3P5J - JenaLib

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:262
 aligned with RNH2A_MOUSE | Q9CWY8 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:292
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299  
          RNH2A_MOUSE    10 NTGRCRLSSPVPAVCLKEPCVLGVDEAGRGPVLGPMVYAICYCPLSRLADLEALKVADSKTLTENERERLFAKMEEDGDFVGWALDVLSPNLISTSMLGRVKYNLNSLSHDTAAGLIQYALDQNVNVTQVFVDTVGMPETYQARLQQHFPGIEVTVKAKADSLFPVVSAASIFAKVARDKAVKNWQFVENLQDLDSDYGSGYPNDPKTKAWLRKHVDPVFGFPQFVRFSWSTAQAILEKEAEDVIWEDSEAEEDPERPGKITSYFSQGPQTCRPQAPHRYFQERGLEAASSL 301
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------RNase_HII-3p5jA01 A:31-242                                                                                                                                                                                          ----------------                           ---------------- Pfam domains
         Sec.struct. author ...eeeee....hhhhhh.eeeeeeee........eeeeeeeee..hhhhhhh....---..hhhhhhhhhhhhhhh....eeeeeeehhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhh...............hhhhhhhhhhhh..ee....---------------------------hhhhhhhhheee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p5j A  10 NTGRCRLSSPVPAVCLKEPCVLGVDEAGRGPVLGPMVYAICYCPLSRLADLEALKVA---TLTENERERLFAKMEEDGDFVGWALDVLSPNLISTSMLGRVKYNLNSLSHDTAAGLIQYALDQNVNVTQVFVDTVGMPETYQARLQQHFPGIEVTVKAKADSLFPVVSAASIFAKVARDKAVKNWQFVENLQDLDSDYGSGYPNDPKTKAWLRKHVDPVFGFPQFVRFSWSTAQAILEKEAEDVIWEDS---------------------------PHRYFQERGLEAASSL 299
                                    19        29        39        49        59      |  -|       79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249        |-         -         -      |287       297  
                                                                                   66  70                                                                                                                                                                                         258                         284

Chain B from PDB  Type:PROTEIN  Length:171
 aligned with RNH2B_MOUSE | Q80ZV0 from UniProtKB/Swiss-Prot  Length:308

    Alignment length:221
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230 
          RNH2B_MOUSE    11 AARQLVFLLPEHLKDASKKKKKSSLLFVKLANPHSGEGATYLIDMCLQQLFEIKVFKEKHHSWFINQSVQSGGLLHFATPMDPLFLLLHYLLKAGKEGKYQPLDQVVVDDTFPDCTLLLRFPELEKSLRHVTEEKEVNSKKYYKYSSEKTLKWLEKKVNQTVVALKANNVNVGARVQSSAYFSGGQVSRDKEEDYVRYAHGLISDYIPKELSDDLSKFLKL 231
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --RNase_H2-Ydr279      -3p5jB01 B:13-231                                                                                                                                                                                      Pfam domains
         Sec.struct. author ....eeeeee.hhhh..------.eeeeee........eeeeee....eeeeeeee.....eeee..eeee...eeeeee.hhhhhhhhhh.....----------------.hhhhhhh..hhhhhhh....-------.....hhhhhhhhhhhhhhhhhhhhhhh...---------------------.hhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p5j B  11 AARQLVFLLPEHLKDAS------SLLFVKLANPHSGEGATYLIDMCLQQLFEIKVFKEKHHSWFINQSVQSGGLLHFATPMDPLFLLLHYLLKAGK----------------PDCTLLLRFPELEKSLRHVTE-------KYYKYSSEKTLKWLEKKVNQTVVALKANNVN---------------------EDYVRYAHGLISDYIPKELSDDLSKFLKL 231
                                    20      |  -   |    40        50        60        70        80        90       100     |   -         -  |    130       140  |      -|      160       170       180|        -         -  |    210       220       230 
                                           27     34                                                                     106              123                 143     151                           181                   203

Chain C from PDB  Type:PROTEIN  Length:116
 aligned with RNH2C_MOUSE | Q9CQ18 from UniProtKB/Swiss-Prot  Length:166

    Alignment length:149
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153         
          RNH2C_MOUSE    14 IHLRPGSLRGAAPAKLHLLPCDVLVSRPAPVDRFFTPAVRHDADGLQASFRGRGLRGEEVAVPPGFAGFVMVTEEKGEGLIGKLNFSGDAEDKADEAQEPLERDFDRLIGATGSFSHFTLWGLETVPGPDAKVHRALGWPSLAAAIHAQ 162
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------RNase_H2_suC-3p5jC01 C:28-159                                                                                                       --- Pfam domains
         Sec.struct. author ...hhhhhhh.ee..eeee..ee...ee.hhhhhhhhhhee....eeeee..eeeeeeeee....eeeeeee.---------------------------------...eeeeee.eeeeeee.......hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p5j C  14 IHLRPGSLRGAAPAKLHLLPCDVLVSRPAPVDRFFTPAVRHDADGLQASFRGRGLRGEEVAVPPGFAGFVMVT---------------------------------RLIGATGSFSHFTLWGLETVPGPDAKVHRALGWPSLAAAIHAQ 162
                                    23        33        43        53        63        73        83  |      -         -         -      |123       133       143       153         
                                                                                                   86                               120

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 (0, 0)

CATH Domains (0, 0)

Pfam Domains (3, 3)

Gene Ontology (22, 32)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (RNH2A_MOUSE | Q9CWY8)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0004523	RNA-DNA hybrid ribonuclease activity	Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
biological process
	GO:0043137	DNA replication, removal of RNA primer	Removal of the Okazaki RNA primer from the lagging strand of replicating DNA, by a combination of the actions of DNA polymerase, DNA helicase and an endonuclease.
	GO:0006401	RNA catabolic process	The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
	GO:0016070	RNA metabolic process	The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
	GO:0090502	RNA phosphodiester bond hydrolysis, endonucleolytic	The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
	GO:0006298	mismatch repair	A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.
	GO:0032299	ribonuclease H2 complex	A protein complex that possesses ribonuclease H activity, in which the catalytic subunit is a member of the RNase H2 (or HII) class. For example, in Saccharomyces the complex contains Rnh201p, Rnh202p and Rnh203p.

Chain B (RNH2B_MOUSE | Q80ZV0)

molecular function
	GO:0004523	RNA-DNA hybrid ribonuclease activity	Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters.
biological process
	GO:0006401	RNA catabolic process	The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
	GO:0090502	RNA phosphodiester bond hydrolysis, endonucleolytic	The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
	GO:0001701	in utero embryonic development	The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
	GO:0010629	negative regulation of gene expression	Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0048146	positive regulation of fibroblast proliferation	Any process that activates or increases the frequency, rate or extent of multiplication or reproduction of fibroblast cells.
	GO:2000001	regulation of DNA damage checkpoint	Any process that modulates the frequency, rate or extent of a DNA damage checkpoint.
	GO:0010389	regulation of G2/M transition of mitotic cell cycle	Any process that modulates the rate or extent of progression from G2 phase to M phase of the mitotic cell cycle.
	GO:0009259	ribonucleotide metabolic process	The chemical reactions and pathways involving a ribonucleotide, a compound consisting of ribonucleoside (a base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
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.
	GO:0032299	ribonuclease H2 complex	A protein complex that possesses ribonuclease H activity, in which the catalytic subunit is a member of the RNase H2 (or HII) class. For example, in Saccharomyces the complex contains Rnh201p, Rnh202p and Rnh203p.

Chain C (RNH2C_MOUSE | Q9CQ18)

molecular function
	GO:0004523	RNA-DNA hybrid ribonuclease activity	Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters.
biological process
	GO:0006401	RNA catabolic process	The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
	GO:0090502	RNA phosphodiester bond hydrolysis, endonucleolytic	The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
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.
	GO:0032299	ribonuclease H2 complex	A protein complex that possesses ribonuclease H activity, in which the catalytic subunit is a member of the RNase H2 (or HII) class. For example, in Saccharomyces the complex contains Rnh201p, Rnh202p and Rnh203p.

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	3p5j
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
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Access by UniProt ID/Accession number
	RNH2A_MOUSE \| Q9CWY8
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	RNH2B_MOUSE \| Q80ZV0
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	RNH2C_MOUSE \| Q9CQ18
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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	3.1.26.4
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments