3C5G - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF A TERNARY COMPLEX OF THE R517K POL LAMBDA MUTANT

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

Date :   31 Jan 08 (Deposition) - 29 Jul 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Helix-Hairpin-Helix, Dna Damage, Dna Repair, Dna Replication, Dna Synthesis, Dna-Binding, Dna-Directed Dna Polymerase, Lyase, Manganese, Metal-Binding, Nucleotidyltransferase, Nucleus, Phosphoprotein, Polymorphism, Transferase, Transferase/Dna, Lyase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Bebenek, M. Garcia-Diaz, M. C. Foley, L. C. Pedersen, T. Schlick, T. A. Kunkel
Substrate-Induced Dna Strand Misalignment During Catalytic Cycling By Dna Polymerase Lambda.
Embo Rep. V. 9 459 2008
PubMed-ID: 18369368 | Reference-DOI: 10.1038/EMBOR.2008.33
(for further references see the PDB file header)

Molecule 1 - DNA POLYMERASE LAMBDA
	Chains	:	A, B
	EC Number	:	2.7.7.7, 4.2.99.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21-CODONPLUS-RIL
	Fragment	:	DNA BINDING REGION
	Gene	:	POLL
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Synonym	:	POL LAMBDA, DNA POLYMERASE KAPPA, DNA POLYMERASE BETA-2, POL BETA2

*Molecule 2 - DNA (5'- D(DCPDGPDGPDCPDAPDAPDTPDAPDCPDTPDG)-3')**
	Chains	:	T, U
	Engineered	:	YES
	Other Details	:	TEMPLATE
	Synthetic	:	YES

*Molecule 3 - DNA (5'-D(DCPDAPDGPDTPDAP(2DT))-3')*
	Chains	:	P, Q
	Engineered	:	YES
	Other Details	:	PRIMER
	Synthetic	:	YES

*Molecule 4 - DNA (5'-D(PDGPDCPDCPDG)-3')*
	Chains	:	D, E
	Engineered	:	YES
	Other Details	:	DOWNSTREAM PRIMER
	Synthetic	:	YES

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	D	E	P	Q	T	U
Biological Unit 1 (1x)	:	A		D		P		T
Biological Unit 2 (1x)	:		B		E		Q		U

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 15)

No.	Name	Count	Type	Full Name
1	2DT	2	Mod. Nucleotide	3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE
2	D3T	2	Ligand/Ion	2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
4	MG	2	Ligand/Ion	MAGNESIUM ION
5	NA	8	Ligand/Ion	SODIUM ION

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	2DT	1	Mod. Nucleotide	3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE
2	D3T	1	Ligand/Ion	2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	2DT	1	Mod. Nucleotide	3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE
2	D3T	1	Ligand/Ion	2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
3	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:427 , ASP A:429 , D3T A:576 , NA A:803 , HOH A:976	BINDING SITE FOR RESIDUE MG A 602
02	AC2	SOFTWARE	ASP A:427 , ASP A:429 , ASP A:490 , D3T A:576 , MG A:602 , HOH P:671	BINDING SITE FOR RESIDUE NA A 803
03	AC3	SOFTWARE	SER A:339 , ILE A:341 , ALA A:344 , DA P:5 , HOH P:170 , HOH P:311	BINDING SITE FOR RESIDUE NA A 804
04	AC4	SOFTWARE	CYS A:300 , ILE A:302 , PRO A:303 , ILE A:305 , HOH B:953 , DC D:3	BINDING SITE FOR RESIDUE NA A 805
05	AC5	SOFTWARE	DG D:1 , DC D:2 , DG T:2 , DG T:3 , HOH T:619	BINDING SITE FOR RESIDUE EDO T 2801
06	AC6	SOFTWARE	GLN A:372 , HOH A:866 , HOH A:934 , DG P:3 , DT P:4 , HOH P:342	BINDING SITE FOR RESIDUE NA P 807
07	AC7	SOFTWARE	ARG B:386 , GLY B:416 , SER B:417 , ARG B:420 , GLY B:426 , ASP B:427 , ASP B:429 , TYR B:505 , PHE B:506 , GLY B:508 , ALA B:510 , ASN B:513 , MG B:601 , NA B:802 , HOH B:840 , HOH B:984 , HOH B:1008 , HOH B:1067 , HOH B:1098 , 2DT Q:6 , HOH Q:16 , DA U:5	BINDING SITE FOR RESIDUE D3T B 577
08	AC8	SOFTWARE	ASP B:427 , ASP B:429 , D3T B:577 , NA B:802 , HOH B:1067	BINDING SITE FOR RESIDUE MG B 601
09	AC9	SOFTWARE	SER B:339 , ILE B:341 , ALA B:344 , DA Q:5 , HOH Q:7 , HOH Q:12	BINDING SITE FOR RESIDUE NA B 801
10	BC1	SOFTWARE	ASP B:427 , ASP B:429 , ASP B:490 , D3T B:577 , MG B:601 , HOH Q:16	BINDING SITE FOR RESIDUE NA B 802
11	BC2	SOFTWARE	LYS A:307 , CYS B:300 , ILE B:302 , ILE B:305 , DC E:3	BINDING SITE FOR RESIDUE NA B 806
12	BC3	SOFTWARE	ARG A:386 , GLY A:416 , SER A:417 , ARG A:420 , GLY A:426 , ASP A:427 , ASP A:429 , TYR A:505 , PHE A:506 , GLY A:508 , ALA A:510 , ASN A:513 , MG A:602 , NA A:803 , HOH A:976 , HOH A:1125 , HOH A:1126 , HOH A:1128 , HOH A:1129 , 2DT P:6 , HOH P:671 , DA T:5	BINDING SITE FOR RESIDUE D3T A 576
13	BC4	SOFTWARE	GLU B:396 , GLN B:400 , CYS B:412 , HOH B:947 , HOH B:949 , HOH B:1076	BINDING SITE FOR RESIDUE NA B 808

Asymmetric Unit

No.	Residues
1	A:543	-	B:543

Asymmetric Unit

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

Asymmetric Unit (1, 2)

								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/B	R	438	W

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

Biological Unit 1 (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)

Biological Unit 2 (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	B	R	438	W

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

Asymmetric Unit (1, 2)

	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	2	A:416-435 B:416-435

Biological Unit 1 (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 -

Biological Unit 2 (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	- B:416-435

Asymmetric Unit (5, 10)

	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	2	A:249-297 B:245-297	49 53
1.6b	ENST00000370169	6b	ENSE00002151653	chr10:103343438-103343265	174	DPOLL_HUMAN	298-355	58	2	A:298-355 B:298-355	58 58
1.7b	ENST00000370169	7b	ENSE00001593760	chr10:103342648-103342520	129	DPOLL_HUMAN	356-398	43	2	A:356-398 B:356-398	43 43
1.8c	ENST00000370169	8c	ENSE00001691940	chr10:103340173-103340005	169	DPOLL_HUMAN	399-455	57	2	A:399-455 B:399-455	57 57
1.9g	ENST00000370169	9g	ENSE00001451993	chr10:103339574-103338639	936	DPOLL_HUMAN	455-575	121	2	A:455-575 (gaps) B:455-575 (gaps)	121 121

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:324
 aligned with DPOLL_HUMAN | Q9UGP5 from UniProtKB/Swiss-Prot  Length:575

    Alignment length:327
                                   258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       
          DPOLL_HUMAN   249 ATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW 575
               SCOP domains d3c5ga1 A:249-328 DNA polymerase lambda                                         d3c5ga2 A:329-385 DNA polymerase lambda                  d3c5ga3 A:386-575 DNA polymerase lambda                                                                                                                                                        SCOP domains
               CATH domains 3c5gA01 A:249-331  [code=1.10.150.110, no name defined]                            3c5gA02 A:332-385                                     3c5gA03 A:386-508 Beta Polymerase, domain 2                                                                                3c5gA04 A:509-575 Beta Polyme   rase, domain 3                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......hhhhhhh....hhhhhhhhhhhhhhh.hhhhhhh.hhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhh.....eeeehhhhhh...ee..eeeeee........hhhhhhhhhhhhh..eeeeee.........eeeeee.........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee....eee...---.........ee...hhhhhhhhh.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------W----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYMERASE_X    -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5e  PDB: A:249-297 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 (gaps) UniProt: 455-575                                                                         Transcript 1 (2)
                 3c5g A 249 ATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMKALAKTKGMSLSEHALSTAVV---HGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW 575
                                   258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528        |-  |    548       558       568       
                                                                                                                                                                                                                                                                                                                          537 541

Chain B from PDB  Type:PROTEIN  Length:329
 aligned with DPOLL_HUMAN | Q9UGP5 from UniProtKB/Swiss-Prot  Length:575

    Alignment length:331
                                   254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574 
          DPOLL_HUMAN   245 SSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW 575
               SCOP domains d3c5gb1 B:245-328 DNA polymerase lambda                                             d3c5gb2 B:329-385 DNA polymerase lambda                  d3c5gb3 B:386-575 DNA polymerase lambda                                                                                                                                                        SCOP domains
               CATH domains 3c5gB01 B:245-331  [code=1.10.150.110, no name defined]                                3c5gB02 B:332-385                                     3c5gB03 B:386-508 Beta Polymerase, domain 2                                                                                3c5gB04 B:509-575 Beta Polymer  ase, domain 3                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......hhhhhhhh...hhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhh.....eeeehhhhhh...ee..eeeeee........hhhhhhhhhhhhh..eeeeeee.......eeeeeeee.......eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee....eee....--.........ee...hhhhhhhhh.....hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------W----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYMERASE_X    -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5e  PDB: B:245-297 UniProt: 192-297           Exon 1.6b  PDB: B:298-355 UniProt: 298-355                Exon 1.7b  PDB: B:356-398 UniProt: 356-398 Exon 1.8c  PDB: B:399-455 UniProt: 399-455               ------------------------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9g  PDB: B:455-575 (gaps) UniProt: 455-575                                                                         Transcript 1 (2)
                 3c5g B 245 SSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMKALAKTKGMSLSEHALSTAVVR--HGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW 575
                                   254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534   |  |544       554       564       574 
                                                                                                                                                                                                                                                                                                                               538  |                                  
                                                                                                                                                                                                                                                                                                                                  541

Chain D from PDB  Type:DNA  Length:4
                                    
                 3c5g D   1 GCCG   4

Chain E from PDB  Type:DNA  Length:4
                                    
                 3c5g E   1 GCCG   4

Chain P from PDB  Type:DNA  Length:6
                                      
                 3c5g P   1 CAGTAt   6
                                 |
                                 6-2DT

Chain Q from PDB  Type:DNA  Length:6
                                      
                 3c5g Q   1 CAGTAt   6
                                 |
                                 6-2DT

Chain T from PDB  Type:DNA  Length:11
                                           
                 3c5g T   1 CGGCAATACTG  11
                                    10

Chain U from PDB  Type:DNA  Length:11
                                           
                 3c5g U   1 CGGCAATACTG  11
                                    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 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)

Human (Homo sapiens) (22)

1a	3c5gA03	A:386-508
1b	3c5gB03	B:386-508

Topology: Beta Polymerase; domain 3 (161)

Homologous Superfamily: Beta Polymerase, domain 3 (161)

Human (Homo sapiens) (21)

2a	3c5gA04	A:509-575
2b	3c5gB04	B: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)

Human (Homo sapiens) (21)

3a	3c5gA01	A:249-331
3b	3c5gB01	B:245-331

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

Human (Homo sapiens) (34)

4a	3c5gA02	A:332-385
4b	3c5gB02	B:332-385

(no "Pfam Domain" information available for 3C5G)

Asymmetric Unit(hide GO term definitions)

Chain A,B (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 Unit
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	Ligands, Modified Residues, Ions
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		D3T	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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	Cis Peptide Bonds
		Gly A:508 - Ser A:509	[ RasMol ]
		Gly B:508 - Ser B:509	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
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Access by PDB/NDB ID
	3c5g
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		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
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	DPOLL_HUMAN \| Q9UGP5
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	2.7.7.7
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		Pathway	:	KEGG \| MetaCyc
	4.2.99.-
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		Pathway	:	KEGG \| MetaCyc

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 15)

Sites (13, 13)

SS Bonds (1, 1)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

PROSITE Motifs (1, 2)

Exons (5, 10)

Sequences/Alignments

Classification and Annotation

SCOP Domains (3, 6)

CATH Domains (4, 8)

Pfam Domains (0, 0)

Gene Ontology (17, 17)

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Databases

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File