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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RIBONUCLEASE H1 FROM CHLOROBIUM TEPIDUM
 
Authors :  K. Ratcliff, J. Corn, S. Marqusee
Date :  08 Apr 09  (Deposition) - 12 May 09  (Release) - 07 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Rnase H, 3D-Structure, Endonuclease, Hydrolase, Magnesium, Metal-Binding, Nuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Ratcliff, J. Corn, S. Marqusee
Structure, Stability, And Folding Of Ribonuclease H1 From The Moderately Thermophilic Chlorobium Tepidum: Comparison With Thermophilic And Mesophilic Homologues.
Biochemistry V. 48 5890 2009
PubMed-ID: 19408959  |  Reference-DOI: 10.1021/BI900305P
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNH (RIBONUCLEASE H)
    Chains: A, B
    EC Number: 3.1.26.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CT1612, RNH, RNHA
    Mutation: YES
    Organism Scientific: CHLOROBACULUM TEPIDUM
    Organism Taxid: 1097

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:10 , GLY A:11 , GLU A:48 , SER A:69 , HOH A:147 , HOH A:173 , HOH A:212BINDING SITE FOR RESIDUE MG A 501
2AC2SOFTWAREASP B:10 , GLY B:11 , GLU B:48 , ASP B:70 , HOH B:147 , HOH B:181 , HOH B:196BINDING SITE FOR RESIDUE MG B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H08)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:16 -Pro A:17
2Asn B:16 -Pro B:17

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3H08)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3H08)

(-) Exons   (0, 0)

(no "Exon" information available for 3H08)

(-) 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:139
 aligned with Q93SU7_CHLTP | Q93SU7 from UniProtKB/TrEMBL  Length:146

    Alignment length:144
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141    
         Q93SU7_CHLTP     2 EKTITIYTDGACSGNPGKGGWGALLMYGSSRKEISGYDPATTNNRMELMAAIKGLEALKEPCRVQLYSDSAYLVNAMNEGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTTLHRVTFHKVKGHSDNPYNSRCDELARLAIKEN 145
               SCOP domains d3h08a_ A: automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeee....eeeeeeeeeee..eeeeeeeeeeeehhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhh...----....hhhhhhhhhhhhhhheeeeee...-..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3h08 A   2 EKTITIYTDGAASGNPGKGGWGALLMYGSSRKEISGYDPATTNNRMELMAAIKGLEALKEPARVQLYSDSAYLVNAMNEGWLKRWVKNGWK----KPVENIDLWQEILKLTTLHRVTFHKVKG-SDNPYNSRADELARLAIKEN 145
                                    11        21        31        41        51        61        71        81        91|    | 101       111       121  | |  131       141    
                                                                                                                     92   97                        124 |                   
                                                                                                                                                      126                   


Chain B from PDB  Type:PROTEIN  Length:142
 aligned with Q93SU7_CHLTP | Q93SU7 from UniProtKB/TrEMBL  Length:146

    Alignment length:144
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141    
         Q93SU7_CHLTP     2 EKTITIYTDGACSGNPGKGGWGALLMYGSSRKEISGYDPATTNNRMELMAAIKGLEALKEPCRVQLYSDSAYLVNAMNEGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTTLHRVTFHKVKGHSDNPYNSRCDELARLAIKEN 145
               SCOP domains d3h08b_ B: automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeee....eeeeeeeeeee..eeeeeeeeeeeehhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhh....-......hhhhhhhhhhhhhhheeeeee...-..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3h08 B   2 EKTITIYTDGAASGNPGKGGWGALLMYGSSRKEISGYDPATTNNRMELMAAIKGLEALKEPARVQLYSDSAYLVNAMNEGWLKRWVKNGWKT-AKKPVENIDLWQEILKLTTLHRVTFHKVKG-SDNPYNSRADELARLAIKEN 145
                                    11        21        31        41        51        61        71        81        91 | |   101       111       121  | |  131       141    
                                                                                                                      93 |                          124 |                   
                                                                                                                        95                            126
   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 3H08)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H08)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q93SU7_CHLTP | Q93SU7)
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: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.

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  3h08
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