3UPQ - JenaLib

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MN A:1 , MN A:2 , HOH A:52 , HOH A:207 , HOH A:208 , HOH A:209 , HOH A:211 , HOH A:213 , HOH A:223 , ARG A:386 , GLY A:416 , SER A:417 , ARG A:420 , CYS A:425 , GLY A:426 , ASP A:427 , ASP A:429 , TYR A:505 , PHE A:506 , THR A:507 , GLY A:508 , ALA A:510 , ASN A:513 , DC P:6 , HOH P:212 , DT T:5	BINDING SITE FOR RESIDUE ZAN A 0
2	AC2	SOFTWARE	ZAN A:0 , MN A:2 , HOH A:215 , ASP A:427 , ASP A:429	BINDING SITE FOR RESIDUE MN A 1
3	AC3	SOFTWARE	ZAN A:0 , MN A:1 , HOH A:213 , ASP A:427 , ASP A:429 , ASP A:490 , DC P:6	BINDING SITE FOR RESIDUE MN A 2
4	AC4	SOFTWARE	HOH A:195 , HOH A:196 , HOH A:197 , HOH A:198 , ASP A:382 , HIS A:486	BINDING SITE FOR RESIDUE MN A 3
5	AC5	SOFTWARE	SER A:339 , ILE A:341 , ALA A:344 , HOH A:578 , DA P:5 , HOH P:50	BINDING SITE FOR RESIDUE NA A 4
6	AC6	SOFTWARE	HOH A:15 , GLY A:442 , ILE A:443 , PHE A:444 , SER A:445	BINDING SITE FOR RESIDUE SO4 A 5
7	AC7	SOFTWARE	HOH A:116 , HIS A:440 , ARG A:441	BINDING SITE FOR RESIDUE SO4 A 6
8	AC8	SOFTWARE	LYS A:273 , TRP A:274	BINDING SITE FOR RESIDUE SO4 A 7
9	AC9	SOFTWARE	HOH A:104 , ARG A:419	BINDING SITE FOR RESIDUE SO4 A 8

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (1, 1)

Exons (5, 5)

Sequences/Alignments

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:308
 aligned with DPOLL_HUMAN | Q9UGP5 from UniProtKB/Swiss-Prot  Length:575

    Alignment length:324
                                   261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571    
          DPOLL_HUMAN   252 HNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW 575
               SCOP domains d3upqa1 A:252-328 DNA polymerase lambda                                      d3upqa2 A:329-385 DNA polymerase lambda                  d3upqa3 A:386-575 DNA polymerase lambda                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.......hhhhhhh....hhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhh......eeeehhhhhh...ee.eeeeeee.........hhhhhhhhhhhh..eeeeeee.-----..eeeeee.........eeeeeee.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: A:252-297 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)
                 3upq A 252 HNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVKG-----ETKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAV-----------GRVLPTPTEKDVFRLLGLPYREPAERDW 575
                                   261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461  |    471       481       491       501       511       521       531    |    -      |551       561       571    
                                                                                                                                                                                                                                              464   470                                                               536         548

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

Chain P from PDB  Type:DNA  Length:6
                                      
                 3upq P   1 CAGTAC   6

Chain T from PDB  Type:DNA  Length:11
                                           
                 3upq T   1 CGGCTGTACTG  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 '\|'

Classification and Annotation

SCOP Domains (3, 3)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (17, 17)

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.

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	DPOLL_HUMAN \| Q9UGP5
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	2.7.7.7
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	4.2.99.-
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (9, 9)