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NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   SOLUTION STRUCTURE OF POLYMERASE-INTERACTING DOMAIN OF HUMAN REV1 IN COMPLEX WITH TRANSLESIONAL SYNTHESIS POLYMERASE KAPPA

Authors :   D. Liu, K. Ryu, J. Ko, B. Choi

Date :   01 May 12 (Deposition) - 29 May 13 (Release) - 29 May 13 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (15x)
NMR Structure *: A,B  (1x)

Keywords :   Polymerase-Interacting Domain, Rev1, Polymerase Kappa, Rev1- Interacting Motif, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Liu, K. Ryu, J. Ko, B. Choi
Insights Into The Scaffold Mechanism Of Human Rev1 In Translesional Synthesis Revealed By The Structural Studies On Its Polymerase-Interacting Domain
To Be Published
PubMed: search

Molecule 1 - DNA REPAIR PROTEIN REV1
	Chains	:	A
	EC Number	:	2.7.7.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector	:	PET28A
	Expression System Vector Type	:	VECTOR
	Fragment	:	PROTEIN INTERACTION DOMAIN, UNP RESIDUES 1156-1251
	Gene	:	REV1, REV1L
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ALPHA INTEGRIN-BINDING PROTEIN 80, AIBP80, REV1-LIKE TERMINAL DEOXYCYTIDYL TRANSFERASE

Molecule 2 - DNA POLYMERASE KAPPA
	Chains	:	B
	EC Number	:	2.7.7.7
	Engineered	:	YES
	Fragment	:	UNP RESIDUES 562-577
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	THE PEPTIDE WAS CHEMICALLY SYNTHESIZED.
	Synonym	:	DINB PROTEIN, DINP
	Synthetic	:	YES

		1	2
NMR Structure (15x)	:	A	B
NMR Structure * (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2LSI)

(no "Site" information available for 2LSI)

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

(no "Cis Peptide Bond" information available for 2LSI)

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

(no "PROSITE Motif" information available for 2LSI)

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000241436	1a	ENSE00002022143	chr5:74807581-74807739	159	POLK_HUMAN	-	0	0	-	-
1.4a	ENST00000241436	4a	ENSE00002160720	chr5:74842835-74842982	148	POLK_HUMAN	1-45	45	0	-	-
1.5b	ENST00000241436	5b	ENSE00001649227	chr5:74848297-74848416	120	POLK_HUMAN	46-85	40	0	-	-
1.7b	ENST00000241436	7b	ENSE00001643362	chr5:74865165-74865317	153	POLK_HUMAN	86-136	51	0	-	-
1.8b	ENST00000241436	8b	ENSE00000827223	chr5:74869563-74869694	132	POLK_HUMAN	137-180	44	0	-	-
1.9b	ENST00000241436	9b	ENSE00000827224	chr5:74872605-74872758	154	POLK_HUMAN	181-232	52	0	-	-
1.10a	ENST00000241436	10a	ENSE00000827225	chr5:74877034-74877273	240	POLK_HUMAN	232-312	81	0	-	-
1.11	ENST00000241436	11	ENSE00000827226	chr5:74879118-74879242	125	POLK_HUMAN	312-353	42	0	-	-
1.12	ENST00000241436	12	ENSE00000827227	chr5:74880585-74880751	167	POLK_HUMAN	354-409	56	0	-	-
1.13	ENST00000241436	13	ENSE00001004825	chr5:74882851-74882883	33	POLK_HUMAN	409-420	12	0	-	-
1.14a	ENST00000241436	14a	ENSE00000827228	chr5:74886169-74886265	97	POLK_HUMAN	420-452	33	0	-	-
1.15a	ENST00000241436	15a	ENSE00000827229	chr5:74889703-74889874	172	POLK_HUMAN	453-510	58	0	-	-
1.16a	ENST00000241436	16a	ENSE00001742078	chr5:74892047-74893003	957	POLK_HUMAN	510-829	320	1	B:561-577 (gaps)	42
1.17b	ENST00000241436	17b	ENSE00001614437	chr5:74893572-74893614	43	POLK_HUMAN	829-843	15	0	-	-
1.17l	ENST00000241436	17l	ENSE00001905813	chr5:74893759-74896969	3211	POLK_HUMAN	843-870	28	0	-	-

2.1a	ENST00000258428	1a	ENSE00001515354	chr2:100106497-100106279	219	REV1_HUMAN	-	0	0	-	-
2.2	ENST00000258428	2	ENSE00000921861	chr2:100081447-100081384	64	REV1_HUMAN	1-18	18	0	-	-
2.3b	ENST00000258428	3b	ENSE00000921860	chr2:100079084-100078958	127	REV1_HUMAN	19-61	43	0	-	-
2.5	ENST00000258428	5	ENSE00001637671	chr2:100065966-100065798	169	REV1_HUMAN	61-117	57	0	-	-
2.6	ENST00000258428	6	ENSE00001757863	chr2:100058931-100058779	153	REV1_HUMAN	117-168	52	0	-	-
2.7a	ENST00000258428	7a	ENSE00001698319	chr2:100055772-100055063	710	REV1_HUMAN	168-405	238	0	-	-
2.9b	ENST00000258428	9b	ENSE00001623485	chr2:100052403-100052296	108	REV1_HUMAN	405-441	37	0	-	-
2.10	ENST00000258428	10	ENSE00001751683	chr2:100050910-100050794	117	REV1_HUMAN	441-480	40	0	-	-
2.12a	ENST00000258428	12a	ENSE00000921854	chr2:100046410-100046302	109	REV1_HUMAN	480-516	37	0	-	-
2.14b	ENST00000258428	14b	ENSE00001685794	chr2:100040742-100040614	129	REV1_HUMAN	516-559	44	0	-	-
2.15	ENST00000258428	15	ENSE00001749185	chr2:100038115-100037961	155	REV1_HUMAN	559-611	53	0	-	-
2.16b	ENST00000258428	16b	ENSE00001690779	chr2:100035409-100035290	120	REV1_HUMAN	611-651	41	0	-	-
2.17b	ENST00000258428	17b	ENSE00001626429	chr2:100029413-100029193	221	REV1_HUMAN	651-724	74	0	-	-
2.18a	ENST00000258428	18a	ENSE00001733763	chr2:100027329-100027157	173	REV1_HUMAN	725-782	58	0	-	-
2.19b	ENST00000258428	19b	ENSE00001627924	chr2:100024593-100024491	103	REV1_HUMAN	782-816	35	0	-	-
2.20b	ENST00000258428	20b	ENSE00001802837	chr2:100022952-100022787	166	REV1_HUMAN	817-872	56	0	-	-
2.20h	ENST00000258428	20h	ENSE00001790412	chr2:100022568-100022372	197	REV1_HUMAN	872-937	66	0	-	-
2.21	ENST00000258428	21	ENSE00001641934	chr2:100021140-100020907	234	REV1_HUMAN	938-1015	78	0	-	-
2.22	ENST00000258428	22	ENSE00001774065	chr2:100020278-100020158	121	REV1_HUMAN	1016-1056	41	0	-	-
2.23d	ENST00000258428	23d	ENSE00001793684	chr2:100019569-100019352	218	REV1_HUMAN	1056-1128	73	0	-	-
2.24a	ENST00000258428	24a	ENSE00000921842	chr2:100019263-100019107	157	REV1_HUMAN	1129-1181	53	1	A:1153-1181 (gaps)	32
2.24e	ENST00000258428	24e	ENSE00000921841	chr2:100018809-100018707	103	REV1_HUMAN	1181-1215	35	1	A:1181-1215	35
2.25b	ENST00000258428	25b	ENSE00000921840	chr2:100017815-100016938	878	REV1_HUMAN	1215-1251	37	1	A:1215-1251	37

NMR Structure

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:99
 aligned with REV1_HUMAN | Q9UBZ9 from UniProtKB/Swiss-Prot  Length:1251

    Alignment length:102
                                  1159      1169      1179      1189      1199      1209      1219      1229      1239      1249  
          REV1_HUMAN   1150 GCVRPPAPNLAGAVEFNDVKTLLREWITTISDPMEEDILQVVKYCTDLIEEKDLEKLDLVIKYMKRLMQQSVESVWNMAFDFILDNVQVVLQQTYGSTLKVT 1251
               SCOP domains ------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...---........hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 2 (1) Exon 2.24a UniProt: 1129-1181   ---------------------------------Exon 2.25b  PDB: A:1215-1251          Transcript 2 (1)
           Transcript 2 (2) -------------------------------Exon 2.24e  PDB: A:1181-1215       ------------------------------------ Transcript 2 (2)
                2lsi A 1153 GHM---APNLAGAVEFNDVKTLLREWITTISDPMEEDILQVVKYCTDLIEEKDLEKLDLVIKYMKRLMQQSVESVWNMAFDFILDNVQVVLQQTYGSTLKVT 1251
                              |   1159      1169      1179      1189      1199      1209      1219      1229      1239      1249  
                           1155   |                                                                                               
                               1156

Chain B from PDB  Type:PROTEIN  Length:17
 aligned with POLK_HUMAN | Q9UBT6 from UniProtKB/Swiss-Prot  Length:870

    Alignment length:42
                                   545       555       565       575  
          POLK_HUMAN    536 GNQALSATECTLEKTDKDKFVKPLEMSHKKSFFDKKRSERKW  577
               SCOP domains ------------------------------------------ SCOP domains
               CATH domains ------------------------------------------ CATH domains
               Pfam domains ------------------------------------------ Pfam domains
         Sec.struct. author .-------------------------....hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------ PROSITE
               Transcript 1 Exon 1.16a  PDB: B:561-577 (gaps)          Transcript 1
                2lsi B  561 G-------------------------SHKKSFFDKKRSERKW  577
                            |        -         -      |565       575  
                            |                       562               
                          561

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 "SCOP Domain" information available for 2LSI)

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

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

NMR Structure(hide GO term definitions)

Chain A (REV1_HUMAN | Q9UBZ9)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003684	damaged DNA binding	Interacting selectively and non-covalently with damaged DNA.
	GO:0017125	deoxycytidyl transferase activity	Catalysis of the insertion of a dCMP residue opposite a template abasic site in DNA.
	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:0042276	error-prone translesion synthesis	The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication by using a specialized DNA polymerase or replication complex to insert a defined nucleotide across the lesion. This process does not remove the replication-blocking lesions and causes an increase in the endogenous mutation level. For example, in E. coli, a low fidelity DNA polymerase, pol V, copies lesions that block replication fork progress. This produces mutations specifically targeted to DNA template damage sites, but it can also produce mutations at undamaged sites.
	GO:0009411	response to UV	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers.
	GO:0019985	translesion synthesis	The replication of damaged DNA by synthesis across a lesion in the template strand; a specialized DNA polymerase or replication complex inserts a defined nucleotide across from the lesion which allows DNA synthesis to continue beyond the lesion. This process can be mutagenic depending on the damaged nucleotide and the inserted nucleotide.
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.

Chain B (POLK_HUMAN | Q9UBT6)

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: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: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:0042276	error-prone translesion synthesis	The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication by using a specialized DNA polymerase or replication complex to insert a defined nucleotide across the lesion. This process does not remove the replication-blocking lesions and causes an increase in the endogenous mutation level. For example, in E. coli, a low fidelity DNA polymerase, pol V, copies lesions that block replication fork progress. This produces mutations specifically targeted to DNA template damage sites, but it can also produce mutations at undamaged sites.
	GO:0006297	nucleotide-excision repair, DNA gap filling	Repair of the gap in the DNA helix by DNA polymerase and DNA ligase after the portion of the strand containing the lesion has been removed by pyrimidine-dimer repair enzymes.
	GO:0033683	nucleotide-excision repair, DNA incision	A process that results in the endonucleolytic cleavage of the damaged strand of DNA. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound.
	GO:0006296	nucleotide-excision repair, DNA incision, 5'-to lesion	The endonucleolytic cleavage of the damaged strand of DNA 5' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision follows the incision formed 3' to the site of damage.
	GO:0006283	transcription-coupled nucleotide-excision repair	The nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway.
	GO:0019985	translesion synthesis	The replication of damaged DNA by synthesis across a lesion in the template strand; a specialized DNA polymerase or replication complex inserts a defined nucleotide across from the lesion which allows DNA synthesis to continue beyond the lesion. This process can be mutagenic depending on the damaged nucleotide and the inserted nucleotide.
cellular component
	GO:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	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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