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(-) Description

Title :  CRYSTAL STRUCTURE OF MAZEF COMPLEX
 
Authors :  K. Kamada, F. Hanaoka, S. K. Burley, New York Sgx Research Center F Structural Genomics (Nysgxrc)
Date :  28 Mar 03  (Deposition) - 20 May 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Toxin, Antidote, Programmed Cell Death, Post-Segregation, Addiction Module, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Kamada, F. Hanaoka, S. K. Burley
Crystal Structure Of The Maze/Mazf Complex. Molecular Bases Of Antidote-Toxin Recognition
Mol. Cell V. 11 875 2003
PubMed-ID: 12718874  |  Reference-DOI: 10.1016/S1097-2765(03)00097-2

(-) Compounds

Molecule 1 - MAZF PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: MODIFIED PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MAZF
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 2 - MAZE PROTEIN
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: MODIFIED PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MAZE
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1UB4)

(-) Sites  (0, 0)

(no "Site" information available for 1UB4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UB4)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asp A:18 -Pro A:19

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UB4)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SPOVT_ABRBPS51740 SpoVT-AbrB domain profile.MAZE_ECO574-49  1C:404-449
MAZE_ECOLI4-49  1C:404-449
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SPOVT_ABRBPS51740 SpoVT-AbrB domain profile.MAZE_ECO574-49  2C:404-449
MAZE_ECOLI4-49  2C:404-449

(-) Exons   (0, 0)

(no "Exon" information available for 1UB4)

(-) 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:103
 aligned with MAZF_ECO57 | P0AE71 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:110
                                    11        21        31        41        51        61        71        81        91       101       111
           MAZF_ECO57     2 VSRYVPDMGDLIWVDFDPTKGSEQAGHRPAVVLSPFMYNNKTGMCLCVPCTTQSKGYPFEVVLSGQERDGVALADQVKSIAWRARGATKKGTVAPEELQLIKAKINVLIG 111
               SCOP domains d1ub4a_ A: MazF pr       otein                                                                                 SCOP domains
               CATH domains 1ub4A00 A:2-111  [       code=2.30.30.110, no name defined]                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeee...-------.eeeeee..hhhhhhhhh.eeeeeee........eeee......eeee....eeehhhhhh.eeeee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1ub4 A   2 VSRYVPDMGDLIWVDFDP-------GHRPAVVLSPFMYNNKTGMCLCVPCTTQSKGYPFEVVLSGQERDGVALADQVKSIAWRARGATKKGTVAPEELQLIKAKINVLIG 111
                                    11       | -     |  31        41        51        61        71        81        91       101       111
                                            19      27                                                                                    


Chain A from PDB  Type:PROTEIN  Length:103
 aligned with MAZF_ECOLI | P0AE70 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:110
                                    11        21        31        41        51        61        71        81        91       101       111
           MAZF_ECOLI     2 VSRYVPDMGDLIWVDFDPTKGSEQAGHRPAVVLSPFMYNNKTGMCLCVPCTTQSKGYPFEVVLSGQERDGVALADQVKSIAWRARGATKKGTVAPEELQLIKAKINVLIG 111
               SCOP domains d1ub4a_ A: MazF pr       otein                                                                                 SCOP domains
               CATH domains 1ub4A00 A:2-111  [       code=2.30.30.110, no name defined]                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeee...-------.eeeeee..hhhhhhhhh.eeeeeee........eeee......eeee....eeehhhhhh.eeeee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1ub4 A   2 VSRYVPDMGDLIWVDFDP-------GHRPAVVLSPFMYNNKTGMCLCVPCTTQSKGYPFEVVLSGQERDGVALADQVKSIAWRARGATKKGTVAPEELQLIKAKINVLIG 111
                                    11       | -     |  31        41        51        61        71        81        91       101       111
                                            19      27                                                                                    


Chain B from PDB  Type:PROTEIN  Length:100
 aligned with MAZF_ECO57 | P0AE71 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:110
                                    11        21        31        41        51        61        71        81        91       101       111
           MAZF_ECO57     2 VSRYVPDMGDLIWVDFDPTKGSEQAGHRPAVVLSPFMYNNKTGMCLCVPCTTQSKGYPFEVVLSGQERDGVALADQVKSIAWRARGATKKGTVAPEELQLIKAKINVLIG 111
               SCOP domains d1ub4b_ B: MazF           protein                                                                              SCOP domains
               CATH domains 1ub4B00 B:202-31          1  [code=2.30.30.110, no name defined]                                               CATH domains
           Pfam domains (1) ------PemK-1ub4B          01 B:208-310                                                                       - Pfam domains (1)
           Pfam domains (2) ------PemK-1ub4B          02 B:208-310                                                                       - Pfam domains (2)
         Sec.struct. author .........eeeee..----------..eeee..hhhhhhhhh.eeeeeee........eee........eee....eeehhhhhheeeeee.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1ub4 B 202 VSRYVPDMGDLIWVDF----------HRPAVVLSPFMYNNKTGMCLCVPCTTQSKGYPFEVVLSGQERDGVALADQVKSIAWRARGATKKGTVAPEELQLIKAKINVLIG 311
                                   211     |   -      |231       241       251       261       271       281       291       301       311
                                         217        228                                                                                   


Chain B from PDB  Type:PROTEIN  Length:100
 aligned with MAZF_ECOLI | P0AE70 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:110
                                    11        21        31        41        51        61        71        81        91       101       111
           MAZF_ECOLI     2 VSRYVPDMGDLIWVDFDPTKGSEQAGHRPAVVLSPFMYNNKTGMCLCVPCTTQSKGYPFEVVLSGQERDGVALADQVKSIAWRARGATKKGTVAPEELQLIKAKINVLIG 111
               SCOP domains d1ub4b_ B: MazF           protein                                                                              SCOP domains
               CATH domains 1ub4B00 B:202-31          1  [code=2.30.30.110, no name defined]                                               CATH domains
           Pfam domains (1) ------PemK-1ub4B          01 B:208-310                                                                       - Pfam domains (1)
           Pfam domains (2) ------PemK-1ub4B          02 B:208-310                                                                       - Pfam domains (2)
         Sec.struct. author .........eeeee..----------..eeee..hhhhhhhhh.eeeeeee........eee........eee....eeehhhhhheeeeee.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1ub4 B 202 VSRYVPDMGDLIWVDF----------HRPAVVLSPFMYNNKTGMCLCVPCTTQSKGYPFEVVLSGQERDGVALADQVKSIAWRARGATKKGTVAPEELQLIKAKINVLIG 311
                                   211     |   -      |231       241       251       261       271       281       291       301       311
                                         217        228                                                                                   


Chain C from PDB  Type:PROTEIN  Length:75
 aligned with MAZE_ECO57 | P0AE73 from UniProtKB/Swiss-Prot  Length:82

    Alignment length:75
                                    11        21        31        41        51        61        71     
           MAZE_ECO57     2 IHSSVKRWGNSPAVRIPATLMQALNLNIDDEVKIDLVDGKLIIEPVRKEPVFTLAELVNDITPENLHENIDWGEP  76
               SCOP domains d1ub4c_ C: MazE                                                             SCOP domains
               CATH domains 1ub4C00 C:402-476  [code=2.10.260.10, no name defined]                      CATH domains
               Pfam domains -----Antitoxin-MazE-1ub4C01 C:407-452              ------------------------ Pfam domains
         Sec.struct. author ....eeee..eeee..hhhhhhhh.......ee..........ee.......hhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --SPOVT_ABRB  PDB: C:404-449 UniProt: 4-49      --------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------- Transcript
                 1ub4 C 402 IHSSVKRWGNSPAVRIPATLMQALNLNIDDEVKIDLVDGKLIIEPVRKEPVFTLAELVNDITPENLHENIDWGEP 476
                                   411       421       431       441       451       461       471     


Chain C from PDB  Type:PROTEIN  Length:75
 aligned with MAZE_ECOLI | P0AE72 from UniProtKB/Swiss-Prot  Length:82

    Alignment length:75
                                    11        21        31        41        51        61        71     
           MAZE_ECOLI     2 IHSSVKRWGNSPAVRIPATLMQALNLNIDDEVKIDLVDGKLIIEPVRKEPVFTLAELVNDITPENLHENIDWGEP  76
               SCOP domains d1ub4c_ C: MazE                                                             SCOP domains
               CATH domains 1ub4C00 C:402-476  [code=2.10.260.10, no name defined]                      CATH domains
               Pfam domains -----Antitoxin-MazE-1ub4C01 C:407-452              ------------------------ Pfam domains
         Sec.struct. author ....eeee..eeee..hhhhhhhh.......ee..........ee.......hhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --SPOVT_ABRB  PDB: C:404-449 UniProt: 4-49      --------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 1ub4 C 402 IHSSVKRWGNSPAVRIPATLMQALNLNIDDEVKIDLVDGKLIIEPVRKEPVFTLAELVNDITPENLHENIDWGEP 476
                                   411       421       431       441       451       461       471
   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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 3)

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

(-) Pfam Domains  (2, 3)

Asymmetric Unit
(-)
Clan: AbrB (11)
(-)
Clan: no clan defined [family: PemK] (4)

(-) Gene Ontology  (17, 29)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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.

Chain A,B   (MAZF_ECO57 | P0AE71)
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: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.
biological process
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

Chain C   (MAZE_ECOLI | P0AE72)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

Chain C   (MAZE_ECO57 | P0AE73)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).

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  1ub4
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 Related Entries

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

UniProtKB/Swiss-Prot
        MAZE_ECO57 | P0AE73: 1mvf
        MAZE_ECOLI | P0AE72: 1mvf 2mrn 2mru 5cqx 5cqy
        MAZF_ECOLI | P0AE70: 3nfc 5ck9 5ckb 5ckd 5cke 5ckf 5ckh 5co7 5cqx 5cqy 5cr2

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1UB4)