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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI RNASE E APOPROTEIN - CATALYTIC DOMAIN
 
Authors :  D. J. Koslover, A. J. Callaghan, M. J. Marcaida, M. Martick, W. G. Scott, B. F. Luisi
Date :  28 Jan 08  (Deposition) - 22 Jul 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Nuclease, Hydrolase, Cytoplasm, Rna-Binding, Rna Turnover, Endonuclease, Rna Processing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. J. Koslover, A. J. Callaghan, M. J. Marcaida, E. F. Garman, M. Martick, W. G. Scott, B. F. Luisi
The Crystal Structure Of The Escherichia Coli Rnase E Apoprotein And A Mechanism For Rna Degradation.
Structure V. 16 1238 2008
PubMed-ID: 18682225  |  Reference-DOI: 10.1016/J.STR.2008.04.017

(-) Compounds

Molecule 1 - RIBONUCLEASE E
    Chains: A, B, C, D
    EC Number: 3.1.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET16B VARIANT
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: CATALYTIC DOMAIN, RESIDUES 1-515
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: RNASE E

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
2ZN2Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:404 , CYS A:407 , CYS B:404 , CYS B:407BINDING SITE FOR RESIDUE ZN B1514
2AC2SOFTWARECYS C:404 , CYS C:407 , CYS D:404 , CYS D:407BINDING SITE FOR RESIDUE ZN D1516
3AC3SOFTWARESER A:140 , ARG A:169 , THR A:170BINDING SITE FOR RESIDUE SO4 A1509
4AC4SOFTWARETHR B:170BINDING SITE FOR RESIDUE SO4 B1515
5AC5SOFTWAREARG C:169 , THR C:170 , ALA C:171BINDING SITE FOR RESIDUE SO4 C1507

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VMK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1S1PS50126 S1 domain profile.RNE_ECOLI39-119
 
 
 		  4A:39-119
B:39-119
C:39-119
D:39-119

(-) Exons   (0, 0)

(no "Exon" information available for 2VMK)

(-) 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:489
 aligned with RNE_ECOLI | P21513 from UniProtKB/Swiss-Prot  Length:1061

    Alignment length:508
                                    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       380       390       400       410       420       430       440       450       460       470       480       490       500        
            RNE_ECOLI     1 MKRMLINATQQEELRVALVDGQRLYDLDIESPGHEQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTTFISLAGSYLVLMPNNPRAGGISRRIEGDDRTELKEALASLELPEGMGLIVRTAGVGKSAEALQWDLSFRLKHWEAIKKAAESRPAPFLIHQESNVIVRAFRDYLRQDIGEILIDNPKVLELARQHIAALGRPDFSSKIKLYTGEIPLFSHYQIESQIESAFQREVRLPSGGSIVIDSTEALTAIDINSARATRGGDIEETAFNTNLEAADEIARQLRLRDLGGLIVIDFIDMTPVRHQRAVENRLREAVRQDRARIQISHISRFGLLEMSRQRLSPSLGESSHHVCPRCSGTGTVRDNESLSLSILRLIEEEALKENTQEVHAIVPVPIASYLLNEKRSAVNAIETRQDGVRCVIVPNDQMETPHYHVLRVRKGEETPTLSYMLPKLHEE 508
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......eeeeeee..eeeeeeee.---......eeeeeeeeeehhh.eeeee......eeee.hhhhhhhh.-------..hhhhh.....eeeeeeee........eee....ee...eeee.......ee....----hhhhhhhhh........eeee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhh......eee...hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhhh..eee.....hhhhhh.hhhhhhhhhh.eee.....eeeeee....eeeeee...-----hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeee....eeeeee...........eee........eeehhhhhhhhhhhhhhhhhh...eeeeeeeeehhhhhhhhhhhhhhhhhhhhhh...eeeeeee........eeeeee.......hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------S1  PDB: A:39-119 UniProt: 39-119                                                ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vmk A   1 MKRMLINATQQEELRVALVDGQRLYDLDIES---EQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFP-------RPNIKDVLREGQEVIVQIDKEERGNKGAALTTFISLAGSYLVLMPNNPRAGGISRRI----RTELKEALASLELPEGMGLIVRTAGVGKSAEALQWDLSFRLKHWEAIKKAAESRPAPFLIHQESNVIVRAFRDYLRQDIGEILIDNPKVLELARQHIAALGRPDFSSKIKLYTGEIPLFSHYQIESQIESAFQREVRLPSGGSIVIDSTEALTAIDINSAR-----DIEETAFNTNLEAADEIARQLRLRDLGGLIVIDFIDMTPVRHQRAVENRLREAVRQDRARIQISHISRFGLLEMSRQRLSPSLGESSHHVCPRCSGTGTVRDNESLSLSILRLIEEEALKENTQEVHAIVPVPIASYLLNEKRSAVNAIETRQDGVRCVIVPNDQMETPHYHVLRVRKGEETPTLSYMLPKLHEE 508
                                    10        20        30|   |   40        50        60        70        |-      | 90       100       110       120       130       140  |    150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       | -   |   320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500        
                                                         31  35                                          79      87                                                     143  148                                                                                                                                                             308   314                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:495
 aligned with RNE_ECOLI | P21513 from UniProtKB/Swiss-Prot  Length:1061

    Alignment length:513
                                    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       380       390       400       410       420       430       440       450       460       470       480       490       500       510   
            RNE_ECOLI     1 MKRMLINATQQEELRVALVDGQRLYDLDIESPGHEQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTTFISLAGSYLVLMPNNPRAGGISRRIEGDDRTELKEALASLELPEGMGLIVRTAGVGKSAEALQWDLSFRLKHWEAIKKAAESRPAPFLIHQESNVIVRAFRDYLRQDIGEILIDNPKVLELARQHIAALGRPDFSSKIKLYTGEIPLFSHYQIESQIESAFQREVRLPSGGSIVIDSTEALTAIDINSARATRGGDIEETAFNTNLEAADEIARQLRLRDLGGLIVIDFIDMTPVRHQRAVENRLREAVRQDRARIQISHISRFGLLEMSRQRLSPSLGESSHHVCPRCSGTGTVRDNESLSLSILRLIEEEALKENTQEVHAIVPVPIASYLLNEKRSAVNAIETRQDGVRCVIVPNDQMETPHYHVLRVRKGEETPTLSYMLPKLHEEAMALP 513
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..----.eeeeee..eeeeee.----.......eeeeeeeeee....eeeee......eeee.hhhhhhhh..------..hhhhhh....eeeeeeee........eee....ee...eeee.......ee....hhhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh........eee...hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhhh..eee.....hhhhhh.hhhhhhhhhh.eee.....eeeeee....eeeeee...----.hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhh......eeeeee....eeeeee...........eee........eeehhhhhhhhhhhhhhhhhh...eeeeeeeeehhhhhhhh..hhhhhhhhhhhh...eeeeeee........eeeeee.......hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------S1  PDB: B:39-119 UniProt: 39-119                                                ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vmk B   1 MKRMLINAT----LRVALVDGQRLYDLDI----HEQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPA------RPNIKDVLREGQEVIVQIDKEERGNKGAALTTFISLAGSYLVLMPNNPRAGGISRRIEGDDRTELKEALASLELPEGMGLIVRTAGVGKSAEALQWDLSFRLKHWEAIKKAAESRPAPFLIHQESNVIVRAFRDYLRQDIGEILIDNPKVLELARQHIAALGRPDFSSKIKLYTGEIPLFSHYQIESQIESAFQREVRLPSGGSIVIDSTEALTAIDINSAR----GDIEETAFNTNLEAADEIARQLRLRDLGGLIVIDFIDMTPVRHQRAVENRLREAVRQDRARIQISHISRFGLLEMSRQRLSPSLGESSHHVCPRCSGTGTVRDNESLSLSILRLIEEEALKENTQEVHAIVPVPIASYLLNEKRSAVNAIETRQDGVRCVIVPNDQMETPHYHVLRVRKGEETPTLSYMLPKLHEEAMALP 513
                                    |-   |    20        |-   |    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       | -  |    320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510   
                                    9   14             29   34                                            80     87                                                                                                                                                                                                                          308  313                                                                                                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:474
 aligned with RNE_ECOLI | P21513 from UniProtKB/Swiss-Prot  Length:1061

    Alignment length:506
                                    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       380       390       400       410       420       430       440       450       460       470       480       490       500      
            RNE_ECOLI     1 MKRMLINATQQEELRVALVDGQRLYDLDIESPGHEQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTTFISLAGSYLVLMPNNPRAGGISRRIEGDDRTELKEALASLELPEGMGLIVRTAGVGKSAEALQWDLSFRLKHWEAIKKAAESRPAPFLIHQESNVIVRAFRDYLRQDIGEILIDNPKVLELARQHIAALGRPDFSSKIKLYTGEIPLFSHYQIESQIESAFQREVRLPSGGSIVIDSTEALTAIDINSARATRGGDIEETAFNTNLEAADEIARQLRLRDLGGLIVIDFIDMTPVRHQRAVENRLREAVRQDRARIQISHISRFGLLEMSRQRLSPSLGESSHHVCPRCSGTGTVRDNESLSLSILRLIEEEALKENTQEVHAIVPVPIASYLLNEKRSAVNAIETRQDGVRCVIVPNDQMETPHYHVLRVRKGEETPTLSYMLPKLH 506
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....--.eeeeee..eeeeeee....---....eeeeeeeeee....eeeee......eeee.hhhhhhhh--------..hhhhhh....eeeeeeee........eee....ee...eeee..........-------..hhhhhhh........eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eee....hhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh.hhhhh..eee.....hhhhhh.hhhhhhhh...eee.....eeeeee....eeeeee..-----.hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhh......eeeeee....eeeeee....-------...........eeehhhhhhhhhhhhhhhhhh...eeeeeeeeehhhhhhhh..hhhhhhhhhhhh...eeeeeee........eeeeee.......hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------S1  PDB: C:39-119 UniProt: 39-119                                                --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vmk C   1 MKRMLINATQQ--LRVALVDGQRLYDLDIESPG---KKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYF--------RPNIKDVLREGQEVIVQIDKEERGNKGAALTTFISLAGSYLVLMPNNPRAGGIS-------RTELKEALASLELPEGMGLIVRTAGVGKSAEALQWDLSFRLKHWEAIKKAAESRPAPFLIHQESNVIVRAFRDYLRQDIGEILIDNPKVLELARQHIAALGRPDFSSKIKLYTGEIPLFSHYQIESQIESAFQREVRLPSGGSIVIDSTEALTAIDINSA-----GDIEETAFNTNLEAADEIARQLRLRDLGGLIVIDFIDMTPVRHQRAVENRLREAVRQDRARIQISHISRFGLLEMSRQRLS-------HHVCPRCSGTGTVRDNESLSLSILRLIEEEALKENTQEVHAIVPVPIASYLLNEKRSAVNAIETRQDGVRCVIVPNDQMETPHYHVLRVRKGEETPTLSYMLPKLH 506
                                    10|  |    20        30  |   | 40        50        60        70       | -      | 90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300      |  -  |    320       330       340       350       360       370       380       390  |      -|      410       420       430       440       450       460       470       480       490       500      
                                     11 14                 33  37                                       78       87                                                  140     148                                                                                                                                                            307   313                                                                             393     401                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:472
 aligned with RNE_ECOLI | P21513 from UniProtKB/Swiss-Prot  Length:1061

    Alignment length:515
                                    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       380       390       400       410       420       430       440       450       460       470       480       490       500       510     
            RNE_ECOLI     1 MKRMLINATQQEELRVALVDGQRLYDLDIESPGHEQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTTFISLAGSYLVLMPNNPRAGGISRRIEGDDRTELKEALASLELPEGMGLIVRTAGVGKSAEALQWDLSFRLKHWEAIKKAAESRPAPFLIHQESNVIVRAFRDYLRQDIGEILIDNPKVLELARQHIAALGRPDFSSKIKLYTGEIPLFSHYQIESQIESAFQREVRLPSGGSIVIDSTEALTAIDINSARATRGGDIEETAFNTNLEAADEIARQLRLRDLGGLIVIDFIDMTPVRHQRAVENRLREAVRQDRARIQISHISRFGLLEMSRQRLSPSLGESSHHVCPRCSGTGTVRDNESLSLSILRLIEEEALKENTQEVHAIVPVPIASYLLNEKRSAVNAIETRQDGVRCVIVPNDQMETPHYHVLRVRKGEETPTLSYMLPKLHEEAMALPSE 515
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------    ----------------      S1-2vmkD01 D:36-119                                                                 -RNase_E_G-2vmkD05        D:121-393                                                                                                                                                                                                                                                 ------------------------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ---------    ----------------      S1-2vmkD02 D:36-119                                                                 -RNase_E_G-2vmkD06        D:121-393                                                                                                                                                                                                                                                 ------------------------------------------------------------------------------------------------------------------------ Pfam domains (2)
           Pfam domains (3) ---------    ----------------      S1-2vmkD03 D:36-119                                                                 -RNase_E_G-2vmkD07        D:121-393                                                                                                                                                                                                                                                 ------------------------------------------------------------------------------------------------------------------------ Pfam domains (3)
           Pfam domains (4) ---------    ----------------      S1-2vmkD04 D:36-119                                                                 -RNase_E_G-2vmkD08        D:121-393                                                                                                                                                                                                                                                 ------------------------------------------------------------------------------------------------------------------------ Pfam domains (4)
         Sec.struct. author .eeeeee..----.eeeeee..eeeeee.------.....eeeeeeeeee....eeeee--....eeee.hhhhhhhh.-------..hhhhh.....eeeeee.....-----.ee....ee...eeee........-------..hhhhhhhhhhh......eeee...----hhhhhhhhhhhhhhhhhhhhhhhh......eee...hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh.hhhhh..eee.....hhhhhh.hhhhhhhh...eee.....eeeeee....eeeeee..------hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhh......eeeeee.....eeeee....--.....eee...........hhhhhhhhhhhhhhhhhhh..eeeeeeeehhhhhhhhh..hhhhhhhhhhhh...eeeeee.........eeeeee.......hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------S1  PDB: D:39-119 UniProt: 39-119                                                ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vmk D   1 MKRMLINAT----LRVALVDGQRLYDLDI------QKKANIYKGKITRIEPSLEAAFVD--AERHGFLPLKEIAREYFP-------RPNIKDVLREGQEVIVQIDKEER-----ALTTFISLAGSYLVLMPNNPRAGG-------DDRTELKEALASLELPEGMGLIVRTA----SAEALQWDLSFRLKHWEAIKKAAESRPAPFLIHQESNVIVRAFRDYLRQDIGEILIDNPKVLELARQHIAALGRPDFSSKIKLYTGEIPLFSHYQIESQIESAFQREVRLPSGGSIVIDSTEALTAIDINSA------DIEETAFNTNLEAADEIARQLRLRDLGGLIVIDFIDMTPVRHQRAVENRLREAVRQDRARIQISHISRFGLLEMSRQRLS--LGESSHHVCPRCSGTGTVRDNESLSLSILRLIEEEALKENTQEVHAIVPVPIASYLLNEKRSAVNAIETRQDGVRCVIVPNDQMETPHYHVLRVRKGEETPTLSYMLPKLHEEAMALPSE 515
                                    |-   |    20        |-     |  40        50        |- |      70        |-      | 90       100        |-    |  120       130       | -     | 150       160       170|    | 180       190       200       210       220       230       240       250       260       270       280       290       300      |  -   |   320       330       340       350       360       370       380       390  |  | 400       410       420       430       440       450       460       470       480       490       500       510     
                                    9   14             29     36                     59 62               79      87                   109   115                    138     146                      171  176                                                                                                                                307    314                                                                            393  |                                                                                                                       
                                                                                                                                                                                                                                                                                                                                                                                                                                     396
   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 2VMK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VMK)

(-) Pfam Domains  (2, 8)

Asymmetric/Biological Unit
(-)
Clan: OB (224)
(-)
Family: S1 (23)
(-)
Escherichia coli (strain K12) (5)
1aS1-2vmkD01D:36-119
1bS1-2vmkD02D:36-119
1cS1-2vmkD03D:36-119
1dS1-2vmkD04D:36-119
(-)
Clan: no clan defined [family: RNase_E_G] (3)

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (RNE_ECOLI | P21513)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0004521    endoribonuclease activity    Catalysis of the hydrolysis of ester linkages within ribonucleic acid 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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0008995    ribonuclease E activity    Catalysis of the cleavage of single-stranded RNA that is monophosphorylated at its 5'-end; cleavage occurs predominantly at 5 nucleotides from the 5'-end and in A + U-rich regions, and is blocked by the presence of a 5'-triphosphate group.
    GO:0004540    ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    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:0006402    mRNA catabolic process    The chemical reactions and pathways resulting in the breakdown of mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0000967    rRNA 5'-end processing    Any process involved in forming the mature 5' end of an rRNA molecule.
    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.
    GO:0009898    cytoplasmic side of plasma membrane    The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

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        RNE_ECOLI | P21513: 1slj 1smx 1sn8 2bx2 2c0b 2c4r 2fym 2vrt 3gcm 3gme 3h1c 3h8a 5f6c

(-) Related Entries Specified in the PDB File

1slj SOLUTION STRUCTURE OF THE S1 DOMAIN OF RNASE E FROM E. COLI
1smx CRYSTAL STRUCTURE OF THE S1 DOMAIN OF RNASE E FROM E. COLI(NATIVE)
1sn8 CRYSTAL STRUCTURE OF THE S1 DOMAIN OF RNASE E FROM E. COLI(PB DERIVATIVE)
2bx2 CATALYTIC DOMAIN OF E. COLI RNASE E
2c0b CATALYTIC DOMAIN OF E. COLI RNASE E IN COMPLEX WITH 13-MER RNA
2c4r CATALYTIC DOMAIN OF E. COLI RNASE E
2fym CRYSTAL STRUCTURE OF E. COLI ENOLASE COMPLEXED WITH THEMINIMAL BINDING SEGMENT OF RNASE E.
2vrt CRYSTAL STRUCTURE OF E. COLI RNASE E POSSESSING M1 RNA FRAGMENTS - CATALYTIC DOMAIN