1N56 | PD0362 - JenaLib

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Title :   Y-FAMILY DNA POLYMERASE DPO4 IN COMPLEX WITH DNA CONTAINING ABASIC LESION

Authors :   H. Ling, F. Boudsocq, R. Woodgate, W. Yang

Date :   04 Nov 02 (Deposition) - 24 Feb 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Y-Family, Dna Polymerase, Dna Lesion Bypass, Protein-Dna Complex, Transferase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Ling, F. Boudsocq, R. Woodgate, W. Yang
A Y-Family Polymerase Complexed With Abasic Lesions: Catching Dna With A Loaded Nucleoside Triphosphate
To Be Published
PubMed: search
(for further references see the PDB file header)

*Molecule 1 - 5'-D(GPGPGPGPGPAPAPGPGPAPCPTPAPA)- 3'*
	Chains	:	C, E
	Engineered	:	YES
	Other Details	:	TEMPLATE
	Synthetic	:	YES

*Molecule 2 - 5'-D(TPCPAPTP(3DR) PAPGPTPCPCPTPTPCPCPCPCPC)-3'**
	Chains	:	D, F
	Engineered	:	YES
	Other Details	:	PRIMER
	Synthetic	:	YES

Molecule 3 - DNA POLYMERASE IV
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET22BB
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	DPO4
	Organism Scientific	:	SULFOLOBUS SOLFATARICUS
	Organism Taxid	:	2287
	Synonym	:	DPO4, POL IV, REPAIR DNA POLYMERASE OF THE DINB/UMUC SUPERFAMILY, DINP

		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 (4, 8)

No.	Name	Count	Type	Full Name
1	3DR	2	Mod. Nucleotide	1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2	ATP	2	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
3	CA	1	Ligand/Ion	CALCIUM ION
4	MG	3	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	3DR	1	Mod. Nucleotide	1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
3	CA	-1	Ligand/Ion	CALCIUM ION
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	3DR	1	Mod. Nucleotide	1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
3	CA	-1	Ligand/Ion	CALCIUM ION
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:7 , GLU A:106 , MG A:402 , HOH A:648 , HOH A:1023 , ATP A:1803	BINDING SITE FOR RESIDUE MG A 401
2	AC2	SOFTWARE	ASP B:7 , ASP B:105 , GLU B:106 , MG B:404 , HOH B:915 , ATP B:1804 , DA E:1814	BINDING SITE FOR RESIDUE CA B 403
3	AC3	SOFTWARE	ASP A:7 , PHE A:8 , ASP A:105 , MG A:401 , HOH A:666 , ATP A:1803	BINDING SITE FOR RESIDUE MG A 402
4	AC4	SOFTWARE	ASP B:7 , PHE B:8 , ASP B:105 , CA B:403 , HOH B:812 , HOH B:822 , ATP B:1804	BINDING SITE FOR RESIDUE MG B 404
5	AC5	SOFTWARE	ASP A:7 , ASP A:9 , TYR A:10 , PHE A:11 , TYR A:12 , ALA A:44 , THR A:45 , TYR A:48 , ARG A:51 , ALA A:57 , GLY A:58 , ASP A:105 , LYS A:159 , MG A:401 , MG A:402 , HOH A:666 , HOH A:808 , HOH A:936 , HOH C:804 , DA C:1814 , DT D:1905	BINDING SITE FOR RESIDUE ATP A 1803
6	AC6	SOFTWARE	ASP B:7 , PHE B:8 , ASP B:9 , TYR B:10 , PHE B:11 , TYR B:12 , ALA B:44 , THR B:45 , TYR B:48 , ARG B:51 , ASP B:105 , LYS B:159 , CA B:403 , MG B:404 , HOH B:677 , HOH B:812 , HOH B:915 , HOH B:934 , HOH E:649 , DA E:1814 , DT F:1905	BINDING SITE FOR RESIDUE ATP B 1804

(no "SS Bond" information available for 1N56)

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 1N56)

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 1N56)

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 d1n56a2 A:1-240 DinB homolog (DBH)                                                                                                                                                                                                              d1n56a1 A:241-341 DinB homolog (DBH)                                                                  SCOP domains
               CATH domains -1n56A02  -------------------------------------------------------------------1n56A02 A:2-10,A:78-166  [code=3.30.70.270, no name defined]                             1n56A03 A:167-233 5' to 3' exonuclease, C-terminal subdomain       ----------1n56A04 A:244-336  [code=3.30.1490.100, no name defined]                                     ----- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhhhh...eeeeee.......eeeeeehhhhhh.......hhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh....eeeee..eeeee......hhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhh...hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.............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
                1n56 A    1 MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFI  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 d1n56b2 B:1-240 DinB homolog (DBH)                                                                                                                                                                                                              d1n56b1 B:241-341 DinB homolog (DBH)                                                                  SCOP domains
               CATH domains -1n56B02  -------------------------------------------------------------------1n56B02 B:2-10,B:78-166  [code=3.30.70.270, no name defined]                             1n56B03 B:167-233 5' to 3' exonuclease, C-terminal subdomain       ----------1n56B04 B:244-336  [code=3.30.1490.100, no name defined]                                     ----- CATH domains
           Pfam domains (1) -----IMS-1n56B03 B:6-156                                                                                                                                    -----------IMS_HHH-1n56B01 B:168-199       -----------IMS_C-1n56B05 B:211-334                                                                                                     ------- Pfam domains (1)
           Pfam domains (2) -----IMS-1n56B04 B:6-156                                                                                                                                    -----------IMS_HHH-1n56B02 B:168-199       -----------IMS_C-1n56B06 B:211-334                                                                                                     ------- Pfam domains (2)
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhhhh...eeeeee.......eeeeeehhhhhh.......hhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh....eeeee..eeeee......hhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhh...hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee....eeeeeee.....hhhhhhhhhhhhhhhhhhhh...eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --UMUC  PDB: B:3-187 UniProt: 3-187                                                                                                                                                        ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1n56 B    1 MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFI  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 C from PDB  Type:DNA  Length:14
                                               
                1n56 C 1801 GGGGGAAGGACTAA 1814
                                  1810

Chain D from PDB  Type:DNA  Length:17
                                                  
                1n56 D 1902 TCATxAGTCCTTCCCCC 1918
                                | 1911       
                             1906-3DR

Chain E from PDB  Type:DNA  Length:14
                                               
                1n56 E 1801 GGGGGAAGGACTAA 1814
                                  1810

Chain F from PDB  Type:DNA  Length:17
                                                  
                1n56 F 1902 TCATxAGTCCTTCCCCC 1918
                                | 1911       
                             1906-3DR

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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.270, no name defined] (278)

[unclassified] (58)

1a	1n56A02	A:2-10,A:78-166
1b	1n56B02	B:2-10,B:78-166

Topology: Dna Ligase; domain 1 (375)

Homologous Superfamily: [code=3.30.1490.100, no name defined] (80)

[unclassified] (29)

2a	1n56A04	A:244-336
2b	1n56B04	B:244-336

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: DNA polymerase; domain 1 (617)

Homologous Superfamily: 5' to 3' exonuclease, C-terminal subdomain (384)

[unclassified] (230)

3a	1n56A03	A:167-233
3b	1n56B03	B:167-233

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:159 - Pro B:160	[ RasMol ]

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	1n56
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1jx4	THIS PROTEIN IN COMPLEXED WITH UNDAMAGED DNA.
1jxl	THIS PROTEIN IN COMPLEXED WITH UNDAMAGED DNA.
1n48	1N48 CONTAINS THE PROTEIN/DNA STRUCTURE WHICH IS IN THE REACTION STAGE JUST BEFORE BYPASSING THE ABASIC LESION

Description

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Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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