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(-) Description

Title :  CRYSTAL STRUCTURE OF ESCHERICHIA COLI RNASE D, AN EXORIBONUCLEASE INVOLVED IN STRUCTURED RNA PROCESSING
 
Authors :  Y. Zuo, Y. Wang, A. Malhotra
Date :  09 Feb 05  (Deposition) - 09 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Rnase; Exoribonuclease; Ribonuclease; Exonuclease; Nuclease; Hydrolase; Trna Processing, Hydrolase, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zuo, Y. Wang, A. Malhotra
Crystal Structure Of Escherichia Coli Rnase D, An Exoribonuclease Involved In Structured Rna Processing
Structure V. 13 973 2005
PubMed-ID: 16004870  |  Reference-DOI: 10.1016/J.STR.2005.04.015
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBONUCLEASE D
    Chains: A
    EC Number: 3.1.26.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: ROSETTA(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RND
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: RNASE D

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1SO47Ligand/IonSULFATE ION
2ZN5Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:301 , GLY A:302 , TYR A:303 , ARG A:304 , LYS A:305 , HOH A:1076 , HOH A:1078 , HOH A:1487BINDING SITE FOR RESIDUE SO4 A 601
02AC2SOFTWARELYS A:227 , ARG A:231 , HIS A:271 , ARG A:331 , HOH A:1010 , HOH A:1117 , HOH A:1118 , HOH A:1472BINDING SITE FOR RESIDUE SO4 A 602
03AC3SOFTWAREGLN A:336 , LYS A:345 , GLN A:347 , HOH A:1055 , HOH A:1112 , HOH A:1114BINDING SITE FOR RESIDUE SO4 A 603
04AC4SOFTWARELYS A:273 , SER A:330 , ARG A:331 , HOH A:1009 , HOH A:1109 , HOH A:1486BINDING SITE FOR RESIDUE SO4 A 604
05AC5SOFTWARESER A:266 , ARG A:269 , LYS A:308 , HOH A:1329BINDING SITE FOR RESIDUE SO4 A 605
06AC6SOFTWAREARG A:240 , SER A:264 , SER A:266 , HOH A:1329 , HOH A:1333BINDING SITE FOR RESIDUE SO4 A 606
07AC7SOFTWAREARG A:189 , SER A:330 , ARG A:332 , HOH A:1109 , HOH A:1110 , HOH A:1199BINDING SITE FOR RESIDUE SO4 A 607
08AC8SOFTWAREASP A:28 , GLU A:30 , TYR A:151 , ASP A:155 , HOH A:1184 , HOH A:1185BINDING SITE FOR RESIDUE ZN A 1001
09AC9SOFTWAREASP A:28 , ASP A:85 , HOH A:1180 , HOH A:1181 , HOH A:1188BINDING SITE FOR RESIDUE ZN A 1002
10BC1SOFTWAREHOH A:1410 , HOH A:1412BINDING SITE FOR RESIDUE ZN A 1003
11BC2SOFTWAREARG A:331 , HOH A:1011 , HOH A:1012 , HOH A:1013 , HOH A:1488BINDING SITE FOR RESIDUE ZN A 1004
12BC3SOFTWAREGLU A:17 , HOH A:1416BINDING SITE FOR RESIDUE ZN A 1005

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YT3)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gln A:98 -Pro A:99
2Arg A:142 -Pro A:143

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YT3)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HRDCPS50967 HRDC domain profile.RND_ECOLI210-289  1A:210-289

(-) Exons   (0, 0)

(no "Exon" information available for 1YT3)

(-) 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:375
 aligned with RND_ECOLI | P09155 from UniProtKB/Swiss-Prot  Length:375

    Alignment length:375
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370     
            RND_ECOLI     1 MNYQMITTDDALASLCEAVRAFPAIALDTEFVRTRTYYPQLGLIQLFDGEHLALIDPLGITDWSPLKAILRDPSITKFLHAGSEDLEVFLNVFGELPQPLIDTQILAAFCGRPMSWGFASMVEEYSGVTLDKSESRTDWLARPLTERQCEYAAADVWYLLPITAKLMVETEASGWLPAALDECRLMQMRRQEVVAPEDAWRDITNAWQLRTRQLACLQLLADWRLRKARERDLAVNFVVREEHLWSVARYMPGSLGELDSLGLSGSEIRFHGKTLLALVEKAQTLPEDALPQPMLNLMDMPGYRKAFKAIKSLITDVSETHKISAELLASRRQINQLLNWHWKLKPQNNLPELISGWRGELMAEALHNLLQEYPQ 375
               SCOP domains d1yt3a3 A:1-193 Ribonuclease D, catalytic domain                                                                                                                                                 d1yt3a1 A:194-294 Ribonuclease D                                                                     d1yt3a2 A:295-375 Ribonuclease D                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --DNA_pol_A_exo1-1yt3A02 A:3-171                                                                                                                                           -----------------------------------------HRDC-1yt3A01 A:213-279                                             ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee.hhhhhhhhhhhhh...eeeeeeeee.......eeeeeeee....eeee.hhhh..hhhhhhhhhh...eeee..hhhhhhhhhhhhh.....eeehhhhhhhh......hhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HRDC  PDB: A:210-289 UniProt: 210-289                                           -------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yt3 A   1 MNYQMITTDDALASLCEAVRAFPAIALDTEFVRTRTYYPQLGLIQLFDGEHLALIDPLGITDWSPLKAILRDPSITKFLHAGSEDLEVFLNVFGELPQPLIDTQILAAFCGRPMSWGFASMVEEYSGVTLDKSESRTDWLARPLTERQCEYAAADVWYLLPITAKLMVETEASGWLPAALDECRLMQMRRQEVVAPEDAWRDITNAWQLRTRQLACLQLLADWRLRKARERDLAVNFVVREEHLWSVARYMPGSLGELDSLGLSGSEIRFHGKTLLALVEKAQTLPEDALPQPMLNLMDMPGYRKAFKAIKSLITDVSETHKISAELLASRRQINQLLNWHWKLKPQNNLPELISGWRGELMAEALHNLLQEYPQ 375
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370
   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, 3)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YT3)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: HRDC-like (19)
(-)
Clan: RNase_H (288)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RND_ECOLI | P09155)
molecular function
    GO:0008408    3'-5' exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004527    exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
    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: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.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0033890    ribonuclease D activity    Catalysis of the exonucleolytic cleavage that removes extra residues from the 3'-terminus of tRNA to produce 5'-mononucleotides.
    GO:0004540    ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    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:0044237    cellular metabolic process    The chemical reactions and pathways by which individual cells transform chemical substances.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
    GO:0042780    tRNA 3'-end processing    The process in which the 3' end of a pre-tRNA molecule is converted to that of a mature tRNA.
    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.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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