2BCR | PD0722 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   DNA POLYMERASE LAMBDA IN COMPLEX WITH A DNA DUPLEX CONTAINING AN UNPAIRED DAMP

Authors :   M. Garcia-Diaz, K. Bebenek, J. M. Krahn, L. C. Pedersen, T. A. Kunkel

Date :   19 Oct 05 (Deposition) - 07 Mar 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   Misalignment, Extrahelical, Mutagenesis, Mutation, Deletion, Streisinger, Slippage, Transferase, Lyase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Garcia-Diaz, K. Bebenek, J. M. Krahn, L. C. Pedersen, T. A. Kunkel
Structural Analysis Of Strand Misalignment During Dna Synthesis By A Human Dna Polymerase
Cell(Cambridge, Mass. ) V. 124 331 2006
PubMed-ID: 16439207 | Reference-DOI: 10.1016/J.CELL.2005.10.039
(for further references see the PDB file header)

*Molecule 1 - 5'-D(PGPCPCPG)-3'*
	Chains	:	D
	Engineered	:	YES
	Other Details	:	TEMPLATE
	Synthetic	:	YES

*Molecule 2 - 5'-D(CPAPGPTPAPCPG)-3'**
	Chains	:	P
	Engineered	:	YES
	Other Details	:	PRIMER
	Synthetic	:	YES

*Molecule 3 - 5'-D(CPGPGPCPCPGPAPTPAPCPTPG)-3'*
	Chains	:	T
	Engineered	:	YES
	Other Details	:	DOWNSTREAM PRIMER
	Synthetic	:	YES

Molecule 4 - DNA POLYMERASE LAMBDA
	Chains	:	A
	EC Number	:	2.7.7.7, 4.2.99.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-22B
	Expression System Strain	:	BL21-CODONPLUS(DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	POL LAMBDA, DNA POLYMERASE KAPPA, DNA POLYMERASE BETA-2, POL BETA2

		1	2	3	4
Asymmetric/Biological Unit	:	A	D	P	T

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 10)

No.	Name	Count	Type	Full Name
1	EDO	5	Ligand/Ion	1,2-ETHANEDIOL
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	NA	3	Ligand/Ion	SODIUM ION
4	PPV	1	Ligand/Ion	PYROPHOSPHATE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:427 , ASP A:429 , PPV A:638 , HOH A:813 , DG P:7	BINDING SITE FOR RESIDUE MG A 600
02	AC2	SOFTWARE	SER A:463 , HOH A:945 , HOH A:946 , HOH T:40 , HOH T:54 , HOH T:98	BINDING SITE FOR RESIDUE NA A 602
03	AC3	SOFTWARE	SER A:339 , ILE A:341 , ALA A:344 , DA P:5 , HOH P:45 , HOH P:251	BINDING SITE FOR RESIDUE NA A 603
04	AC4	SOFTWARE	CYS A:300 , ILE A:302 , ILE A:305 , HOH A:1105 , DC D:3 , HOH D:406	BINDING SITE FOR RESIDUE NA A 604
05	AC5	SOFTWARE	ARG A:386 , GLY A:416 , SER A:417 , ARG A:420 , GLY A:426 , MG A:600 , HOH A:839 , HOH A:846 , HOH A:967 , HOH A:1041 , DG P:7 , HOH P:96	BINDING SITE FOR RESIDUE PPV A 638
06	AC6	SOFTWARE	ARG A:452 , LEU A:457 , ASP A:460 , HOH A:1135	BINDING SITE FOR RESIDUE EDO A 801
07	AC7	SOFTWARE	GLN A:471 , VAL A:494 , HIS A:530 , HOH A:856 , HOH A:950 , HOH A:981 , DA T:9	BINDING SITE FOR RESIDUE EDO A 802
08	AC8	SOFTWARE	THR A:348 , MET A:351 , GLU A:385 , ARG A:485 , DG P:3	BINDING SITE FOR RESIDUE EDO P 803
09	AC9	SOFTWARE	ARG A:419 , THR A:555 , GLU A:556 , LYS A:557 , TYR A:567 , HOH A:835 , HOH A:1000 , HOH A:1068	BINDING SITE FOR RESIDUE EDO A 804
10	BC1	SOFTWARE	LYS A:347 , GLY A:481 , PRO A:482 , GLY A:483 , ARG A:484 , HOH A:896	BINDING SITE FOR RESIDUE EDO A 805

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

Asymmetric/Biological Unit

No.	Residues
1	Gly A:508	-	Ser A:509

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_020269	R	438	W	DPOLL_HUMAN	Polymorphism	3730477	A	R	438	W

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_POLYMERASE_X	PS00522	DNA polymerase family X signature.	DPOLL_HUMAN	416-435	1	A:416-435

Asymmetric/Biological Unit (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1k	ENST00000370169	1k	ENSE00001451987	chr10:103347178-103347003	176	DPOLL_HUMAN	1-39	39	0	-	-
1.3	ENST00000370169	3	ENSE00001731892	chr10:103345913-103345619	295	DPOLL_HUMAN	39-137	99	0	-	-
1.4b	ENST00000370169	4b	ENSE00001100422	chr10:103345235-103345073	163	DPOLL_HUMAN	137-191	55	0	-	-
1.5e	ENST00000370169	5e	ENSE00001617344	chr10:103344676-103344359	318	DPOLL_HUMAN	192-297	106	1	A:251-297	47
1.6b	ENST00000370169	6b	ENSE00002151653	chr10:103343438-103343265	174	DPOLL_HUMAN	298-355	58	1	A:298-355	58
1.7b	ENST00000370169	7b	ENSE00001593760	chr10:103342648-103342520	129	DPOLL_HUMAN	356-398	43	1	A:356-398	43
1.8c	ENST00000370169	8c	ENSE00001691940	chr10:103340173-103340005	169	DPOLL_HUMAN	399-455	57	1	A:399-455	57
1.9g	ENST00000370169	9g	ENSE00001451993	chr10:103339574-103338639	936	DPOLL_HUMAN	455-575	121	1	A:455-575	121

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
	(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:325
 aligned with DPOLL_HUMAN | Q9UGP5 from UniProtKB/Swiss-Prot  Length:575

    Alignment length:325
                                   260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570     
          DPOLL_HUMAN   251 NHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW 575
               SCOP domains d2bcra1 A:251-328 automated matches                                           d2bcra2 A:329-385 automated matches                      d2bcra3 A:386-575 automated matches                                                                                                                                                            SCOP domains
               CATH domains 2bcrA01 A:251-331  [code=1.10.150.110, no name defined]                          2bcrA02 A:332-385                                     2bcrA03 A:386-508 Beta Polymerase, domain 2                                                                                2bcrA04 A:509-575 Beta Polymerase, domain 3                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.......hhhhhhh....hhhhhhhhhhhhh...hhhhhh...hhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhh.hhhhh.eehhhhhhhhhhhhhhhhhhh...eeeehhhhhh...ee..eeeeee.........hhhhhhhhhhhh..eeeeee.........eeeeee.........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee....eee..ee.....eee..ee....hhhhhhhhh.....hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------W----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYMERASE_X    -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5e  PDB: A:251-297 UniProt: 192-297     Exon 1.6b  PDB: A:298-355 UniProt: 298-355                Exon 1.7b  PDB: A:356-398 UniProt: 356-398 Exon 1.8c  PDB: A:399-455 UniProt: 399-455               ------------------------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9g  PDB: A:455-575 UniProt: 455-575                                                                                Transcript 1 (2)
                 2bcr A 251 NHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW 575
                                   260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570

Chain D from PDB  Type:DNA  Length:4
                                    
                 2bcr D   1 GCCG   4

Chain P from PDB  Type:DNA  Length:7
                                       
                 2bcr P   1 CAGTACG   7

Chain T from PDB  Type:DNA  Length:12
                                            
                 2bcr T   1 CGGCCGATACTG  12
                                    10

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/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Beta Polymerase; domain 2 (187)

Homologous Superfamily: Beta Polymerase, domain 2 (183)

[unclassified] (117)

2bcrA03

A:386-508

Topology: Beta Polymerase; domain 3 (161)

Homologous Superfamily: Beta Polymerase, domain 3 (161)

[unclassified] (116)

2bcrA04

A:509-575

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: DNA polymerase; domain 1 (617)

Homologous Superfamily: [code=1.10.150.110, no name defined] (150)

[unclassified] (116)

2bcrA01

A:251-331

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

[unclassified] (230)

2bcrA02

A:332-385

(no "Pfam Domain" information available for 2BCR)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (DPOLL_HUMAN | Q9UGP5)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0034061	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 nucleic acid template and a 3'hydroxyl group.
	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:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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: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.
	GO:0006303	double-strand break repair via nonhomologous end joining	The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.
	GO:0006289	nucleotide-excision repair	A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
	GO:0016446	somatic hypermutation of immunoglobulin genes	Mutations occurring somatically that result in amino acid changes in the rearranged V regions of immunoglobulins.
cellular component
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:508 - Ser A:509	[ RasMol ]

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	2bcr
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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (4, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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