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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE TRANSCRIPTION FACTOR SC-MTTFB OFFERS INTRIGUING INSIGHTS INTO MITOCHONDRIAL TRANSCRIPTION
 
Authors :  F. D. Schubot, C. -J. Chen, J. P. Rose, T. A. Dailey, H. A. Dailey, B. - C. Wang
Date :  23 Feb 01  (Deposition) - 03 Oct 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Mitochondrial Transcription Factor, Transcription Initiation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. D. Schubot, C. J. Chen, J. P. Rose, T. A. Dailey, H. A. Dailey, B. C. Wang
Crystal Structure Of The Transcription Factor Sc-Mttfb Offers Insights Into Mitochondrial Transcription.
Protein Sci. V. 10 1980 2001
PubMed-ID: 11567089  |  Reference-DOI: 10.1110/PS.11201
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MITOCHONDRIAL REPLICATION PROTEIN MTF1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTRCHISC
    Expression System StrainJM109
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneMTF1
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymMITOCHONDRIAL TRANSCRIPTION FACTOR MTTFB

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1XE3Ligand/IonXENON

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:68BINDING SITE FOR RESIDUE XE A 342
2AC2SOFTWAREGLN A:60BINDING SITE FOR RESIDUE XE A 343
3AC3SOFTWARETYR A:108BINDING SITE FOR RESIDUE XE A 344

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1I4W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1I4W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1I4W)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_RNA_A_N6_MTPS51689 rRNA adenine N(6)-methyltransferase family profile.MTF1_YEAST14-322  1A:14-322

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YMR228W1YMR228W.1XIII:724625-7256501026MTF1_YEAST1-3413411A:4-325322

(-) 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    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:322
 aligned with MTF1_YEAST | P14908 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:322
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323  
           MTF1_YEAST     4 PIPGIKDISKLKFFYGFKYLWNPTVYNKIFDKLDLTKTYKHPEELKVLDLYPGVGIQSAIFYNKYCPRQYSLLEKRSSLYKFLNAKFEGSPLQILKRDPYDWSTYSNLIDEERIFVPEVQSSDHINDKFLTVANVTGEGSEGLIMQWLSCIGNKNWLYRFGKVKMLLWMPSTTARKLLARPGMHSRSKCSVVREAFTDTKLIAISDANELKGFDSQCIEEWDPILFSAAEIWPTKGKPIALVEMDPIDFDFDVDNWDYVTRHLMILKRTPLNTVMDSLGHGGQQYFNSRITDKDLLKKCPIDLTNDEFIYLTKLFMEWPFKP 325
               SCOP domains d1i4wa_ A: Transcription factor sc-mtTFB                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1i4wA01 A:4-250 Vaccinia Virus protein VP39                                                                                                                                                                                                            1i4wA02 A:251-325  [code=1.10.8.100, no name defined]                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhh....hhhhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhhh..eeeee..hhhhhhhhhhhh.....eee.....hhhhhhhhh...............eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhheeeeeeeeehhhhhhhhh.......hhhhhhhhhheeeeeeee.hhhhhhhhhhhhhhhhh.ee.hhhh........eeeeeeee.....hhhhhhhhhhhhhh.......hhhhhh..hhhhhhh...........hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------SAM_RNA_A_N6_MT  PDB: A:14-322 UniProt: 14-322                                                                                                                                                                                                                                                                       --- PROSITE
               Transcript 1 Exon 1.1  PDB: A:4-325 UniProt: 1-341 [INCOMPLETE]                                                                                                                                                                                                                                                                                 Transcript 1
                 1i4w A   4 PIPGIKDISKLKFFYGFKYLWNPTVYNKIFDKLDLTKTYKHPEELKVLDLYPGVGIQSAIFYNKYCPRQYSLLEKRSSLYKFLNAKFEGSPLQILKRDPYDWSTYSNLIDEERIFVPEVQSSDHINDKFLTVANVTGEGSEGLIMQWLSCIGNKNWLYRFGKVKMLLWMPSTTARKLLARPGMHSRSKCSVVREAFTDTKLIAISDANELKGFDSQCIEEWDPILFSAAEIWPTKGKPIALVEMDPIDFDFDVDNWDYVTRHLMILKRTPLNTVMDSLGHGGQQYFNSRITDKDLLKKCPIDLTNDEFIYLTKLFMEWPFKP 325
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323  

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1I4W)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MTF1_YEAST | P14908)
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:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0034246    mitochondrial RNA polymerase binding promoter specificity activity    Interacting selectively and non-covalently with a mitochondrial RNA polymerase to form a holoenzyme complex and also, while present in the holoenzyme, interacting with promoter sequences in order to confer sequence specific recognition of mitochondrial promoter DNA sequence motifs.
    GO:0000997    mitochondrial RNA polymerase core promoter sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is part of the core promoter for the mitochondrial RNA polymerase.
    GO:0000179    rRNA (adenine-N6,N6-)-dimethyltransferase activity    Catalysis of the dimethylation two adjacent A residues in the loop closing the 3'-terminal stem of the 18S rRNA, using S-adenosyl-L-methionine as a methyl donor.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:1903108    regulation of transcription from mitochondrial promoter    Any process that modulates the frequency, rate or extent of transcription from mitochondrial promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006391    transcription initiation from mitochondrial promoter    A transcription initiation process that takes place at a promoter on the mitochondrial chromosome, and results in RNA synthesis by a mitochondrial RNA polymerase.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0034245    mitochondrial DNA-directed RNA polymerase complex    A DNA-directed RNA polymerase complex located in the mitochondrion. Mitochondrial RNA polymerase is composed of two subunits, a catalytic core, which resembles the enzymes from bacteriophage T7 and T3, and a specificity factor required for promoter recognition, which is similar to members of the eubacterial sigma factor family. In S. cerevisiae, these are encoded by the nuclear genes RPO41 and MTF1 and the specificity factor, required for promoter recognition and initiation, is not present in the elongating form.
    GO:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    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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