2VA2 - JenaLib

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Title :   COMPLEX STRUCTURE OF SULFOLOBUS SOLFATARICUS DPO4 AND DNA DUPLEX CONTAINING A HYDROPHOBIC THYMINE ISOSTERE 2,4-DIFLUOROTOLUENE NUCLEOTIDE IN THE TEMPLATE STRAND

Authors :   A. Irimia, P. S. Pallan, M. Egli

Date :   28 Aug 07 (Deposition) - 30 Oct 07 (Release) - 09 Apr 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Transferase-Dna Complex, Dna-Directed Dna Polymerase, P2 Dna Polymerase Iv, Transferase, Nucleotidyltransferase, Mutator Protein, Dna Replication, Dna Repair, Dna-Binding, Metal-Binding, Translesion Dna Polymerase, 2, Ddctp, Magnesium, Dna Damage (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Irimia, R. L. Eoff, P. S. Pallan, F. P. Guengerich, M. Egli
Structure And Activity Of Y-Class Dna Polymerase Dpo4 From Sulfolobus Solfataricus With Templates Containing The Hydrophobic Thymine Analog 2, 4- Difluorotoluene.
J. Biol. Chem. V. 282 36421 2007
PubMed-ID: 17951245 | Reference-DOI: 10.1074/JBC.M707267200

Molecule 1 - DNA POLYMERASE IV
	Chains	:	A, B
	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	:	273057
	Other Details	:	DPO4
	Strain	:	P2
	Synonym	:	POL IV

*Molecule 2 - 5'-D(GPGPGPGPGPAPAPGPGPAP CPTPA)-3'**
	Chains	:	C, E
	Other Details	:	13-MER PRIMER
	Synthetic	:	YES

*Molecule 3 - 5'-D(TPTPCPAPGPDFTPAPGPTPCPCP TPTPCPCPCPCPC)-3'*
	Chains	:	D, F
	Other Details	:	18-MER TEMPLATE
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 10)

No.	Name	Count	Type	Full Name
1	CA	6	Ligand/Ion	CALCIUM ION
2	DCT	2	Ligand/Ion	2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE
3	DFT	2	Mod. Nucleotide	1-[2-DEOXYRIBOFURANOSYL]-2,4-DIFLUORO-5-METHYL-BENZENE-5'MONOPHOSPHATE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	DCT	1	Ligand/Ion	2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE
3	DFT	1	Mod. Nucleotide	1-[2-DEOXYRIBOFURANOSYL]-2,4-DIFLUORO-5-METHYL-BENZENE-5'MONOPHOSPHATE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	DCT	1	Ligand/Ion	2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE
3	DFT	1	Mod. Nucleotide	1-[2-DEOXYRIBOFURANOSYL]-2,4-DIFLUORO-5-METHYL-BENZENE-5'MONOPHOSPHATE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:7 , PHE A:8 , ASP A:105 , DCT A:1345 , HOH A:2089	BINDING SITE FOR RESIDUE CA A1343
2	AC2	SOFTWARE	ALA A:181 , ILE A:186 , HOH A:2023 , HOH A:2048 , HOH A:2050 , HOH C:2014	BINDING SITE FOR RESIDUE CA A1344
3	AC3	SOFTWARE	ASP A:7 , TYR A:10 , ALA A:44 , THR A:45 , TYR A:48 , ARG A:51 , ALA A:57 , GLY A:58 , ASP A:105 , LYS A:159 , CA A:1343 , CA A:1346 , HOH A:2002 , HOH A:2003 , HOH A:2006 , HOH A:2014 , HOH A:2088 , HOH A:2089 , HOH A:2090 , DA C:13 , DG D:5	BINDING SITE FOR RESIDUE DCT A1345
4	AC4	SOFTWARE	DCT A:1345 , HOH A:2002 , HOH C:2017	BINDING SITE FOR RESIDUE CA A1346
5	AC5	SOFTWARE	HOH B:2049 , DCT E:1014 , HOH E:2010	BINDING SITE FOR RESIDUE CA B3002
6	AC6	SOFTWARE	ASP B:7 , PHE B:8 , ASP B:105 , HOH B:2037 , DCT E:1014	BINDING SITE FOR RESIDUE CA B1343
7	AC7	SOFTWARE	ALA B:181 , ILE B:186 , HOH B:2053 , HOH B:2054 , HOH B:2055	BINDING SITE FOR RESIDUE CA B1344
8	AC8	SOFTWARE	ASP B:7 , PHE B:8 , TYR B:10 , THR B:45 , TYR B:48 , ARG B:51 , ASP B:105 , LYS B:159 , CA B:1343 , CA B:3002 , DA E:13 , HOH E:2009 , HOH E:2010 , HOH E:2011 , DG F:5	BINDING SITE FOR RESIDUE DCT E1014

(no "SS Bond" information available for 2VA2)

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 2VA2)

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	A: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	- B:3-187

(no "Exon" information available for 2VA2)

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
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Chain A from PDB  Type:PROTEIN  Length:343
 aligned with DPO4_SULSO | Q97W02 from UniProtKB/Swiss-Prot  Length:352

    Alignment length:343
                                    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 MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFIEA 343
               SCOP domains d2va2a2 A:1-240 automated matches                                                                                                                                                                                                               d2va2a1 A:241-343 automated matches                                                                     SCOP domains
               CATH domains -2va2A01  -------------------------------------------------------------------2va2A01 A:2-10,A:78-166  [code=3.30.70.270, no name defined]                             2va2A03 A:167-233 5' to 3' exonuclease, C-terminal subdomain       ----------2va2A04 A:244-336  [code=3.30.1490.100, no name defined]                                     ------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhhhh...eeeee.........eeeeehhhhhh.......hhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh....eeeee..eeeee.hhh...hhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh...eee.hhhhhhhhhhhh.hhhh...hhhhhhhhhh.....hhhhhh.hhhhhh...hhhhhhhhhhhhh.............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhh....eeeeeeeeee....eeeeeee.....hhhhhhhhhhhhhhhhhhhh...eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --UMUC  PDB: A:3-187 UniProt: 3-187                                                                                                                                                        ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2va2 A   1 MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFIEA 343
                                    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 B from PDB  Type:PROTEIN  Length:344
 aligned with DPO4_SULSO | Q97W02 from UniProtKB/Swiss-Prot  Length:352

    Alignment length:344
                             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     - -MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFIEA 343
               SCOP domains d2va2b2 B:0-240 automated matches                                                                                                                                                                                                                d2va2b1 B:241-343 automated matches                                                                     SCOP domains
               CATH domains --2va2B01  -------------------------------------------------------------------2va2B01 B:2-10,B:78-166  [code=3.30.70.270, no name defined]                             2va2B03 B:167-233 5' to 3' exonuclease, C-terminal subdomain       ----------2va2B04 B:244-336  [code=3.30.1490.100, no name defined]                                     ------- CATH domains
           Pfam domains (1) ------IMS-2va2B03 B:6-156                                                                                                                                    -----------IMS_HHH-2va2B01 B:168-199       -----------IMS_C-2va2B05 B:211-334                                                                                                     --------- Pfam domains (1)
           Pfam domains (2) ------IMS-2va2B04 B:6-156                                                                                                                                    -----------IMS_HHH-2va2B02 B:168-199       -----------IMS_C-2va2B06 B:211-334                                                                                                     --------- Pfam domains (2)
         Sec.struct. author ...eeeeee.hhhhhhhhhhhhhhh...eeeeee.......eeeeeehhhhhh.......hhhhhhh.....eeee.hhhhhhhhhhhhhhhhh.....eee....eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh...eeeehhhhhhhhh....hhhh...hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeeeeee.....hhhhhhhhhhhhhhhhhhhh...eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---UMUC  PDB: B:3-187 UniProt: 3-187                                                                                                                                                        ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2va2 B   0 HMIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFIEA 343
                                     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 C from PDB  Type:DNA  Length:13
                                             
                 2va2 C   1 GGGGGAAGGACTA  13
                                    10

Chain D from PDB  Type:DNA  Length:16
                                                
                 2va2 D   3 CAGtAGTCCTTCCCCC  18
                               |    12      
                               6-DFT

Chain E from PDB  Type:DNA  Length:13
                                             
                 2va2 E   1 GGGGGAAGGACTA  13
                                    10

Chain F from PDB  Type:DNA  Length:18
                                                  
                 2va2 F   1 TTCAGtAGTCCTTCCCCC  18
                                 |  10        
                                 6-DFT

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 '\|'

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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2v9w	COMPLEX STRUCTURE OF SULFOLOBUS SOLFATARICUS DPO4 AND DNA DUPLEX CONTAINING A HYDROPHOBIC THYMINE ISOSTERE 2, 4-DIFLUOROTOLUENE NUCLEOTIDE IN THE TEMPLATE STRAND
2va3	COMPLEX STRUCTURE OF SULFOLOBUS SOLFATARICUS DPO4 AND DNA DUPLEX CONTAINING A HYDROPHOBIC THYMINE ISOSTERE 2, 4-DIFLUOROTOLUENE NUCLEOTIDE IN THE TEMPLATE STRAND

Description

Compounds

Structural Features

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Ligands, Modified Residues, Ions (3, 10)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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Exons (0, 0)

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SCOP Domains (2, 4)

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