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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   HUMAN RNASE H CATALYTIC DOMAIN MUTANT D210N IN COMPLEX WITH 20-MER RNA/DNA HYBRID

Authors :   M. Nowotny, S. A. Gaidamakov, R. Ghirlando, S. M. Cerritelli, R. J. Crouch, W. Yang

Date :   10 Jul 07 (Deposition) - 13 Nov 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

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
(for further references see the PDB file header)

Molecule 1 - RIBONUCLEASE H1
	Chains	:	A, B
	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(GPGPAPGPUPGPCPGPAPCPAPCPCPUPGPAPUPUPCP C)-3')*
	Chains	:	C
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 3 - 5'- D(DGPDGPDAPDAPDTPDCPDAPDGPDGPDTPDGPDTPDCPDGP DCPDAPDCPDTPDCPDT)-3'*
	Chains	:	D
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 12)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:153 , ARG A:154	BINDING SITE FOR RESIDUE SO4 A 9001
2	AC2	SOFTWARE	ARG B:157 , ARG B:175 , SER B:284	BINDING SITE FOR RESIDUE SO4 B 9002
3	AC3	SOFTWARE	ARG A:179 , ARG A:184 , ILE A:239 , ASP A:243 , HOH A:9017 , HOH A:9018	BINDING SITE FOR RESIDUE EDO A 9003
4	AC4	SOFTWARE	ARG B:179 , ARG B:184 , ILE B:239 , GLU B:242 , ASP B:243 , HOH B:9029	BINDING SITE FOR RESIDUE EDO B 9004

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

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

Asymmetric/Biological Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_074561	V	142	I	RNH1_HUMAN	Disease (PEOB2)	766294940	A/B	V	142	I
2	UniProt	VAR_074562	A	185	V	RNH1_HUMAN	Disease (PEOB2)	---	A/B	A	185	V

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_H	PS50879	RNase H domain profile.	RNH1_HUMAN	136-282	2	A:136-282 B:136-282

Asymmetric/Biological Unit (6, 12)

	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	2	A:133-137 (gaps) B:134-137	33 4
1.5b	ENST00000315212	5b	ENSE00001792991	chr2:3598062-3597963	100	RNH1_HUMAN	137-170	34	2	A:137-170 B:137-170 (gaps)	34 34
1.6	ENST00000315212	6	ENSE00001703361	chr2:3596702-3596648	55	RNH1_HUMAN	170-188	19	2	A:170-188 B:170-188	19 19
1.7	ENST00000315212	7	ENSE00001702047	chr2:3596314-3596230	85	RNH1_HUMAN	189-217	29	2	A:189-217 B:189-217	29 29
1.8	ENST00000315212	8	ENSE00001759845	chr2:3595645-3595521	125	RNH1_HUMAN	217-258	42	2	A:217-258 B:217-258	42 42
1.9a	ENST00000315212	9a	ENSE00001253775	chr2:3593461-3592705	757	RNH1_HUMAN	259-286	28	2	A:259-284 B:259-284	26 26

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:152
 aligned with RNH1_HUMAN | O60930 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:180
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284
           RNH1_HUMAN   105 GDGHESAEPYAKHMKPSVEPAPPVSRDTFSYMGDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTDSMFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQGMDIQWMHVPGHSGFIGNEEADRLAREGAKQS 284
               SCOP domains d                            2qkba_ A: automated matches                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .----------------------------.ee..eeeeeeeeeee.......eeeeeee........eeee.....hhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------I------------------------------------------V--------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------RNASE_H  PDB: A:136-282 UniProt: 136-282                                                                                                           -- PROSITE
           Transcript 1 (1) Exon 1.4  PDB: A:133-137 (gaps)  --------------------------------Exon 1.6           Exon 1.7  PDB: A:189-217     -----------------------------------------Exon 1.9a  PDB: A:259-284  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)
                 2qkb A 133 G----------------------------SHmGDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTNSmFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQGmDIQWmHVPGHSGFIGNEEADRLAREGAKQS 284
                            |        -         -       134 |     144       154       164       174       184       194       204       214       224       234       244       254    |  264       274       284
                            |                          134 |                                                                         212-MSE                                   254-MSE|                         
                          133                            136-MSE                                                                                                                    259-MSE

Chain B from PDB  Type:PROTEIN  Length:150
 aligned with RNH1_HUMAN | O60930 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:151
                                   143       153       163       173       183       193       203       213       223       233       243       253       263       273       283 
           RNH1_HUMAN   134 SYMGDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTDSMFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQGMDIQWMHVPGHSGFIGNEEADRLAREGAKQS 284
               SCOP domains d2qkbb_ B: automat ed matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---RNase_H-2qkbB01  B:137-282                                                                                                                        -- Pfam domains (1)
           Pfam domains (2) ---RNase_H-2qkbB02  B:137-282                                                                                                                        -- Pfam domains (2)
         Sec.struct. author .ee..eeeeeeeeeee..-....eeeeeee........eeee.....hhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh.............hhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------I------------------------------------------V--------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --RNASE_H  PDB: B:136-282 UniProt: 136-282                                                                                                           -- PROSITE
           Transcript 1 (1) 1.4 --------------------------------Exon 1.6           Exon 1.7  PDB: B:189-217     -----------------------------------------Exon 1.9a  PDB: B:259-284  Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.5b  PDB: B:137-170 (gaps)  ----------------------------------------------Exon 1.8  PDB: B:217-258 UniProt: 217-258 -------------------------- Transcript 1 (2)
                 2qkb B 134 SHmGDFVVVYTDGCCSSN-RRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTNSmFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQGmDIQWmHVPGHSGFIGNEEADRLAREGAKQS 284
                              |    143       153       163       173       183       193       203       213       223       233       243       253|    | 263       273       283 
                            136-MSE        151 |                                                        212-MSE                                   254-MSE|                         
                                             153                                                                                                       259-MSE

Chain C from PDB  Type:DNA/RNA  Length:20
                                                    
                 2qkb C   1 GGAGUGCGACACCUGAUUCC  20
                                    10        20

Chain D from PDB  Type:DNA  Length:20
                                                    
                 2qkb D  21 GGAATCAGGTGTCGCACTCT  40
                                    30        40

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Ribonuclease H-like motif (1424)

Superfamily: Ribonuclease H-like (775)

Family: automated matches (127)

Protein domain: automated matches (127)

Human (Homo sapiens) [TaxId: 9606] (2)

1a	d2qkba_	A:
1b	d2qkbb_	B:

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: RNase_H (288)

Family: RNase_H (128)

Homo sapiens (Human) (3)

1a	RNase_H-2qkbB01	B:137-282
1b	RNase_H-2qkbB02	B:137-282

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (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.

Asymmetric/Biological Unit
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	RNH1_HUMAN \| O60930	:	2qk9 2qkk 3bsu

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 4)

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Exons (6, 12)

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