2QK9 - JenaLib

Title :   HUMAN RNASE H CATALYTIC DOMAIN MUTANT D210N IN COMPLEX WITH 18-MER RNA/DNA HYBRID

Authors :   M. Nowotny, S. A. Gaidamakov, R. Ghirlando, S. M. Cerritelli, R. J. Crou

Date :   10 Jul 07 (Deposition) - 13 Nov 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.55

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Rnase H; Rna/Dna Hybrid, Hydrolase-Dna-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Nowotny, S. A. Gaidamakov, R. Ghirlando, S. M. Cerritelli, R. J. Crouch, W. Yang
Structure Of Human Rnase H1 Complexed With An Rna/Dna Hybrid: Insight Into Hiv Reverse Transcription
Mol. Cell V. 28 264 2007
PubMed-ID: 17964265 | Reference-DOI: 10.1016/J.MOLCEL.2007.08.015

Compounds

Molecule 1 - RIBONUCLEASE H1
	Chains	:	A
	EC Number	:	3.1.26.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET15
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL DOMAIN (RESIDUES 134-286)
	Gene	:	RNASEH1, RNH1
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HS-RNASE HC; RNASE H1; RIBONUCLEASE H TYPE II

*Molecule 2 - 5'-R(APGPUPGPCPGPAPCPAPCPCPUPGPAPUPUPCPC) -3'*
	Chains	:	B
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 3 - 5'-D(GPGPAPAPTPCPAPGPGPTPGPTPCPGPCPAPCPT) -3'*
	Chains	:	C
	Engineered	:	YES
	Synthetic	:	YES

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 12)

Sites (12, 12)

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC2	SOFTWARE	C B:8 , A B:9 , 16D C:1004	BINDING SITE FOR RESIDUE SO4 B 1007
02	AC3	SOFTWARE	G B:13 , A B:14 , DA C:25	BINDING SITE FOR RESIDUE SO4 B 1008
03	AC4	SOFTWARE	DT C:30 , DC C:31	BINDING SITE FOR RESIDUE SO4 C 1009
04	AC5	SOFTWARE	ASP A:145 , GLU A:186 , ASN A:210 , HOH A:9037 , A B:9 , C B:10	BINDING SITE FOR RESIDUE NA A 9001
05	AC6	SOFTWARE	VAL A:140 , TRP A:164 , HIS A:168 , GLY A:173 , GLN A:200 , ILE A:202 , GLN A:283 , HOH A:9014 , HOH A:9018 , HOH A:9021 , HOH A:9038 , HOH A:9041 , HOH A:9045	BINDING SITE FOR RESIDUE FLC A 1001
06	AC7	SOFTWARE	ARG A:157 , ARG A:175 , SER A:284 , GLU A:285	BINDING SITE FOR RESIDUE SO4 A 1005
07	AC8	SOFTWARE	HIS A:264 , HOH A:9054 , C B:10 , C B:11	BINDING SITE FOR RESIDUE SO4 A 1006
08	AC9	SOFTWARE	ARG A:153 , DG C:26 , DG C:27	BINDING SITE FOR RESIDUE SO4 A 1010
09	AD1	SOFTWARE	ARG A:153 , ARG A:154 , HOH A:9058	BINDING SITE FOR RESIDUE SO4 A 1011
10	BC1	SOFTWARE	A B:7 , SO4 B:1007 , HOH B:1027 , DT C:28 , DG C:29 , DT C:30 , HOH C:1033	BINDING SITE FOR RESIDUE 16D C 1004
11	BC2	SOFTWARE	ARG A:179 , ARG A:184 , ILE A:239 , ASN A:240 , GLU A:242 , ASP A:243	BINDING SITE FOR RESIDUE GOL A 1002
12	BC3	SOFTWARE	HIS A:188 , CYS A:191 , GLU A:195	BINDING SITE FOR RESIDUE GOL A 1003

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

PROSITE Motifs (1, 1)

Exons (6, 6)

Asymmetric/Biological Unit (6, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000315212	1a	ENSE00001253796	chr2:3606206-3605723	484	RNH1_HUMAN	1-43	43	0	-	-
1.3	ENST00000315212	3	ENSE00001764472	chr2:3604494-3604379	116	RNH1_HUMAN	43-82	40	0	-	-
1.4	ENST00000315212	4	ENSE00001613471	chr2:3599898-3599734	165	RNH1_HUMAN	82-137	56	1	A:134-137	4
1.5b	ENST00000315212	5b	ENSE00001792991	chr2:3598062-3597963	100	RNH1_HUMAN	137-170	34	1	A:137-170	34
1.6	ENST00000315212	6	ENSE00001703361	chr2:3596702-3596648	55	RNH1_HUMAN	170-188	19	1	A:170-188	19
1.7	ENST00000315212	7	ENSE00001702047	chr2:3596314-3596230	85	RNH1_HUMAN	189-217	29	1	A:189-217	29
1.8	ENST00000315212	8	ENSE00001759845	chr2:3595645-3595521	125	RNH1_HUMAN	217-258	42	1	A:217-258	42
1.9a	ENST00000315212	9a	ENSE00001253775	chr2:3593461-3592705	757	RNH1_HUMAN	259-286	28	1	A:259-286	28

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:153
 aligned with RNH1_HUMAN | O60930 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:153
                                   143       153       163       173       183       193       203       213       223       233       243       253       263       273       283   
           RNH1_HUMAN   134 SYMGDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTDSMFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQGMDIQWMHVPGHSGFIGNEEADRLAREGAKQSED 286
               SCOP domains d2qk9a_ A: automated matches                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---RNase_H-2qk9A01 A:137-282                                                                                                                         ---- Pfam domains
         Sec.struct. author ......eeeeeeeeee.......eeeeeee........eeee.....hhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------I------------------------------------------V----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --RNASE_H  PDB: A:136-282 UniProt: 136-282                                                                                                           ---- PROSITE
           Transcript 1 (1) 1.4 --------------------------------Exon 1.6           Exon 1.7  PDB: A:189-217     -----------------------------------------Exon 1.9a  PDB: A:259-286    Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.5b  PDB: A:137-170         ----------------------------------------------Exon 1.8  PDB: A:217-258 UniProt: 217-258 ---------------------------- Transcript 1 (2)
                 2qk9 A 134 SHMGDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTNSMFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQGMDIQWMHVPGHSGFIGNEEADRLAREGAKQSED 286
                                   143       153       163       173       183       193       203       213       223       233       243       253       263       273       283

Chain B from PDB  Type:RNA  Length:18
                                                  
                 2qk9 B   1 AGUGCGACACCUGAUUCC  18
                                    10

Chain C from PDB  Type:DNA  Length:18
                                                  
                 2qk9 C  19 GGAATCAGGTGTCGCACT  36
                                    28

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 (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (RNH1_HUMAN | O60930)

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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	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.
	GO:0004540	ribonuclease activity	Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
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:0090501	RNA phosphodiester bond hydrolysis	The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
	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:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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