3KHR - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   DPO4 POST-EXTENSION TERNARY COMPLEX WITH THE CORRECT C OPPOSITE THE 2-AMINOFLUORENE-GUANINE [AF]G LESION

Authors :   O. Rechkoblit, L. Malinina, D. J. Patel

Date :   30 Oct 09 (Deposition) - 16 Feb 10 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.01

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

Keywords :   Lesion Bypass, Dna Polymerase, Y-Family Polymerase, 2-Aminofluorene, Semi-Targeted Mutagenesis, Dna Damage, Dna Repair, Dna Replication, Dna-Binding, Dna-Directed Dna Polymerase, Magnesium, Metal-Binding, Mutator Protein, Nucleotidyltransferase, Transferase, Transferase- Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   O. Rechkoblit, A. Kolbanovskiy, L. Malinina, N. E. Geacintov, S. Broyde, D. J. Patel
Mechanism Of Error-Free And Semitargeted Mutagenic Bypass O An Aromatic Amine Lesion By Y-Family Polymerase Dpo4.
Nat. Struct. Mol. Biol. V. 17 379 2010
PubMed-ID: 20154704 | Reference-DOI: 10.1038/NSMB.1771

Molecule 1 - DNA POLYMERASE IV
	Chains	:	A, B
	EC Number	:	2.7.7.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)-RIL(STRATAGENE)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DBH, DPO4, SSO2448
	Organism Scientific	:	SULFOLOBUS SOLFATARICUS P2
	Organism Taxid	:	273057
	Strain	:	P2 / DSM 1617 / JCM 11322
	Synonym	:	POL IV

*Molecule 2 - 5'-D(TPTPGPGPAPTPGPGPTPAPGPCP(DDG))-3'**
	Chains	:	D, H
	Engineered	:	YES
	Other Details	:	DNA PRIMER STRAND (DIDEOXY-TERMINATED AT THE 3'-END)
	Other Details - Source	:	DNA PRIMER STRAND (DIDEOXY-TERMINATED AT THE 3'-END)
	Synthetic	:	YES

*Molecule 3 - 5'-D(CPCTPAPAPCPGPCPTPAPCPCPAPTPCPCPAPAP CPC)-3'*
	Chains	:	E, J
	Engineered	:	YES
	Other Details	:	DNA [AF]G-MODIFIED TEMPLATE STRAND
	Other Details - Source	:	DNA [AF]G-MODIFIED TEMPLATE STRAND
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 12)

No.	Name	Count	Type	Full Name
1	AF	2	Ligand/Ion	2-AMINOFLUORENE
2	CA	6	Ligand/Ion	CALCIUM ION
3	DDG	2	Mod. Nucleotide	2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE
4	TTP	2	Ligand/Ion	THYMIDINE-5'-TRIPHOSPHATE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	AF	-1	Ligand/Ion	2-AMINOFLUORENE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	DDG	1	Mod. Nucleotide	2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE
4	TTP	1	Ligand/Ion	THYMIDINE-5'-TRIPHOSPHATE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	AF	-1	Ligand/Ion	2-AMINOFLUORENE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	DDG	1	Mod. Nucleotide	2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE
4	TTP	1	Ligand/Ion	THYMIDINE-5'-TRIPHOSPHATE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:7 , PHE A:8 , TYR A:10 , PHE A:11 , TYR A:12 , ALA A:44 , THR A:45 , TYR A:48 , ARG A:51 , ALA A:57 , ASP A:105 , LYS A:159 , CA A:415 , CA A:416 , HOH A:524 , HOH A:553 , HOH A:567 , HOH A:587 , HOH A:597 , DDG D:815 , DA E:904	BINDING SITE FOR RESIDUE TTP A 414
02	AC2	SOFTWARE	ASP A:7 , ASP A:105 , GLU A:106 , TTP A:414 , CA A:416 , HOH A:510 , DDG D:815	BINDING SITE FOR RESIDUE CA A 415
03	AC3	SOFTWARE	ASP A:7 , PHE A:8 , ASP A:105 , TTP A:414 , CA A:415	BINDING SITE FOR RESIDUE CA A 416
04	AC4	SOFTWARE	ALA A:181 , ILE A:186 , HOH A:513 , HOH A:585 , HOH D:514	BINDING SITE FOR RESIDUE CA A 417
05	AC5	SOFTWARE	ARG A:247 , ILE A:248 , HIS A:285 , VAL A:287 , VAL A:335 , ARG A:336 , DC E:905 , DG E:906 , DC E:907	BINDING SITE FOR RESIDUE AF E 926
06	AC6	SOFTWARE	HOH B:21 , HOH B:25 , HOH B:39 , HOH B:65 , HOH B:167 , HOH B:400 , ASP B:1007 , PHE B:1008 , ASP B:1009 , TYR B:1010 , PHE B:1011 , TYR B:1012 , ALA B:1044 , THR B:1045 , TYR B:1048 , ARG B:1051 , ALA B:1057 , ASP B:1105 , LYS B:1159 , CA B:1416 , DDG H:1815 , DA J:1904	BINDING SITE FOR RESIDUE TTP B 1414
07	AC7	SOFTWARE	ASP B:1007 , GLU B:1106 , LYS B:1152 , HOH B:1519 , DDG H:1815	BINDING SITE FOR RESIDUE CA B 1415
08	AC8	SOFTWARE	ASP B:1007 , PHE B:1008 , ASP B:1105 , TTP B:1414 , HOH B:1519	BINDING SITE FOR RESIDUE CA B 1416
09	AC9	SOFTWARE	HOH B:344 , ALA B:1181 , ILE B:1186 , HOH B:1511 , HOH B:1512 , HOH B:1513 , HOH H:331	BINDING SITE FOR RESIDUE CA B 1417
10	BC1	SOFTWARE	ILE B:1248 , HIS B:1285 , VAL B:1287 , VAL B:1335 , ARG B:1336 , DC J:1905 , DG J:1906 , DC J:1907	BINDING SITE FOR RESIDUE AF J 1926

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

Asymmetric Unit

No.	Residues
1	Lys A:159	-	Pro A:160
2	Lys B:1159	-	Pro B:1160

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

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:1003-1187

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:1003-1187

(no "Exon" information available for 3KHR)

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:341
 aligned with DPO4_SULSO | Q97W02 from UniProtKB/Swiss-Prot  Length:352

    Alignment length:341
                                    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 MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFI  341
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhhhh...eeeeee.......eeeeeehhhhhh.......hhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhh..eeeee..eeeee......hhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhh...hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............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
                3khr A    1 GIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFI  341
                                    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:341
 aligned with DPO4_SULSO | Q97W02 from UniProtKB/Swiss-Prot  Length:352

    Alignment length:341
                                    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 MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFI  341
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----IMS-3khrB03 B:1006-1156                                                                                                                                -----------IMS_HHH-3khrB01 B:1168-1199     -----------IMS_C-3khrB05 B:1211-1334                                                                                                   ------- Pfam domains (1)
           Pfam domains (2) -----IMS-3khrB04 B:1006-1156                                                                                                                                -----------IMS_HHH-3khrB02 B:1168-1199     -----------IMS_C-3khrB06 B:1211-1334                                                                                                   ------- Pfam domains (2)
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhhhh...eeeeee.......eeeeeehhhhhhh......hhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh....eeeee..eeeee......hhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhh....eeeeeeeeee....eeeeeee.....hhhhhhhhhhhhhhhhhh.....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --UMUC  PDB: B:1003-1187 UniProt: 3-187                                                                                                                                                    ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3khr B 1001 GIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFI 1341
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260      1270      1280      1290      1300      1310      1320      1330      1340

Chain D from PDB  Type:DNA  Length:13
                                              
                3khr D  803 TTGGATGGTAGCg  815
                                   812  |
                                      815-DDG

Chain E from PDB  Type:DNA  Length:17
                                                  
                3khr E  902 TAACGCTACCATCCAAC  918
                                   911

Chain H from PDB  Type:DNA  Length:13
                                              
                3khr H 1803 TTGGATGGTAGCg 1815
                                  1812  |
                                     1815-DDG

Chain J from PDB  Type:DNA  Length:18
                                                   
                3khr J 1901 CTAACGCTACCATCCAAC 1918
                                  1910

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 3KHR)

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

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
		Lys A:159 - Pro A:160	[ RasMol ]
		Lys B:1159 - Pro B:1160	[ RasMol ]

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	3khr
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	DPO4_SULSO \| Q97W02
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3khg	DPO4 EXTENSION TERNARY COMPLEX WITH MISINSERTED A OPPOSITE THE 2-AMINOFLUORENE-GUANINE [AF]G LESION.
3khh	DPO4 EXTENSION TERNARY COMPLEX WITH A C BASE OPPOSITE THE 2-AMINOFLUORENE-GUANINE [AF]G LESION.
3khl	DPO4 POST-EXTENSION TERNARY COMPLEX WITH MISINSERTED A OPPOSITE THE 2-AMINOFLUORENE-GUANINE [AF]G LESION.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 12)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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Pfam Domains (3, 6)

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