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(-) Description

Title :  CRYSTAL STRUCTURE OF E.COLI MAZF TOXIN
 
Authors :  X. Wang, K. Wang, X. Su, J. Zhang
Date :  10 Jun 10  (Deposition) - 15 Jun 11  (Release) - 15 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B,C  (1x)
Biol. Unit 3:  D,E  (1x)
Biol. Unit 4:  F  (2x)
Keywords :  Mazf, Mazef System, Rna Cleavage, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Wang, K. Wang, X. Gao, X. Zhang, L. Li, X. Su, J. Zhang
Biochemical And Structural Analysis Of E. Coli Mazf Toxin
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PEMK-LIKE PROTEIN 1
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: PROTEIN MAZF

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (2x): A     
Biological Unit 2 (1x):  BC   
Biological Unit 3 (1x):    DE 
Biological Unit 4 (2x):      F

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3NFC)

(-) Sites  (0, 0)

(no "Site" information available for 3NFC)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NFC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NFC)

(-) 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:94
 aligned with MAZF_ECOLI | P0AE70 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:107
                                    14        24        34        44        54        64        74        84        94       104       
           MAZF_ECOLI     5 YVPDMGDLIWVDFDPTKGSEQAGHRPAVVLSPFMYNNKTGMCLCVPCTTQSKGYPFEVVLSGQERDGVALADQVKSIAWRARGATKKGTVAPEELQLIKAKINVLIG 111
               SCOP domains d3nfca_ A: Maz         F protein                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee....---------...eee..hhhhhhhhh.eeeeeee........eee...----.eee.hhheee.......eeeee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 3nfc A   5 YVPDMGDLIWVDFD---------HRPAVVLSPFMYNNKTGMCLCVPCTTQSKGYPFEVVLSG----GVALADQVKSIAWRARGATKKGTVAPEELQLIKAKINVLIG 111
                                    14   |     -   |    34        44        54        64 |    | 74        84        94       104       
                                        18        28                                    66   71                                        


Chain B from PDB  Type:PROTEIN  Length:92
 aligned with MAZF_ECOLI | P0AE70 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:107
                                    14        24        34        44        54        64        74        84        94       104       
           MAZF_ECOLI     5 YVPDMGDLIWVDFDPTKGSEQAGHRPAVVLSPFMYNNKTGMCLCVPCTTQSKGYPFEVVLSGQERDGVALADQVKSIAWRARGATKKGTVAPEELQLIKAKINVLIG 111
               SCOP domains d3nfcb_ B: Ma           zF protein                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee...-----------..eee..hhhhhhhhh.eeeeeee........eee...----.eee.hhheee.......eeeee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 3nfc B   5 YVPDMGDLIWVDF-----------RPAVVLSPFMYNNKTGMCLCVPCTTQSKGYPFEVVLSG----GVALADQVKSIAWRARGATKKGTVAPEELQLIKAKINVLIG 111
                                    14  |      -    |   34        44        54        64 |    | 74        84        94       104       
                                       17          29                                   66   71                                        


Chain C from PDB  Type:PROTEIN  Length:93
 aligned with MAZF_ECOLI | P0AE70 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:107
                                    14        24        34        44        54        64        74        84        94       104       
           MAZF_ECOLI     5 YVPDMGDLIWVDFDPTKGSEQAGHRPAVVLSPFMYNNKTGMCLCVPCTTQSKGYPFEVVLSGQERDGVALADQVKSIAWRARGATKKGTVAPEELQLIKAKINVLIG 111
               SCOP domains d3nfcc_ C: Ma          zF protein                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee...----------...eee..hhhhhhhhh.eeeeeee........eee...----.eee.hhheee.......eeeee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 3nfc C   5 YVPDMGDLIWVDF----------HRPAVVLSPFMYNNKTGMCLCVPCTTQSKGYPFEVVLSG----GVALADQVKSIAWRARGATKKGTVAPEELQLIKAKINVLIG 111
                                    14  |      -   |    34        44        54        64 |    | 74        84        94       104       
                                       17         28                                    66   71                                        


Chain D from PDB  Type:PROTEIN  Length:93
 aligned with MAZF_ECOLI | P0AE70 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:107
                                    14        24        34        44        54        64        74        84        94       104       
           MAZF_ECOLI     5 YVPDMGDLIWVDFDPTKGSEQAGHRPAVVLSPFMYNNKTGMCLCVPCTTQSKGYPFEVVLSGQERDGVALADQVKSIAWRARGATKKGTVAPEELQLIKAKINVLIG 111
               SCOP domains d3nfcd_ D: Ma          zF protein                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee...----------...eee..hhhhhhhhh.eeeeeee........eee...----.eee.hhheee.......eeeee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 3nfc D   5 YVPDMGDLIWVDF----------HRPAVVLSPFMYNNKTGMCLCVPCTTQSKGYPFEVVLSG----GVALADQVKSIAWRARGATKKGTVAPEELQLIKAKINVLIG 111
                                    14  |      -   |    34        44        54        64 |    | 74        84        94       104       
                                       17         28                                    66   71                                        


Chain E from PDB  Type:PROTEIN  Length:94
 aligned with MAZF_ECOLI | P0AE70 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:107
                                    14        24        34        44        54        64        74        84        94       104       
           MAZF_ECOLI     5 YVPDMGDLIWVDFDPTKGSEQAGHRPAVVLSPFMYNNKTGMCLCVPCTTQSKGYPFEVVLSGQERDGVALADQVKSIAWRARGATKKGTVAPEELQLIKAKINVLIG 111
               SCOP domains d3nfce_ E: Maz         F protein                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee....---------...eee..hhhhhhhhh.eeeeeee........eee...----.eee.hhheee.......eeeee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 3nfc E   5 YVPDMGDLIWVDFD---------HRPAVVLSPFMYNNKTGMCLCVPCTTQSKGYPFEVVLSG----GVALADQVKSIAWRARGATKKGTVAPEELQLIKAKINVLIG 111
                                    14   |     -   |    34        44        54        64 |    | 74        84        94       104       
                                        18        28                                    66   71                                        


Chain F from PDB  Type:PROTEIN  Length:93
 aligned with MAZF_ECOLI | P0AE70 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:108
                                    13        23        33        43        53        63        73        83        93       103        
           MAZF_ECOLI     4 RYVPDMGDLIWVDFDPTKGSEQAGHRPAVVLSPFMYNNKTGMCLCVPCTTQSKGYPFEVVLSGQERDGVALADQVKSIAWRARGATKKGTVAPEELQLIKAKINVLIG 111
               SCOP domains d3nfcf_ F: Maz           F protein                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ----PemK-3nfcF           01 F:8-110                                                                        - Pfam domains (1)
           Pfam domains (2) ----PemK-3nfcF           02 F:8-110                                                                        - Pfam domains (2)
           Pfam domains (3) ----PemK-3nfcF           03 F:8-110                                                                        - Pfam domains (3)
           Pfam domains (4) ----PemK-3nfcF           04 F:8-110                                                                        - Pfam domains (4)
           Pfam domains (5) ----PemK-3nfcF           05 F:8-110                                                                        - Pfam domains (5)
           Pfam domains (6) ----PemK-3nfcF           06 F:8-110                                                                        - Pfam domains (6)
         Sec.struct. author .......eeee...-----------..eee..hhhhhhhhh.eeeeeee........eee...----.eee.hhheee.......eeeee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 3nfc F   4 RYVPDMGDLIWVDF-----------RPAVVLSPFMYNNKTGMCLCVPCTTQSKGYPFEVVLSG----GVALADQVKSIAWRARGATKKGTVAPEELQLIKAKINVLIG 111
                                    13   |     -     |  33        43        53        63  |    |73        83        93       103        
                                        17          29                                   66   71
   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, 6)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NFC)

(-) Pfam Domains  (1, 6)

Asymmetric Unit
(-)
Clan: no clan defined [family: PemK] (4)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (MAZF_ECOLI | P0AE70)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    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).
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:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    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:0030308    negative regulation of cell growth    Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0009372    quorum sensing    The process in which single-celled organisms monitor their population density by detecting the concentration of small, diffusible signal molecules produced by the cells themselves.
    GO:0016075    rRNA catabolic process    The chemical reactions and pathways resulting in the breakdown of rRNA, ribosomal RNA, a structural constituent of ribosomes.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MAZF_ECOLI | P0AE70: 1ub4 5ck9 5ckb 5ckd 5cke 5ckf 5ckh 5co7 5cqx 5cqy 5cr2

(-) Related Entries Specified in the PDB File

1ub4 MAZEF COMPLEX