2IHM | PD0880 - JenaLib

Biol.Unit 1 - 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 :   POLYMERASE MU IN TERNARY COMPLEX WITH GAPPED 11MER DNA DUPLEX AND BOUND INCOMING NUCLEOTIDE

Authors :   A. F. Moon, L. C Pedersen, T. A. Kunkel

Date :   26 Sep 06 (Deposition) - 12 Dec 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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 :   Polymerase, Helix-Turn-Helix, Transferase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. F. Moon, M. Garcia-Diaz, K. Bebenek, B. J. Davis, X. Zhong, D. A. Ramsden, T. A. Kunkel, L. C. Pedersen
Structural Insight Into The Substrate Specificity Of Dna Polymerase Mu.
Nat. Struct. Mol. Biol. V. 14 45 2007
PubMed-ID: 17159995 | Reference-DOI: 10.1038/NSMB1180
(for further references see the PDB file header)

*Molecule 1 - 5'-D(CPGPGPCPAPAPTPAPCPTPG)-3'**
	Chains	:	T, U
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 2 - 5'-D(CPAPGPTPAPT)-3'*
	Chains	:	P, Q
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 3 - 5'-D(PGPCPCPG)-3'*
	Chains	:	D, E
	Engineered	:	YES
	Synthetic	:	YES

Molecule 4 - DNA POLYMERASE MU
	Chains	:	A, B
	EC Number	:	2.7.7.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX4T3
	Expression System Strain	:	BL21 (DE3) - RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN
	Gene	:	POLM
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	POL MU

		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 (3, 7)

No.	Name	Count	Type	Full Name
1	D3T	2	Ligand/Ion	2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	NA	3	Ligand/Ion	SODIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	D3T	2	Ligand/Ion	2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	D3T	-1	Ligand/Ion	2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:330 , ASP A:332 , D3T A:538 , HOH A:903	BINDING SITE FOR RESIDUE MG A 700
2	AC2	SOFTWARE	D3T A:638 , ASP B:330 , ASP B:332 , HOH B:902	BINDING SITE FOR RESIDUE MG B 800
3	AC3	SOFTWARE	THR A:241 , VAL A:243 , VAL A:246 , DA P:5	BINDING SITE FOR RESIDUE NA A 900
4	AC4	SOFTWARE	THR B:241 , VAL B:243 , VAL B:246 , DA Q:5	BINDING SITE FOR RESIDUE NA B 901
5	AC5	SOFTWARE	ASP A:330 , ASP A:332 , ASP A:420 , D3T A:538 , DT P:6	BINDING SITE FOR RESIDUE NA A 902
6	AC6	SOFTWARE	GLY A:319 , GLY A:320 , ARG A:323 , LYS A:325 , GLN A:327 , GLY A:328 , HIS A:329 , ASP A:330 , ASP A:332 , GLY A:435 , TRP A:436 , GLY A:438 , GLN A:440 , GLU A:443 , MG A:700 , NA A:902 , HOH A:905 , HOH A:910 , HOH A:924 , HOH A:926 , DT P:6 , DA T:5	BINDING SITE FOR RESIDUE D3T A 538
7	AC7	SOFTWARE	HOH A:953 , HOH A:983 , HOH A:984 , GLY B:319 , GLY B:320 , ARG B:323 , LYS B:325 , GLY B:328 , HIS B:329 , ASP B:330 , ASP B:332 , GLY B:435 , TRP B:436 , GLY B:438 , GLN B:440 , GLU B:443 , MG B:800 , DT Q:6 , DA U:5	BINDING SITE FOR RESIDUE D3T A 638

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

Asymmetric Unit

No.	Residues
1	Gly A:438	-	Ser A:439
2	Gly B:438	-	Ser B:439

(no "SAP(SNP)/Variant" information available for 2IHM)

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.	DPOLM_MOUSE	319-338	2	A:319-338 B:319-338

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.	DPOLM_MOUSE	319-338	1	A:319-338 -

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.	DPOLM_MOUSE	319-338	1	- B:319-338

Asymmetric Unit (9, 18)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENSMUST00000020767	1a	ENSMUSE00000105186	chr11:5738019-5737564	456	DPOLM_MOUSE	1-64	64	0	-	-
1.2d	ENSMUST00000020767	2d	ENSMUSE00000105181	chr11:5736377-5736197	181	DPOLM_MOUSE	64-124	61	0	-	-
1.3a	ENSMUST00000020767	3a	ENSMUSE00000105174	chr11:5735802-5735704	99	DPOLM_MOUSE	125-157	33	2	A:137-157 B:137-157	21 21
1.4a	ENSMUST00000020767	4a	ENSMUSE00000105189	chr11:5735589-5735419	171	DPOLM_MOUSE	158-214	57	2	A:158-214 B:158-214	57 57
1.5b	ENSMUST00000020767	5b	ENSMUSE00000105179	chr11:5734816-5734745	72	DPOLM_MOUSE	215-238	24	2	A:215-238 B:215-238	24 24
1.6	ENSMUST00000020767	6	ENSMUSE00000105187	chr11:5731783-5731663	121	DPOLM_MOUSE	239-279	41	2	A:239-279 B:239-279	41 41
1.7	ENSMUST00000020767	7	ENSMUSE00000105172	chr11:5730203-5730071	133	DPOLM_MOUSE	279-323	45	2	A:279-323 B:279-323	45 45
1.8a	ENSMUST00000020767	8a	ENSMUSE00000105175	chr11:5729931-5729829	103	DPOLM_MOUSE	323-357	35	2	A:323-357 B:323-357	35 35
1.8c	ENSMUST00000020767	8c	ENSMUSE00000105176	chr11:5729728-5729480	249	DPOLM_MOUSE	358-440	83	2	A:358-440 (gaps) B:358-440 (gaps)	83 83
1.8d	ENSMUST00000020767	8d	ENSMUSE00000105180	chr11:5729397-5729314	84	DPOLM_MOUSE	441-468	28	2	A:441-468 B:441-468	28 28
1.9a	ENSMUST00000020767	9a	ENSMUSE00000377438	chr11:5729118-5727864	1255	DPOLM_MOUSE	469-496	28	2	A:469-496 B:469-496	28 28

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:332
 aligned with DPOLM_MOUSE | Q9JIW4 from UniProtKB/Swiss-Prot  Length:496

    Alignment length:360
                                   146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496
          DPOLM_MOUSE   137 SMPAYACQRPSPLTHHNTLLSEALETLAEAAGFEANEGRLLSFSRAASVLKSLPCPVASLSQLHGLPYFGEHSTRVIQELLEHGTCEEVKQVRCSERYQTMKLFTQVFGVGVKTANRWYQEGLRTLDELREQPQRLTQQQKAGLQYYQDLSTPVRRADAEALQQLIEAAVRQTLPGATVTLTGGFRRGKLQGHDVDFLITHPEEGQEVGLLPKVMSCLQSQGLVLYHQYHRSHLADSAHNLRQRSSTMDAFERSFCILGLPQPQQAALAGALPPCPTWKAVRVDLVVTPSSQFPFALLGWTGSQFFERELRRFSRQEKGLWLNSHGLFDPEQKRVFHATSEEDVFRLLGLKYLPPEQRNA 496
               SCOP domains d2ihma1 A:137-230 automated matches                                                           d2ihma2 A:231-289 automated matches                        d2ihma3 A:290-496 automated matches                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhh.......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh...hhhhhhh.....hhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhh.....eeeehhhhhh...ee.eeeeeee........hhhhhhhhhhhhh..eeeeeee...---------------....eeeeeeeee.-------------..eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee....ee...........hhhhhhhhh.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYMERASE_X    -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a            Exon 1.4a  PDB: A:158-214 UniProt: 158-214               Exon 1.5b  PDB: A:215-23Exon 1.6  PDB: A:239-279 UniProt: 239-279-------------------------------------------Exon 1.8a  PDB: A:323-357          Exon 1.8c  PDB: A:358-440 (gaps) UniProt: 358-440                                  Exon 1.8d  PDB: A:441-468   Exon 1.9a  PDB: A:469-496    Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------------------Exon 1.7  PDB: A:279-323 UniProt: 279-323    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2ihm A 137 SMPAYACQRPSPLTHHNTLLSEALETLAEAAGFEANEGRLLSFSRAASVLKSLPCPVASLSQLHGLPYFGEHSTRVIQELLEHGTCEEVKQVRCSERYQTMKLFTQVFGVGVKTANRWYQEGLRTLDELREQPQRLTQQQKAGLQYYQDLSTPVRRADAEALQQLIEAAVRQTLPGATVTLTGGFRRGKLQGHDVDFLITHPEEGQEVGLLPKVMSCLQSQGLVLYHQYHRSH---------------DVFERSFCILGLPQ-------------PTWKAVRVDLVVTPSSQFPFALLGWTGSQFFERELRRFSRQEKGLWLNSHGLFDPEQKRVFHATSEEDVFRLLGLKYLPPEQRNA 496
                                   146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366  |      -       386       396 |       -     | 416       426       436       446       456       466       476       486       496
                                                                                                                                                                                                                                                                  369             385          398           412

Chain B from PDB  Type:PROTEIN  Length:336
 aligned with DPOLM_MOUSE | Q9JIW4 from UniProtKB/Swiss-Prot  Length:496

    Alignment length:360
                                   146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496
          DPOLM_MOUSE   137 SMPAYACQRPSPLTHHNTLLSEALETLAEAAGFEANEGRLLSFSRAASVLKSLPCPVASLSQLHGLPYFGEHSTRVIQELLEHGTCEEVKQVRCSERYQTMKLFTQVFGVGVKTANRWYQEGLRTLDELREQPQRLTQQQKAGLQYYQDLSTPVRRADAEALQQLIEAAVRQTLPGATVTLTGGFRRGKLQGHDVDFLITHPEEGQEVGLLPKVMSCLQSQGLVLYHQYHRSHLADSAHNLRQRSSTMDAFERSFCILGLPQPQQAALAGALPPCPTWKAVRVDLVVTPSSQFPFALLGWTGSQFFERELRRFSRQEKGLWLNSHGLFDPEQKRVFHATSEEDVFRLLGLKYLPPEQRNA 496
               SCOP domains d2ihmb1 B:137-230 automated matches                                                           d2ihmb2 B:231-289 automated matches                        d2ihmb3 B:290-496 automated matches                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhh.......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......hhhhh......hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhh.....eeeehhhhhh...ee..eeeeee........hhhhhhhhhhhh...eee...---------------------..eeeeeeeee.....---........eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee....ee...........hhhhhhhhhh....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYMERASE_X    -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a            Exon 1.4a  PDB: B:158-214 UniProt: 158-214               Exon 1.5b  PDB: B:215-23Exon 1.6  PDB: B:239-279 UniProt: 239-279-------------------------------------------Exon 1.8a  PDB: B:323-357          Exon 1.8c  PDB: B:358-440 (gaps) UniProt: 358-440                                  Exon 1.8d  PDB: B:441-468   Exon 1.9a  PDB: B:469-496    Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------------------Exon 1.7  PDB: B:279-323 UniProt: 279-323    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2ihm B 137 SMPAYACQRPSPLTHHNTLLSEALETLAEAAGFEANEGRLLSFSRAASVLKSLPCPVASLSQLHGLPYFGEHSTRVIQELLEHGTCEEVKQVRCSERYQTMKLFTQVFGVGVKTANRWYQEGLRTLDELREQPQRLTQQQKAGLQYYQDLSTPVRRADAEALQQLIEAAVRQTLPGATVTLTGGFRRGKLQGHDVDFLITHPEEGQEVGLLPKVMSCLQSQGLVLYHQY---------------------FERSFCILGLPQPQQA---GALPPCPTWKAVRVDLVVTPSSQFPFALLGWTGSQFFERELRRFSRQEKGLWLNSHGLFDPEQKRVFHATSEEDVFRLLGLKYLPPEQRNA 496
                                   146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356        |-         -         -|      396     | 406       416       426       436       446       456       466       476       486       496
                                                                                                                                                                                                                                                              365                   387            402 406

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

Chain E from PDB  Type:DNA  Length:4
                                    
                 2ihm E   1 GCCG   4

Chain P from PDB  Type:DNA  Length:6
                                      
                 2ihm P   1 CAGTAT   6

Chain Q from PDB  Type:DNA  Length:6
                                      
                 2ihm Q   1 CAGTAT   6

Chain T from PDB  Type:DNA  Length:11
                                           
                 2ihm T   1 CGGCAATACTG  11
                                    10

Chain U from PDB  Type:DNA  Length:11
                                           
                 2ihm 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 '\|'

(no "CATH Domain" information available for 2IHM)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (DPOLM_MOUSE | Q9JIW4)

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: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:0030183	B cell differentiation	The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
	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:0006310	DNA recombination	Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
	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: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: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: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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	Cis Peptide Bonds
		Gly A:438 - Ser A:439	[ RasMol ]
		Gly B:438 - Ser B:439	[ RasMol ]

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	2ihm
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	DPOLM_MOUSE \| Q9JIW4
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (9, 18)

Sequences/Alignments

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SCOP Domains (3, 6)

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