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Title :   CRYSTAL STRUCTURE OF CLASS II RIBONUCLEASE H (RNASE HII) WITH MES LIGAND

Authors :   L. H. Lai, H. Yokota, L. W. Hung, R. Kim, S. H. Kim, Berkeley Structural Genomics Center (Bsgc)

Date :   07 Mar 00 (Deposition) - 13 Sep 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Nuclease, Endonuclease, Structural Genomics, Bsgc Structure Funded By Nih, Protein Structure Initiative, Psi, Berkeley Structural Genomics Center, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Lai, H. Yokota, L. W. Hung, R. Kim, S. H. Kim
Crystal Structure Of Archaeal Rnase Hii: A Homologue Of Human Major Rnase H
Structure V. 8 897 2000
PubMed-ID: 10997908 | Reference-DOI: 10.1016/S0969-2126(00)00179-9
(for further references see the PDB file header)

Molecule 1 - RIBONUCLEASE HII
	Chains	:	A, B
	EC Number	:	3.1.26.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	METHANOCALDOCOCCUS JANNASCHII
	Organism Taxid	:	2190

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 8)

No.	Name	Count	Type	Full Name
1	MES	2	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:212 , LYS A:213 , HOH A:403 , HOH A:422	BINDING SITE FOR RESIDUE MES A 301
2	AC2	SOFTWARE	TRP B:212 , LYS B:213 , HOH B:680	BINDING SITE FOR RESIDUE MES B 302

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

(no "Cis Peptide Bond" information available for 1EKE)

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

(no "PROSITE Motif" information available for 1EKE)

(no "Exon" information available for 1EKE)

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:222
 aligned with RNH2_METJA | Q57599 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:225
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220     
           RNH2_METJA     1 MIIIGIDEAGRGPVLGPMVVCAFAIEKEREEELKKLGVKDSKELTKNKRAYLKKLLENLGYVEKRILEAEEINQLMNSINLNDIEINAFSKVAKNLIEKLNIRDDEIEIYIDACSTNTKKFEDSFKDKIEDIIKERNLNIKIIAEHKADAKYPVVSAASIIAKAERDEIIDYYKKIYGDIGSGYPSDPKTIKFLEDYFKKHKKLPDIARTHWKTCKRILDKSKQT 225
               SCOP domains d1ekea_ A: Class II ribonuclease H (RNa   se HII)                                                                                                                                                                                 SCOP domains
               CATH domains -1ekeA01 A:2-175  [code=3.30.420.10, no    name defined]                                                                                                                       1ekeA02 A:176-225 Ribonuclease hii. Domain 2       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee........eeeeeeeee..hhhhhhh....---..hhhhhhhhhhhhhhhheeeeeeehhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhhhhhh....eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhh.........hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1eke A   1 mIIIGIDEAGRGPVLGPmVVCAFAIEKEREEELKKLGVK---ELTKNKRAYLKKLLENLGYVEKRILEAEEINQLmNSINLNDIEINAFSKVAKNLIEKLNIRDDEIEIYIDACSTNTKKFEDSFKDKIEDIIKERNLNIKIIAEHKADAKYPVVSAASIIAKAERDEIIDYYKKIYGDIGSGYPSDPKTIKFLEDYFKKHKKLPDIARTHWKTCKRILDKSKQT 225
                            |       10       |20        30        |-  |     50        60        70     |  80        90       100       110       120       130       140       150       160       170       180       190       200       210       220     
                            |               18-MSE               39  43                               76-MSE                                                                                                                                                 
                            1-MSE

Chain B from PDB  Type:PROTEIN  Length:225
 aligned with RNH2_METJA | Q57599 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:225
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220     
           RNH2_METJA     1 MIIIGIDEAGRGPVLGPMVVCAFAIEKEREEELKKLGVKDSKELTKNKRAYLKKLLENLGYVEKRILEAEEINQLMNSINLNDIEINAFSKVAKNLIEKLNIRDDEIEIYIDACSTNTKKFEDSFKDKIEDIIKERNLNIKIIAEHKADAKYPVVSAASIIAKAERDEIIDYYKKIYGDIGSGYPSDPKTIKFLEDYFKKHKKLPDIARTHWKTCKRILDKSKQT 225
               SCOP domains d1ekeb_ B: Class II ribonuclease H (RNase HII)                                                                                                                                                                                    SCOP domains
               CATH domains -1ekeB01 B:2-175  [code=3.30.420.10, no name defined]                                                                                                                          1ekeB02 B:176-222 Ribonuclease hii. Domain 2   --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee........eeeeeeeee..hhhhhhhh........hhhhhhhhhhhhhhhheeeeeeehhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh....eeeeeeee....hhhhhhhhhhhhhhhhhhhh.eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh.........hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1eke B   1 mIIIGIDEAGRGPVLGPmVVCAFAIEKEREEELKKLGVKDSKELTKNKRAYLKKLLENLGYVEKRILEAEEINQLmNSINLNDIEINAFSKVAKNLIEKLNIRDDEIEIYIDACSTNTKKFEDSFKDKIEDIIKERNLNIKIIAEHKADAKYPVVSAASIIAKAERDEIIDYYKKIYGDIGSGYPSDPKTIKFLEDYFKKHKKLPDIARTHWKTCKRILDKSKQT 225
                            |       10       |20        30        40        50        60        70     |  80        90       100       110       120       130       140       150       160       170       180       190       200       210       220     
                            1-MSE           18-MSE                                                    76-MSE

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(

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Folds(

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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: Class II ribonuclease H (RNase HII) (7)

Methanococcus jannaschii [TaxId: 2190] (1)

1a	d1ekea_	A:
1b	d1ekeb_	B:

Asymmetric/Biological 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)

Methanocaldococcus jannaschii. Organism_taxid: 2190. (1)

1a	1ekeA01	A:2-175
1b	1ekeB01	B:2-175

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: Ribonuclease hii. Domain 2 (8)

Methanocaldococcus jannaschii. Organism_taxid: 2190. (1)

2a	1ekeB02	B:176-222
2b	1ekeA02	A:176-225

(no "Pfam Domain" information available for 1EKE)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (RNH2_METJA | Q57599)

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:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) 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: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.
	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.
	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.

Asymmetric/Biological Unit
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Description

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Ligands, Modified Residues, Ions (2, 8)

Sites (2, 2)

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Cis Peptide Bonds (0, 0)

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