1WSF - JenaLib

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)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CO-CRYSTAL STRUCTURE OF E.COLI RNASE HI ACTIVE SITE MUTANT (D134A*) WITH MN2+

Authors :   Y. Tsunaka, K. Takano, H. Matsumura, Y. Yamagata, S. Kanaya

Date :   05 Nov 04 (Deposition) - 08 Feb 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Rnase H, Active-Site Mutant, Co-Crystal Structure With Mn2+, X-Ray Crystallography, Metal Fluctuation Model, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Tsunaka, K. Takano, H. Matsumura, Y. Yamagata, S. Kanaya
Identification Of Single Mn(2+) Binding Sites Required For Activation Of The Mutant Proteins Of E. Coli Rnase Hi At Glu48 And/Or Asp134 By X-Ray Crystallography
J. Mol. Biol. V. 345 1171 2005
PubMed-ID: 15644213 | Reference-DOI: 10.1016/J.JMB.2004.11.007
(for further references see the PDB file header)

Molecule 1 - RIBONUCLEASE HI
	Chains	:	A, B, C, D
	EC Number	:	3.1.26.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PJAL600
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	RNASE HI, RIBONUCLEASE H, RNASE H

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	MN	3	Ligand/Ion	MANGANESE (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:10 , ASP A:70 , HOH A:1037	BINDING SITE FOR RESIDUE MN A 1001
2	AC2	SOFTWARE	ASP B:10 , GLY B:11 , HIS B:124 , HOH B:1003 , HOH B:1035	BINDING SITE FOR RESIDUE MN B 1002
3	AC3	SOFTWARE	ASP D:10 , GLU D:48 , ASP D:70 , HOH D:1016 , HOH D:1018	BINDING SITE FOR RESIDUE MN D 1003

(no "SS Bond" information available for 1WSF)

Asymmetric Unit

No.	Residues
1	Asn A:16	-	Pro A:17
2	Asn B:16	-	Pro B:17
3	Asn C:16	-	Pro C:17
4	Asn D:16	-	Pro D:17

(no "SAP(SNP)/Variant" information available for 1WSF)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_H	PS50879	RNase H domain profile.	RNH_ECOLI	1-142	4	A:1-142 B:1-142 C:1-142 D:1-142

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_H	PS50879	RNase H domain profile.	RNH_ECOLI	1-142	1	A:1-142 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_H	PS50879	RNase H domain profile.	RNH_ECOLI	1-142	1	- B:1-142 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_H	PS50879	RNase H domain profile.	RNH_ECOLI	1-142	1	- - C:1-142 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_H	PS50879	RNase H domain profile.	RNH_ECOLI	1-142	1	- - - D:1-142

(no "Exon" information available for 1WSF)

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:155
 aligned with RNH_ECOLI | P0A7Y4 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150     
            RNH_ECOLI     1 MLKQVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHCEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERCDELARAAAMNPTLEDTGYQVEV 155
               SCOP domains d1wsfa1 A:1-155 RNase H (RNase HI)                                                                                                                          SCOP domains
               CATH domains 1wsfA00 A:1-155  [code=3.30.420.10, no name defined]                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee....eeeeeeeeeee..eeeeeeeeeeeehhhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh.eeeeee......hhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RNASE_H  PDB: A:1-142 UniProt: 1-142                                                                                                          ------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wsf A   1 MLKQVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHCEVILSTDSQYVRQGITQWIHNWKARGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERCAELARAAAMNPTLEDTGYQVEV 155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:PROTEIN  Length:155
 aligned with RNH_ECOLI | P0A7Y4 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150     
            RNH_ECOLI     1 MLKQVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHCEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERCDELARAAAMNPTLEDTGYQVEV 155
               SCOP domains d1wsfb_ B: RNase H (RNase HI)                                                                                                                               SCOP domains
               CATH domains 1wsfB00 B:1-155  [code=3.30.420.10, no name defined]                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee....eeeeeeeeee.....eeeeeeeeeehhhhhhhhhhhhhhhh....eeeeeee.hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RNASE_H  PDB: B:1-142 UniProt: 1-142                                                                                                          ------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wsf B   1 MLKQVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHCEVILSTDSQYVRQGITQWIHNWKARGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERCAELARAAAMNPTLEDTGYQVEV 155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain C from PDB  Type:PROTEIN  Length:155
 aligned with RNH_ECOLI | P0A7Y4 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150     
            RNH_ECOLI     1 MLKQVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHCEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERCDELARAAAMNPTLEDTGYQVEV 155
               SCOP domains d1wsfc_ C: RNase H (RNase HI)                                                                                                                               SCOP domains
               CATH domains 1wsfC00 C:1-155  [code=3.30.420.10, no name defined]                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee....eeeeeeeeee....eeeeeeeeeeehhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhheeeeee......hhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RNASE_H  PDB: C:1-142 UniProt: 1-142                                                                                                          ------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wsf C   1 MLKQVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHCEVILSTDSQYVRQGITQWIHNWKARGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERCAELARAAAMNPTLEDTGYQVEV 155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain D from PDB  Type:PROTEIN  Length:155
 aligned with RNH_ECOLI | P0A7Y4 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150     
            RNH_ECOLI     1 MLKQVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHCEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERCDELARAAAMNPTLEDTGYQVEV 155
               SCOP domains d1wsfd_ D: RNase H (RNase HI)                                                                                                                               SCOP domains
               CATH domains 1wsfD00 D:1-155  [code=3.30.420.10, no name defined]                                                                                                        CATH domains
           Pfam domains (1) -RNase_H-1wsfD01 D:2-142                                                                                                                      ------------- Pfam domains (1)
           Pfam domains (2) -RNase_H-1wsfD02 D:2-142                                                                                                                      ------------- Pfam domains (2)
           Pfam domains (3) -RNase_H-1wsfD03 D:2-142                                                                                                                      ------------- Pfam domains (3)
           Pfam domains (4) -RNase_H-1wsfD04 D:2-142                                                                                                                      ------------- Pfam domains (4)
         Sec.struct. author ...eeeeeeeeee....eeeeeeeee......eeeeeeeeeehhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RNASE_H  PDB: D:1-142 UniProt: 1-142                                                                                                          ------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wsf D   1 MLKQVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHCEVILSTDSQYVRQGITQWIHNWKARGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERCAELARAAAMNPTLEDTGYQVEV 155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

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 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: Ribonuclease H (190)

Protein domain: RNase H (RNase HI) (36)

Escherichia coli [TaxId: 562] (33)

1a	d1wsfa1	A:1-155
1b	d1wsfb_	B:
1c	d1wsfc_	C:
1d	d1wsfd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Nucleotidyltransferase; domain 5 (788)

Homologous Superfamily: [code=3.30.420.10, no name defined] (372)

Escherichia coli. Organism_taxid: 562. (17)

1a	1wsfA00	A:1-155
1b	1wsfB00	B:1-155
1c	1wsfC00	C:1-155
1d	1wsfD00	D:1-155

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: RNase_H (288)

Family: RNase_H (128)

Escherichia coli (strain K12) (28)

1a	RNase_H-1wsfD01	D:2-142
1b	RNase_H-1wsfD02	D:2-142
1c	RNase_H-1wsfD03	D:2-142
1d	RNase_H-1wsfD04	D:2-142

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (RNH_ECOLI | P0A7Y4)

molecular function
	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.
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: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 Unit
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		Asn C:16 - Pro C:17	[ RasMol ]
		Asn D:16 - Pro D:17	[ RasMol ]

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	1wsf
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1wse	THE SAME PROTEIN MUTANT (E48A*) WITH MN2+
1wsg	THE SAME PROTEIN MUTANT (E48A/D134N*) WITH MN2+
1wsh	THE SAME PROTEIN MUTANT (E48A/K87A)
1wsi	THE SAME PROTEIN MUTANT (E48A/K87A/D134N)
1wsj	THE SAME PROTEIN MUTANT (K87A/H124A)

Description

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