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(-) Description

Title :  CRYSTAL STRUCTURE OF Q54A MUTANT PROTEIN OF BST-RNASE HIII
 
Authors :  C. Angkawidjaja, S. Kanaya
Date :  16 Dec 10  (Deposition) - 08 Jun 11  (Release) - 23 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Rnase, Dna/Rna Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Miyashita, T. Tadokoro, C. Angkawidjaja, D. -J. You, Y. Koga, K. Takano, S. Kanaya
Identification Of The Substrate Binding Site In The N-Terminal Tbp-Like Domain Of Rnase H3.
Febs Lett. V. 585 2313 2011
PubMed-ID: 21664908  |  Reference-DOI: 10.1016/J.FEBSLET.2011.05.064

(-) Compounds

Molecule 1 - RIBONUCLEASE HIII
    Chains: A
    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
    Mutation: YES
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
    Synonym: RNASE HIII

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 3ASM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:192 -Pro A:193

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ASM)

(-) Sequences/Alignments

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:308
 aligned with Q6L6Q4_GEOSE | Q6L6Q4 from UniProtKB/TrEMBL  Length:310

    Alignment length:308
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301        
         Q6L6Q4_GEOSE     2 SNYVIQADQQLLDALRAHYEGALSDRLPAGALFAVKRPDVVITAYRSGKVLFQGKAAEQEAAKWISGASASNETADHQPSALAAHQLGSLSAIGSDEVGTGDYFGPIVVAAAYVDRPHIAKIAALGVKDSKQLNDEAIKRIAPAIMETVPHAVTVLDNPQYNRWQRSGMPQTKMKALLHNRTLVKLVDAIAPAEPEAIIIDEFLKRDSYFRYLSDEDRIIRERVHCLPKAESVHVSVAAASIIARYVFLEEMEQLSRAVGLLLPKGAGAIVDEAAARIIRARGEEMLETCAKLHFANTKKALAIAKRR 309
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhh...........eeeeeee..eeeeee...eeeee..hhhhhhhh.....eee......hhhhhhhhhhh...eeeeeee........eeeeeeeehhhhhhhhhhh........hhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhh...........eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3asm A   2 SNYVIQADQQLLDALRAHYEGALSDRLPAGALFAVKRPDVVITAYRSGKVLFAGKAAEQEAAKWISGASASNETADHQPSALAAHQLGSLSAIGSDEVGTGDYFGPIVVAAAYVDRPHIAKIAALGVKDSKQLNDEAIKRIAPAIMETVPHAVTVLDNPQYNRWQRSGMPQTKMKALLHNRTLVKLVDAIAPAEPEAIIIDEFLKRDSYFRYLSDEDRIIRERVHCLPKAESVHVSVAAASIIARYVFLEEMEQLSRAVGLLLPKGAGAIVDEAAARIIRARGEEMLETCAKLHFANTKKALAIAKRR 309
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301
   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  (0, 0)

(no "SCOP Domain" information available for 3ASM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q6L6Q4_GEOSE | Q6L6Q4)
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.
biological process
    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: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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  Sites
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  Cis Peptide Bonds
    Ala A:192 - Pro A:193   [ RasMol ]  
 

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  3.1.26.4
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 Related Entries

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

UniProtKB/TrEMBL
        Q6L6Q4_GEOSE | Q6L6Q4: 2d0a 2d0b 2d0c

(-) Related Entries Specified in the PDB File

2d0a WILD TYPE PROTEIN