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(-) Description

Title :  A CONFORMATIONAL TRANSITION IN THE STRUCTURE OF A 2'-THIOMETHYL-MODIFIED DNA VISUALIZED AT HIGH RESOLUTION
 
Authors :  M. Egli, P. S. Pallan
Date :  17 Oct 08  (Deposition) - 28 Apr 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Rnase H-Dna Complex, Protein-Dna Complex, Endonuclease, 2'-Thiomethyl Uridine Ribonucleic Acid, Hydrolase, Magnesium, Manganese, Metal- Binding, Nuclease, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. S. Pallan, T. P. Prakash, F. Li, R. L. Eoff, M. Manoharan, M. Egli
A Conformational Transition In The Structure Of A 2'-Thiomethyl-Modified Dna Visualized At High Resolution.
Chem. Commun. (Camb. ) V. 15 2017 2009
PubMed-ID: 19333476  |  Reference-DOI: 10.1039/B822781K

(-) Compounds

Molecule 1 - RIBONUCLEASE H
    Chains: A
    EC Number: 3.1.26.4
    Engineered: YES
    Fragment: RNASE H DOMAIN, UNP RESIDUES 59-196
    Gene: RNHA, BH0863
    Mutation: YES
    Organism Scientific: BACILLUS HALODURANS
    Organism Taxid: 86665
    Synonym: RNASE H
 
Molecule 2 - 5'-D(*CP*GP*CP*GP*AP*AP*(USM)P*(USM)P*CP*GP*CP*G)-3'
    Chains: B
    Engineered: YES
    Other Details: 2'-THIOMETHYL URIDINE (USM) MODIFIED DECAMER NUCLEIC ACID 5'-DC DG DC DG DA DA USM USM DC DG DC DG-3'
    Other Details - Source: CHEMICALLY SYNTHESIZED MODIFIED DODECAMER DNA (OLIGONUCLEOTIDE)
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2USM2Mod. Nucleotide2'-S-METHYL-2'-THIOURIDINE 5'-(DIHYDROGEN PHOSPHATE)
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2USM4Mod. Nucleotide2'-S-METHYL-2'-THIOURIDINE 5'-(DIHYDROGEN PHOSPHATE)

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:76 , ASN A:77 , DC B:301 , DG B:302BINDING SITE FOR RESIDUE GOL B 601
2AC2SOFTWAREUSM B:307 , USM B:308BINDING SITE FOR RESIDUE GOL B 602
3AC3SOFTWARELYS A:138 , DA B:305 , DA B:306BINDING SITE FOR RESIDUE GOL B 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3EY1)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:77 -Pro A:78
2Tyr A:193 -Gly A:194

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EY1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3EY1)

(-) Exons   (0, 0)

(no "Exon" information available for 3EY1)

(-) Sequences/Alignments

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:137
 aligned with RNH1_BACHD | Q9KEI9 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:137
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       
           RNH1_BACHD    59 AKEEIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSDSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKADYGR 195
               SCOP domains d3ey1a_ A: BH0863-like Ribonuclease H                                                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeee.....eeeeeeeee.....eeeeeeeeeeehhhhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhh...........hhhhhhhhhhhhhhhh.......eee.hhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ey1 A  59 AKEEIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSNSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKADYGR 195
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       


Chain B from PDB  Type:DNA  Length:12
                                            
                 3ey1 B 301 CGCGAAxxCGCG 312
                                  |310  
                                307-USM 
                                 308-USM
   Legend:   → Mismatch (orange background)
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  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)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3EY1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EY1)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (RNH1_BACHD | Q9KEI9)
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: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: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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  3.1.26.4
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RNH1_BACHD | Q9KEI9: 1zbf 1zbi 1zbl 2g8f 2g8h 2g8i 2g8k 2g8u 2g8v 2g8w 2r7y 3d0p 3i8d 3twh 3uld 4htu 4hue 4huf 4hug 4opj 4opk 5swm 5us2 5usa 5use 5usg 5w7n 5w7o

(-) Related Entries Specified in the PDB File

3ey2 3ey3