE	ASP A:7 , ASP A:105 , GLU A:106 , DCP A:401 , MG A:402 , HOH A:604	BINDING SITE FOR RESIDUE MG A 403
5	AC5	SOFTWARE	ALA A:181 , VAL A:183 , ILE A:186 , HOH A:535 , HOH A:585 , HOH A:613	BINDING SITE FOR RESIDUE CA A 404
6	AC6	SOFTWARE	ASP B:7 , PHE B:8 , TYR B:10 , PHE B:11 , TYR B:12 , ALA B:44 , THR B:45 , TYR B:48 , ARG B:51 , GLY B:58 , ASP B:105 , LYS B:159 , MG B:402 , MG B:404 , HOH B:512 , HOH B:521 , HOH B:526 , HOH B:547 , HOH B:558 , HOH B:559 , HOH B:560 , DOC P:13 , EFG T:5	BINDING SITE FOR RESIDUE DCP B 401
7	AC7	SOFTWARE	ASP B:7 , PHE B:8 , ASP B:105 , DCP B:401 , MG B:404	BINDING SITE FOR RESIDUE MG B 402
8	AC8	SOFTWARE	ILE B:104 , DOC P:13	BINDING SITE FOR RESIDUE CA B 403
9	AC9	SOFTWARE	ASP B:7 , ASP B:105 , GLU B:106 , DCP B:401 , MG B:402	BINDING SITE FOR RESIDUE MG B 404

(no "SS Bond" information available for 3V6H)

Asymmetric Unit

No.	Residues
1	Lys A:159	-	Pro A:160
2	Lys B:159	-	Pro B:160

(no "SAP(SNP)/Variant" information available for 3V6H)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UMUC	PS50173	UmuC domain profile.	DPO4_SULSO	3-187	2	A:3-187 B:3-187

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UMUC	PS50173	UmuC domain profile.	DPO4_SULSO	3-187	1	- B:3-187

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UMUC	PS50173	UmuC domain profile.	DPO4_SULSO	3-187	1	A:3-187 -

(no "Exon" information available for 3V6H)

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:343
 aligned with DPO4_SULSO | Q97W02 from UniProtKB/Swiss-Prot  Length:352

    Alignment length:343
                             1                                                                                                                                                                                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339   
           DPO4_SULSO     - -MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFIE 342
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.hhhhhhhhhhh.......eeeeee.......eeeeeehhhhhh.......hhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh....eee....eeeee......hhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhh...hhhhhhhhhhh...hhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee....eeeeeee.....hhhhhhhhhhhhhhhhhhhh...eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---UMUC  PDB: A:3-187 UniProt: 3-187                                                                                                                                                        ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v6h A   0 HMIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFIE 342
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339

Chain B 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 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhhhh...eeeeee.......eeeeeehhhhhh.......hhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh....eee....eeeee.......hhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh...eee.hhhhhhhhhh..hhhhh...hhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhh.....eeeeeeee....eeeeeee.....hhhhhhhhhhhhhhhhhhh....eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --UMUC  PDB: B:3-187 UniProt: 3-187                                                                                                                                                        ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3v6h B   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 C from PDB  Type:DNA  Length:17
                                                 
                 3v6h C   1 TCACgGAATCCTTCCCC  17
                                |   10       
                                5-EFG

Chain D from PDB  Type:DNA  Length:12
                                            
                 3v6h D   2 GGGGAAGGATTc  13
                                    11 |
                                      13-DOC

Chain P from PDB  Type:DNA  Length:11
                                           
                 3v6h P   3 GGGAAGGATTc  13
                                    12|
                                     13-DOC

Chain T from PDB  Type:DNA  Length:13
                                             
                 3v6h T   4 CgGAATCCTTCCC  16
                             |      13   
                             |           
                             5-EFG

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 3V6H)

(no "CATH Domain" information available for 3V6H)

(no "Pfam Domain" information available for 3V6H)

Asymmetric Unit(hide GO term definitions)

Chain A,B (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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	Cis Peptide Bonds
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		Lys B:159 - Pro B:160	[ RasMol ]

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	3v6h
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 13)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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