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(-) Description

Title :  THE E. COLI BIOTIN HOLOENZYME SYNTHETASE(SLASH)BIO REPRESSOR CRYSTAL STRUCTURE DELINEATES THE BIOTIN AND DNA-BINDING DOMAINS
 
Authors :  K. P. Wilson, L. M. Shewchuk, B. W. Matthews
Date :  06 Jul 92  (Deposition) - 31 Oct 93  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. P. Wilson, L. M. Shewchuk, R. G. Brennan, A. J. Otsuka, B. W. Matthews
Escherichia Coli Biotin Holoenzyme Synthetase/Bio Repressor Crystal Structure Delineates The Biotin- And Dna-Binding Domains.
Proc. Natl. Acad. Sci. Usa V. 89 9257 1992
PubMed-ID: 1409631  |  Reference-DOI: 10.1073/PNAS.89.19.9257
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BIR A
    Chains: A
    EC Number: 6.3.4.15
    Engineered: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1BTN1Ligand/IonBIOTIN

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:89 , THR A:90 , ASN A:91 , GLN A:112 , GLY A:115 , ARG A:116 , TYR A:132 , SER A:134 , LYS A:183 , GLY A:186 , ILE A:187 , GLY A:204 , ALA A:205BINDING SITE FOR RESIDUE BTN A 500
2CATUNKNOWNSER A:89 , THR A:90 , ASN A:91 , GLN A:112 , GLY A:115 , ARG A:116 , GLY A:117 , ARG A:118 , TYR A:132 , LYS A:183 , ILE A:187 , LEU A:188 , GLY A:204 , ALA A:205NULL
3HTHUNKNOWNGLY A:22 , GLU A:23 , GLN A:24 , LEU A:25 , GLY A:26 , GLU A:27 , THR A:28 , LEU A:29 , GLY A:30 , MET A:31 , SER A:32 , ARG A:33 , ALA A:34 , ALA A:35 , ILE A:36 , ASN A:37 , LYS A:38 , HIS A:39 , ILE A:40 , GLN A:41 , THR A:42 , LEU A:43 , ARG A:44 , ASP A:45 , TRP A:46NULL

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Trp A:173 -Pro A:174

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_BIRA_ECOLI_001 *P61ABIRA_ECOLI  ---  ---AP61A
2UniProtVAR_BIRA_ECOLI_002 *K70EBIRA_ECOLI  ---  ---AK70E
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BPL_LPL_CATALYTICPS51733 Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile.BIRA_ECOLI66-254  1A:66-254

(-) Exons   (0, 0)

(no "Exon" information available for 1BIB)

(-) 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:294
 aligned with BIRA_ECOLI | P06709 from UniProtKB/Swiss-Prot  Length:321

    Alignment length:316
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311      
           BIRA_ECOLI     2 KDNTVPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDWGVDVFTVPGKGYSLPEPIQLLNAKQILGQLDGGSVAVLPVIDSTNQYLLDRIGELKSGDACIAEYQQAGRGRRGRKWFSPFGANLYLSMFWRLEQGPAAAIGLSLVIGIVMAEVLRKLGADKVRVKWPNDLYLQDRKLAGILVELTGKTGDAAQIVIGAGINMAMRRVEESVVNQGWITLQEAGINLDRNTLAAMLIRELRAALELFEQEGLAPYLSRWEKLDNFINRPVKLIIGDKEIFGISRGIDKQGALLLEQDGIIKPWMGGEISLR 317
               SCOP domains d1biba1 A:2-63 Biotin repressor, N-terminal domain            d1biba3 A:64-270 Biotin repressor/biotin holoenzyme syn      thetase, catalyti c (central) domain                                                                                                              d1biba2 A:271-317                               SCOP domains
               CATH domains 1bibA01 A:2-64 'winged helix' repressor DNA binding domain     1bibA02 A:65-270 Bira Bifunctional Protein; Domain 2                                                                                                                                                          1bibA03 A:271-313                          ---- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh......hhhhhhhh...hhhhhhhhhhhhhh..eeeeee.eeeee.......hhhhhhhhh...eeeee....hhhhhhhhh......eeeeee.........------....eeeeeeeeeee..-....hhhhhhhhhhhhhhhhhh.....eeee.eeeeee.eeeeeeeeeee.----..eeeeeeeeeee.-----------...........hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh....eeeeeee..eeeeeeeeeee..eeeeeee..eeeee...eeeee Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------A--------E------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------BPL_LPL_CATALYTIC  PDB: A:66-254 UniProt: 66-254                                                                                                                                             --------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bib A   2 KDNTVPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDWGVDVFTVPGKGYSLPEPIQLLNAKQILGQLDGGSVAVLPVIDSTNQYLLDRIGELKSGDACIAEYQQAGRGR------SPFGANLYLSMFWRLEQ-PAAAIGLSLVIGIVMAEVLRKLGADKVRVKWPNDLYLQDRKLAGILVELTG----AAQIVIGAGINMAM-----------WITLQEAGINLDRNTLAAMLIRELRAALELFEQEGLAPYLSRWEKLDNFINRPVKLIIGDKEIFGISRGIDKQGALLLEQDGIIKPWMGGEISLR 317
                                    11        21        31        41        51        61        71        81        91       101       111      |  -   |   131       141 |     151       161       171       181       191 |    |201       211         - |     231       241       251       261       271       281       291       301       311      
                                                                                                                                              118    125             141 |                                               193  198          211         223                                                                                              
                                                                                                                                                                       143
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BIRA_ECOLI | P06709)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0004077    biotin-[acetyl-CoA-carboxylase] ligase activity    Catalysis of the reaction: ATP + biotin + apo-(acetyl-CoA:carbon-dioxide ligase (ADP forming)) = AMP + diphosphate + (acetyl-CoA:carbon-dioxide ligase (ADP forming)).
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    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.
biological process
    GO:0009102    biotin biosynthetic process    The chemical reactions and pathways resulting in the formation of biotin, cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid.
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    GO:0009305    protein biotinylation    The addition of biotin (vitamin B7 / vitamin H) to a protein amino acid.
    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.

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 Related Entries

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UniProtKB/Swiss-Prot
        BIRA_ECOLI | P06709: 1bia 1hxd 1k67 2ewn 4wf2

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