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(-) Description

Title :  CRYSTAL STRUCTURE OF RIBONUCLEASE III (TM1102) FROM THERMOTOGA MARITIMA AT 2.0 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  13 Sep 02  (Deposition) - 13 Nov 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tm1102, Ribonuclease Iii, Structural Genomics, Jcsg, Psi, Protein Structure Initiative, Joint Center For Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Ribonuclease Iii (Tm1102) From Thermotoga Maritima At 2. 0 A Resolution
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBONUCLEASE III
    Chains: A, B
    EC Number: 3.1.26.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TM1102
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: RNASE III

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1O0W)

(-) Sites  (0, 0)

(no "Site" information available for 1O0W)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1O0W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1O0W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1O0W)

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RNASE_3_2PS50142 Ribonuclease III family domain profile.RNC_THEMA9-141
 		  2A:9-141
B:9-141
2RNASE_3_1PS00517 Ribonuclease III family signature.RNC_THEMA51-59
 		  2A:51-59
B:51-59
3DS_RBDPS50137 Double stranded RNA-binding domain (dsRBD) profile.RNC_THEMA168-237
 		  2A:168-236
B:168-237

(-) Exons   (0, 0)

(no "Exon" information available for 1O0W)

(-) 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:238
 aligned with RNC_THEMA | Q9X0I6 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:238
                              1                                                                                                                                                                                                                                           
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228        
            RNC_THEMA     - --MNESERKIVEEFQKETGINFKNEELLFRALCHSSYANEQNQAGRKDVESNEKLEFLGDAVLELFVCEILYKKYPEAEVGDLARVKSAAASEEVLAMVSRKMNLGKFLFLGKGEEKTGGRDRDSILADAFEALLAAIYLDQGYEKIKELFEQEFEFYIEKIMKGEMLFDYKTALQEIVQSEHKVPPEYILVRTEKNDGDRIFVVEVRVNGKTIATGKGRTKKEAEKEAARIAYEKLL 236
               SCOP domains d1o0wa1 A:-1-167 RNase III endonuclease catalytic domain                                                                                                                 d1o0wa2 A:168-236 RNase III, C-terminal domain                        SCOP domains
               CATH domains --------1o0wA01 A:7-160  [code=1.10.1520.10, no name defined]                                                                                                     -------1o0wA02 A:168-235  [code=3.30.160.20, no name defined]              - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...eeeeeeee......eeeeeeee..eeeeeeee.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------RNASE_3_2  PDB: A:9-141 UniProt: 9-141                                                                                               --------------------------DS_RBD  PDB: A:168-236 UniProt: 168-237                               PROSITE (1)
                PROSITE (2) ----------------------------------------------------RNASE_3_1--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o0w A  -1 HHMNESERKIVEEFQKETGINFKNEELLFRALCHSSYANEQNQAGRKDVESNEKLEFLGDAVLELFVCEILYKKYPEAEVGDLARVKSAAASEEVLAMVSRKMNLGKFLFLGKGEEKTGGRDRDSILADAFEALLAAIYLDQGYEKIKELFEQEFEFYIEKIMKGEMLFDYKTALQEIVQSEHKVPPEYILVRTEKNDGDRIFVVEVRVNGKTIATGKGRTKKEAEKEAARIAYEKLL 236
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228        


Chain B from PDB  Type:PROTEIN  Length:239
 aligned with RNC_THEMA | Q9X0I6 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:239
                              1                                                                                                                                                                                                                                            
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228         
            RNC_THEMA     - --MNESERKIVEEFQKETGINFKNEELLFRALCHSSYANEQNQAGRKDVESNEKLEFLGDAVLELFVCEILYKKYPEAEVGDLARVKSAAASEEVLAMVSRKMNLGKFLFLGKGEEKTGGRDRDSILADAFEALLAAIYLDQGYEKIKELFEQEFEFYIEKIMKGEMLFDYKTALQEIVQSEHKVPPEYILVRTEKNDGDRIFVVEVRVNGKTIATGKGRTKKEAEKEAARIAYEKLLK 237
               SCOP domains d1o0wb1 B:-1-167 RNase III endonuclease catalytic domain                                                                                                                 d1o0wb2 B:168-237 RNase III, C-terminal domain                         SCOP domains
               CATH domains --------1o0wB01 B:7-160  [code=1.10.1520.10, no name defined]                                                                                                     -------1o0wB02 B:168-235  [code=3.30.160.20, no name defined]              -- CATH domains
           Pfam domains (1) ----------------------------------------------------Ribonuclease_3-1o0wB03 B:51-141                                                            ---------------------------dsrm-1o0wB01 B:169-235                                             -- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------Ribonuclease_3-1o0wB04 B:51-141                                                            ---------------------------dsrm-1o0wB02 B:169-235                                             -- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...eeeeeeeee....eeeeeeeee..eeeeeeee.hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------RNASE_3_2  PDB: B:9-141 UniProt: 9-141                                                                                               --------------------------DS_RBD  PDB: B:168-237 UniProt: 168-237                                PROSITE (1)
                PROSITE (2) ----------------------------------------------------RNASE_3_1---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o0w B  -1 HHMNESERKIVEEFQKETGINFKNEELLFRALCHSSYANEQNQAGRKDVESNEKLEFLGDAVLELFVCEILYKKYPEAEVGDLARVKSAAASEEVLAMVSRKMNLGKFLFLGKGEEKTGGRDRDSILADAFEALLAAIYLDQGYEKIKELFEQEFEFYIEKIMKGEMLFDYKTALQEIVQSEHKVPPEYILVRTEKNDGDRIFVVEVRVNGKTIATGKGRTKKEAEKEAARIAYEKLLK 237
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: DSRM (45)
(-)
Family: dsrm (27)
(-)
Thermotoga maritima (1)
1adsrm-1o0wB01B:169-235
1bdsrm-1o0wB02B:169-235
(-)
Clan: no clan defined [family: Ribonuclease_3] (11)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RNC_THEMA | Q9X0I6)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003725    double-stranded RNA binding    Interacting selectively and non-covalently with double-stranded RNA.
    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:0019843    rRNA binding    Interacting selectively and non-covalently with ribosomal RNA.
    GO:0004525    ribonuclease III activity    Catalysis of the endonucleolytic cleavage of RNA with 5'-phosphomonoesters and 3'-OH termini; makes two staggered cuts in both strands of dsRNA, leaving a 3' overhang of 2 nt.
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:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0016075    rRNA catabolic process    The chemical reactions and pathways resulting in the breakdown of rRNA, ribosomal RNA, a structural constituent of ribosomes.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
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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