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(-) Description

Title :  CRYSTAL STRUCTURE OF RIBONUCLEASE II FAMILY PROTEIN FROM DEINOCOCCUS RADIODURANS, TRICLINIC CRYSTAL FORM. NORTHEAST STRUCTURAL GENOMICS TARGET DRR63
 
Authors :  J. Seetharaman, H. Neely, F. Forouhar, D. Wang, Y. Fang, K. Cunningham, R. Xia, J. Liu, M. C. Baran, T. B. Acton, B. Rost, G. T. Montelione, J. F. H L. Tong, Northeast Structural Genomics Consortium (Nesg)
Date :  07 Sep 07  (Deposition) - 02 Oct 07  (Release) - 01 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Ribonuclease Ii Family Protein, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. J. Schmier, J. Seetharaman, M. P. Deutscher, J. F. Hunt, A. Malhotra
The Structure And Enzymatic Properties Of A Novel Rnase Ii Family Enzyme From Deinococcus Radiodurans.
J. Mol. Biol. V. 415 547 2012
PubMed-ID: 22133431  |  Reference-DOI: 10.1016/J.JMB.2011.11.031

(-) Compounds

Molecule 1 - RIBONUCLEASE II FAMILY PROTEIN
    Atcc: 13939
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DR_0020
    Organism Scientific: DEINOCOCCUS RADIODURANS R1
    Organism Taxid: 243230
    Strain: R1, DSM 20539, IFO 15346, LMG 4051

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 30)

Asymmetric Unit (2, 30)
No.NameCountTypeFull Name
1MG3Ligand/IonMAGNESIUM ION
2MSE27Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 9)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MSE9Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 9)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MSE9Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 9)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MSE9Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:93 , ASP A:102 , HOH A:1001 , HOH A:1002 , HOH A:1026 , HOH A:1453BINDING SITE FOR RESIDUE MG A 1000
2AC2SOFTWAREASP B:93 , ASP B:102 , HOH B:2001 , HOH B:2003 , HOH B:2009 , HOH B:2132BINDING SITE FOR RESIDUE MG B 2000
3AC3SOFTWAREASP C:93 , ASP C:102 , HOH C:3001 , HOH C:3002 , HOH C:3017 , HOH C:3021BINDING SITE FOR RESIDUE MG C 3000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R7D)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Glu A:214 -Pro A:215
2Glu B:214 -Pro B:215
3Glu C:214 -Pro C:215

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R7D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R7D)

(-) Exons   (0, 0)

(no "Exon" information available for 2R7D)

(-) 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:461
 aligned with Q9RYD0_DEIRA | Q9RYD0 from UniProtKB/TrEMBL  Length:461

    Alignment length:461
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    461  
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452        |- 
         Q9RYD0_DEIRA     3 QPELTPAQRTEVELLARGRADKSRVLRDLKLPETPEAAHALLLRLGVWDEARTPYADRLRAALNAVELPVPDFDPAEERLDLTHLPTFAIDDEGNQDPDDAVGVEDLGGGLTRLWVHVADVAALVAPDSPLDLEARARGATLYLPDRTIGMLPDELVAKAGLGLHEVSPALSICLDLDPDGNAEAVDVLLTRVKVQRLAYQEAQARLEAGEEPFVTLARLARASRRLREGEGALSIDLPEVRVKADETGASVFPLPKPEMRTVVQECMTLAGWGTAIFADDNEIPLPFATQDYPTREVAGDTLPAMWARRKTLARTRFQPSPGPHHGMGLDLYAQATSPMRRYLDLVVHQQLRAFLAGRDPLSSKVMAAHIAESQMNADATRQAERLSRRHHTLRFIAAQPERVWDAVVVDRRGAQATLLIPDLAFDVQVNTPAAPGTALQVQFADIDLPQMRVRARSV--   -
               SCOP domains d2r7da2 A:3-403 Ribonuclease II family protein DR0020                                                                                                                                                                                                                                                                                                                                                            d2r7da1 A:404-461 Ribonuclease II family protein DR0020   -- SCOP domains
               CATH domains 2r7dA01 A:3-71 'winged helix' repressor DNA binding domain           --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2r7dA03 A:404-463 Nucleic acid-binding proteins              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh.....hhhhhhh....hhhhhhhhhhhh........hhhhhh....................ee.....eeeee........eeeeeee.....eeeeeeee.hhhh....hhhhhhhhhhh..ee....ee...hhhhhhhhh......eeeeeeeeee.....eeeeeeeeeee.eeeeehhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.........eeeeee..eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhh.....eeee..........hhhhhhhhhhhh..eeee......................hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeee..eeeeeehhhheeeeee.......eeeeeeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r7d A   3 QPELTPAQRTEVELLARGRADKSRVLRDLKLPETPEAAHALLLRLGVWDEARTPYADRLRAALNAVELPVPDFDPAEERLDLTHLPTFAIDDEGNQDPDDAVGVEDLGGGLTRLWVHVADVAALVAPDSPLDLEARARGATLYLPDRTIGmLPDELVAKAGLGLHEVSPALSICLDLDPDGNAEAVDVLLTRVKVQRLAYQEAQARLEAGEEPFVTLARLARASRRLREGEGALSIDLPEVRVKADETGASVFPLPKPEmRTVVQECmTLAGWGTAIFADDNEIPLPFATQDYPTREVAGDTLPAmWARRKTLARTRFQPSPGPHHGmGLDLYAQATSPmRRYLDLVVHQQLRAFLAGRDPLSSKVmAAHIAESQmNADATRQAERLSRRHHTLRFIAAQPERVWDAVVVDRRGAQATLLIPDLAFDVQVNTPAAPGTALQVQFADIDLPQmRVRARSVLE 463
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152|      162       172       182       192       202       212       222       232       242       252       262       272       282       292       302     | 312       322       332       342       352       362      |372     | 382       392       402       412       422       432       442       452 |     462 
                                                                                                                                                                                153-MSE                                                                                                      262-MSE 270-MSE                               308-MSE               330-MSE     342-MSE                    369-MSE  378-MSE                                                                     454-MSE     


Chain B from PDB  Type:PROTEIN  Length:459
 aligned with Q9RYD0_DEIRA | Q9RYD0 from UniProtKB/TrEMBL  Length:461

    Alignment length:459
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452         
         Q9RYD0_DEIRA     3 QPELTPAQRTEVELLARGRADKSRVLRDLKLPETPEAAHALLLRLGVWDEARTPYADRLRAALNAVELPVPDFDPAEERLDLTHLPTFAIDDEGNQDPDDAVGVEDLGGGLTRLWVHVADVAALVAPDSPLDLEARARGATLYLPDRTIGMLPDELVAKAGLGLHEVSPALSICLDLDPDGNAEAVDVLLTRVKVQRLAYQEAQARLEAGEEPFVTLARLARASRRLREGEGALSIDLPEVRVKADETGASVFPLPKPEMRTVVQECMTLAGWGTAIFADDNEIPLPFATQDYPTREVAGDTLPAMWARRKTLARTRFQPSPGPHHGMGLDLYAQATSPMRRYLDLVVHQQLRAFLAGRDPLSSKVMAAHIAESQMNADATRQAERLSRRHHTLRFIAAQPERVWDAVVVDRRGAQATLLIPDLAFDVQVNTPAAPGTALQVQFADIDLPQMRVRARSV 461
               SCOP domains d2r7db2 B:3-403 Ribonuclease II family protein DR0020                                                                                                                                                                                                                                                                                                                                                            d2r7db1 B:404-461 Ribonuclease II family protein DR0020    SCOP domains
               CATH domains 2r7dB01 B:3-71 'winged helix' repressor DNA binding domain           --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2r7dB03 B:404-461 Nucleic acid-binding proteins            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh.....hhhhhhh....hhhhhhhhhhhh........hhhhhh....................ee.....eeeee........eeeeeeeee..eeeeeeeee.hhhh....hhhhhhhhhhh..ee....ee...hhhhhhhhh......eeeeeeeeee.....eeeeeeeeeee.eeeeehhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.........eeeeee..eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhh.....eee...........hhhhhhhhhh.....eee......................hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee...eeeeeehhhheeeeee........eeeeeeeee....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r7d B   3 QPELTPAQRTEVELLARGRADKSRVLRDLKLPETPEAAHALLLRLGVWDEARTPYADRLRAALNAVELPVPDFDPAEERLDLTHLPTFAIDDEGNQDPDDAVGVEDLGGGLTRLWVHVADVAALVAPDSPLDLEARARGATLYLPDRTIGmLPDELVAKAGLGLHEVSPALSICLDLDPDGNAEAVDVLLTRVKVQRLAYQEAQARLEAGEEPFVTLARLARASRRLREGEGALSIDLPEVRVKADETGASVFPLPKPEmRTVVQECmTLAGWGTAIFADDNEIPLPFATQDYPTREVAGDTLPAmWARRKTLARTRFQPSPGPHHGmGLDLYAQATSPmRRYLDLVVHQQLRAFLAGRDPLSSKVmAAHIAESQmNADATRQAERLSRRHHTLRFIAAQPERVWDAVVVDRRGAQATLLIPDLAFDVQVNTPAAPGTALQVQFADIDLPQmRVRARSV 461
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152|      162       172       182       192       202       212       222       232       242       252       262       272       282       292       302     | 312       322       332       342       352       362      |372     | 382       392       402       412       422       432       442       452 |       
                                                                                                                                                                                153-MSE                                                                                                      262-MSE 270-MSE                               308-MSE               330-MSE     342-MSE                    369-MSE  378-MSE                                                                     454-MSE   


Chain C from PDB  Type:PROTEIN  Length:459
 aligned with Q9RYD0_DEIRA | Q9RYD0 from UniProtKB/TrEMBL  Length:461

    Alignment length:459
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452         
         Q9RYD0_DEIRA     3 QPELTPAQRTEVELLARGRADKSRVLRDLKLPETPEAAHALLLRLGVWDEARTPYADRLRAALNAVELPVPDFDPAEERLDLTHLPTFAIDDEGNQDPDDAVGVEDLGGGLTRLWVHVADVAALVAPDSPLDLEARARGATLYLPDRTIGMLPDELVAKAGLGLHEVSPALSICLDLDPDGNAEAVDVLLTRVKVQRLAYQEAQARLEAGEEPFVTLARLARASRRLREGEGALSIDLPEVRVKADETGASVFPLPKPEMRTVVQECMTLAGWGTAIFADDNEIPLPFATQDYPTREVAGDTLPAMWARRKTLARTRFQPSPGPHHGMGLDLYAQATSPMRRYLDLVVHQQLRAFLAGRDPLSSKVMAAHIAESQMNADATRQAERLSRRHHTLRFIAAQPERVWDAVVVDRRGAQATLLIPDLAFDVQVNTPAAPGTALQVQFADIDLPQMRVRARSV 461
               SCOP domains d2r7dc2 C:3-403 Ribonuclease II family protein DR0020                                                                                                                                                                                                                                                                                                                                                            d2r7dc1 C:404-461 Ribonuclease II family protein DR0020    SCOP domains
               CATH domains 2r7dC01 C:3-71 'winged helix' repressor DNA binding domain           --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2r7dC03 C:404-461 Nucleic acid-binding proteins            CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------RNB-2r7dC01 C:81-360                                                                                                                                                                                                                                                                    ----------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------RNB-2r7dC02 C:81-360                                                                                                                                                                                                                                                                    ----------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------RNB-2r7dC03 C:81-360                                                                                                                                                                                                                                                                    ----------------------------------------------------------------------------------------------------- Pfam domains (3)
         Sec.struct. author ....hhhhhhhhhhhhh.....hhhhhhhh...hhhhhhhhhhhh........hhhhhh....................ee.....eeeee........eeeeeeeee..eeeeeeeee.hhhh....hhhhhhhhhhh..ee....ee...hhhhhhhhh......eeeeeeeeee.....eeeeeeeeeee.eeeeehhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.........eeeeee..eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhh.....eeee..........hhhhhhhhhhhh..eeee......................hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeee..eeeeeehhhheeeeee.......eeeeeeeeee....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r7d C   3 QPELTPAQRTEVELLARGRADKSRVLRDLKLPETPEAAHALLLRLGVWDEARTPYADRLRAALNAVELPVPDFDPAEERLDLTHLPTFAIDDEGNQDPDDAVGVEDLGGGLTRLWVHVADVAALVAPDSPLDLEARARGATLYLPDRTIGmLPDELVAKAGLGLHEVSPALSICLDLDPDGNAEAVDVLLTRVKVQRLAYQEAQARLEAGEEPFVTLARLARASRRLREGEGALSIDLPEVRVKADETGASVFPLPKPEmRTVVQECmTLAGWGTAIFADDNEIPLPFATQDYPTREVAGDTLPAmWARRKTLARTRFQPSPGPHHGmGLDLYAQATSPmRRYLDLVVHQQLRAFLAGRDPLSSKVmAAHIAESQmNADATRQAERLSRRHHTLRFIAAQPERVWDAVVVDRRGAQATLLIPDLAFDVQVNTPAAPGTALQVQFADIDLPQmRVRARSV 461
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152|      162       172       182       192       202       212       222       232       242       252       262       272       282       292       302     | 312       322       332       342       352       362      |372     | 382       392       402       412       422       432       442       452 |       
                                                                                                                                                                                153-MSE                                                                                                      262-MSE 270-MSE                               308-MSE               330-MSE     342-MSE                    369-MSE  378-MSE                                                                     454-MSE
   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, 6)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 6)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: RNB] (4)
(-)
Family: RNB (4)
(-)
Deinococcus radiodurans (2)
1aRNB-2r7dC01C:81-360
1bRNB-2r7dC02C:81-360
1cRNB-2r7dC03C:81-360

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q9RYD0_DEIRA | Q9RYD0)
molecular function
    GO:0000175    3'-5'-exoribonuclease activity    Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule.
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:0090503    RNA phosphodiester bond hydrolysis, exonucleolytic    The chemical reactions and pathways involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
cellular component
    GO:0000178    exosome (RNase complex)    A ribonuclease complex that has 3-prime to 5-prime exoribonuclease activity and possibly endoribonuclease activity, producing 5-prime-phosphomonoesters. Participates in a multitude of cellular RNA processing and degradation events preventing nuclear export and/or translation of aberrant RNAs. Restricted to processing linear and circular single-stranded RNAs (ssRNA) only. RNAs with complex secondary structures may have to be unwound or pre-processed by co-factors prior to entering the complex, esp if the 3-prime end is structured.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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  2r7d
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 Related Entries

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

UniProtKB/TrEMBL
        Q9RYD0_DEIRA | Q9RYD0: 2r7f

(-) Related Entries Specified in the PDB File

2r7f CRYSTAL STRUCTURE OF RIBONUCLEASE II FAMILY PROTEIN FROM DEINOCOCCUS RADIODURANS, HEXAGONAL CRYSTAL FORM.