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(-) Description

Title :  CRYSTAL STRUCTURE OF RNASE HI FROM SULFOLOBUS TOKODAII WITH C-TERMINAL DELETION
 
Authors :  C. Angkawidjaja, K. Takano, S. Kanaya
Date :  10 Aug 10  (Deposition) - 22 Jun 11  (Release) - 22 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.66
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Thermostable Rnase Hi, C-Terminal Anchor Deletion, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Takano, T. Okamoto, J. Okada, S. Tanaka, C. Angkawidjaja, Y. Koga, S. Kanaya
Stabilization By Fusion To The C-Terminus Of Hyperthermophile Sulfolobus Tokodaii Rnase Hi: A Possibilit Of Protein Stabilization Tag
Plos One V. 6 E1622 2011
PubMed-ID: 21283826  |  Reference-DOI: 10.1371/JOURNAL.PONE.0016226

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN ST0753
    Chains: A, B
    EC Number: 3.1.26.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET25B+
    Expression System Strain: MIC2067(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-143
    Gene: ST0753
    Organism Scientific: SULFOLOBUS TOKODAII
    Organism Taxid: 273063
    Strain: STR. 7
    Synonym: RIBONUCLEASE HI, RNASE HI

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3ALY)

(-) Sites  (0, 0)

(no "Site" information available for 3ALY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu A:11 -Pro A:12
2Asn A:14 -Pro A:15
3Glu B:11 -Pro B:12
4Asn B:14 -Pro B:15

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RNASE_HPS50879 RNase H domain profile.RNH_SULTO1-140
 		  2A:1-140
B:1-140
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RNASE_HPS50879 RNase H domain profile.RNH_SULTO1-140
 		  1A:1-140
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RNASE_HPS50879 RNase H domain profile.RNH_SULTO1-140
 		  1-
B:1-140
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RNASE_HPS50879 RNase H domain profile.RNH_SULTO1-140
 		  2A:1-140
B:1-140

(-) Exons   (0, 0)

(no "Exon" information available for 3ALY)

(-) 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:141
 aligned with RNH_SULTO | F9VN79 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 
            RNH_SULTO     1 MIIGYFDGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRLGISSPIIKGDSQLVIKQMNGEYKVKAKRIIPLYEKAIELKKKLNATLIWVPREENKEADRLSRVAYELVRRGKLR 141
               SCOP domains d3alya_ A: automated matches                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee......eeeeeeeee...eeeeeeee.........hhhhhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhh.........hhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RNASE_H  PDB: A:1-140 UniProt: 1-140                                                                                                        - PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3aly A   1 MIIGYFDGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRLGISSPIIKGDSQLVIKQMNGEYKVKAKRIIPLYEKAIELKKKLNATLIWVPREENKEADRLSRVAYELVRRGKLR 141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 


Chain B from PDB  Type:PROTEIN  Length:141
 aligned with RNH_SULTO | F9VN79 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 
            RNH_SULTO     1 MIIGYFDGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRLGISSPIIKGDSQLVIKQMNGEYKVKAKRIIPLYEKAIELKKKLNATLIWVPREENKEADRLSRVAYELVRRGKLR 141
               SCOP domains d3alyb_ B: automated matches                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee......eeeeeeeee...eeeeeeee.........hhhhhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhh.........hhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RNASE_H  PDB: B:1-140 UniProt: 1-140                                                                                                        - PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3aly B   1 MIIGYFDGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRLGISSPIIKGDSQLVIKQMNGEYKVKAKRIIPLYEKAIELKKKLNATLIWVPREENKEADRLSRVAYELVRRGKLR 141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
   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, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RNH_SULTO | F9VN79)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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: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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    Asn A:14 - Pro A:15   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        RNH_SULTO | F9VN79: 2ehg

(-) Related Entries Specified in the PDB File

2ehg THE SAME PROTEIN WITH RESIDUE NO. 144-149 DELETED