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Theoretical Model  (Jmol Viewer)

(-) Description

Title :  MODEL INTERACTION BETWEEN BIRA AND BCCP
 
Authors :  L. H. Weaver, K. Kwon, D. Beckett, B. W. Matthews
Date :  15 Oct 01  (Deposition) - 21 Nov 01  (Release) - 05 Dec 01  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,B,_#
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 
Keywords :  Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. H. Weaver, K. Kwon, D. Beckett, B. W. Matthews
Competing Protein:Protein Interactions Are Proposed To Control The Biological Switch Of The E Coli Biotin Repressor.
Protein Sci. V. 10 2618 2001
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BIRA BIFUNCTIONAL PROTEIN
    Chains: A
    EC Number: 6.3.4.15
    Organism Common: BACTERIA
    Organism Scientific: ESCHERICHIA COLI
    Other Details: FROM PDB ENTRY 1HXD
    Synonym: BIRA, BIOTIN OPERON REPRESSOR
 
Molecule 2 - BIOTIN CARBOXYL CARRIER PROTEIN OF ACETYL-COA CARBOXYLASE
    Chains: B
    Organism Common: BACTERIA
    Organism Scientific: ESCHERICHIA COLI
    Other Details: FROM PDB ENTRY 1BDO
    Synonym: BCCP

 Structural Features

(-) Chains, Units

  
Theoretical Model : 
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 

Summary Information (see also Sequences/Alignments below)

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

Theoretical Model (1, 1)
No.NameCountTypeFull Name
1BTN1Ligand/IonBIOTIN

(-) Sites  (0, 0)

(no "Site" information available for 1K67)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K67)

(-) Cis Peptide Bonds  (1, 1)

Theoretical Model
No.Residues
1Trp A:173 -Pro A:174

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Theoretical Model (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_BIRA_ECOLI_002 *K70EBIRA_ECOLI  ---  ---AK70E
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Theoretical Model (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BPL_LPL_CATALYTICPS51733 Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile.BIRA_ECOLI66-254  1A:66-254
2BIOTINPS00188 Biotin-requiring enzymes attachment site.BCCP_ECO57112-129  1B:112-129
BCCP_ECOL6112-129  1B:112-129
BCCP_ECOLI112-129  1B:112-129
BCCP_SHIFL112-129  1B:112-129

(-) Exons   (0, 0)

(no "Exon" information available for 1K67)

(-) Sequences/Alignments

Theoretical Model
   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:244
 aligned with BIRA_ECOLI | P06709 from UniProtKB/Swiss-Prot  Length:321

    Alignment length:253
                                    74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314   
           BIRA_ECOLI    65 QLLNAKQILGQLDGGSVAVLPVIDSTNQYLLDRIGELKSGDACIAEYQQAGRGRRGRKWFSPFGANLYLSMFWRLEQGPAAAIGLSLVIGIVMAEVLRKLGADKVRVKWPNDLYLQDRKLAGILVELTGKTGDAAQIVIGAGINMAMRRVEESVVNQGWITLQEAGINLDRNTLAAMLIRELRAALELFEQEGLAPYLSRWEKLDNFINRPVKLIIGDKEIFGISRGIDKQGALLLEQDGIIKPWMGGEISLR 317
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh.....eee.....hhhhhhhh.........eee......................eeeeeeeee......hhhhhhhhhhhhhhhhhhhh....eee...eeee..eeeeeeeeeee......eeeeeeeee....---------.....hhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh.......eeeeee..eeeeeeeeee.....eeee....eeee...eeee. Sec.struct. author
                 SAPs(SNPs) -----E------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -BPL_LPL_CATALYTIC  PDB: A:66-254 UniProt: 66-254                                                                                                                                             --------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k67 A  65 QLLNAKQILGQLDGGSVAVLPVIDSTNQYLLDRIGELKSGDACIAEYQQAGRGRRGRKWFSPFGANLYLSMFWRLEQGPAAAIGLSLVIGIVMAEVLRKLGADKVRVKWPNDLYLQDRKLAGILVELTGKTGDAAQIVIGAGINMAM---------QGWITLQEAGINLDRNTLAAMLIRELRAALELFEQEGLAPYLSRWEKLDNFINRPVKLIIGDKEIFGISRGIDKQGALLLEQDGIIKPWMGGEISLR 317
                                    74        84        94       104       114       124       134       144       154       164       174       184       194       204      |  -      |224       234       244       254       264       274       284       294       304       314   
                                                                                                                                                                            211       221                                                                                                


Chain B from PDB  Type:PROTEIN  Length:79
 aligned with BCCP_ECO57 | P0ABE0 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:79
                                    86        96       106       116       126       136       146         
           BCCP_ECO57    77 EISGHIVRSPMVGTFYRTPSPDAKAFIEVGQKVNVGDTLCIVEAMKMMNQIEADKSGTVKAILVESGQPVEFDEPLVVI 155
               SCOP domains ------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....eeee...............ee....eeeeeee..eeeeee....ee..ee......ee....eeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ------------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) -----------------------------------BIOTIN            -------------------------- PROSITE (5)
                 Transcript ------------------------------------------------------------------------------- Transcript
                 1k67 B  77 EISGHIVRSPMVGTFYRTPSPDAKAFIEVGQKVNVGDTLCIVEAMKMMNQIEADKSGTVKAILVESGQPVEFDEPLVVI 155
                                    86        96       106       116       126       136       146         


Chain B from PDB  Type:PROTEIN  Length:79
 aligned with BCCP_ECOL6 | P0ABD9 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:79
                                    86        96       106       116       126       136       146         
           BCCP_ECOL6    77 EISGHIVRSPMVGTFYRTPSPDAKAFIEVGQKVNVGDTLCIVEAMKMMNQIEADKSGTVKAILVESGQPVEFDEPLVVI 155
               SCOP domains ------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....eeee...............ee....eeeeeee..eeeeee....ee..ee......ee....eeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) -----------------------------------BIOTIN            -------------------------- PROSITE (4)
                 Transcript ------------------------------------------------------------------------------- Transcript
                 1k67 B  77 EISGHIVRSPMVGTFYRTPSPDAKAFIEVGQKVNVGDTLCIVEAMKMMNQIEADKSGTVKAILVESGQPVEFDEPLVVI 155
                                    86        96       106       116       126       136       146         


Chain B from PDB  Type:PROTEIN  Length:79
 aligned with BCCP_ECOLI | P0ABD8 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:79
                                    86        96       106       116       126       136       146         
           BCCP_ECOLI    77 EISGHIVRSPMVGTFYRTPSPDAKAFIEVGQKVNVGDTLCIVEAMKMMNQIEADKSGTVKAILVESGQPVEFDEPLVVI 155
               SCOP domains ------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....eeee...............ee....eeeeeee..eeeeee....ee..ee......ee....eeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -----------------------------------BIOTIN            -------------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------- Transcript
                 1k67 B  77 EISGHIVRSPMVGTFYRTPSPDAKAFIEVGQKVNVGDTLCIVEAMKMMNQIEADKSGTVKAILVESGQPVEFDEPLVVI 155
                                    86        96       106       116       126       136       146         


Chain B from PDB  Type:PROTEIN  Length:79
 aligned with BCCP_SHIFL | P0ABE1 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:79
                                    86        96       106       116       126       136       146         
           BCCP_SHIFL    77 EISGHIVRSPMVGTFYRTPSPDAKAFIEVGQKVNVGDTLCIVEAMKMMNQIEADKSGTVKAILVESGQPVEFDEPLVVI 155
               SCOP domains ------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....eeee...............ee....eeeeeee..eeeeee....ee..ee......ee....eeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -----------------------------------BIOTIN            -------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------- Transcript
                 1k67 B  77 EISGHIVRSPMVGTFYRTPSPDAKAFIEVGQKVNVGDTLCIVEAMKMMNQIEADKSGTVKAILVESGQPVEFDEPLVVI 155
                                    86        96       106       116       126       136       146
   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 1K67)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1K67)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1K67)

(-) Gene Ontology  (19, 34)

Theoretical Model(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.

Chain B   (BCCP_SHIFL | P0ABE1)
molecular function
    GO:0003989    acetyl-CoA carboxylase activity    Catalysis of the reaction: ATP + acetyl-CoA + HCO3- = ADP + phosphate + malonyl-CoA.
biological process
    GO:0006633    fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
    GO:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
cellular component
    GO:0009317    acetyl-CoA carboxylase complex    A protein complex that catalyzes the first step in long-chain fatty acid biosynthesis. For example, in E. coli the complex is heterohexameric and composed of biotin carbonyl carrier protein, biotin carboxylase and the acetate CoA-transferase complex.

Chain B   (BCCP_ECOL6 | P0ABD9)
molecular function
    GO:0003989    acetyl-CoA carboxylase activity    Catalysis of the reaction: ATP + acetyl-CoA + HCO3- = ADP + phosphate + malonyl-CoA.
biological process
    GO:0006633    fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
    GO:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
cellular component
    GO:0009317    acetyl-CoA carboxylase complex    A protein complex that catalyzes the first step in long-chain fatty acid biosynthesis. For example, in E. coli the complex is heterohexameric and composed of biotin carbonyl carrier protein, biotin carboxylase and the acetate CoA-transferase complex.

Chain B   (BCCP_ECO57 | P0ABE0)
molecular function
    GO:0003989    acetyl-CoA carboxylase activity    Catalysis of the reaction: ATP + acetyl-CoA + HCO3- = ADP + phosphate + malonyl-CoA.
biological process
    GO:0006633    fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
    GO:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
cellular component
    GO:0009317    acetyl-CoA carboxylase complex    A protein complex that catalyzes the first step in long-chain fatty acid biosynthesis. For example, in E. coli the complex is heterohexameric and composed of biotin carbonyl carrier protein, biotin carboxylase and the acetate CoA-transferase complex.

Chain B   (BCCP_ECOLI | P0ABD8)
molecular function
    GO:0003989    acetyl-CoA carboxylase activity    Catalysis of the reaction: ATP + acetyl-CoA + HCO3- = ADP + phosphate + malonyl-CoA.
    GO:0009374    biotin binding    Interacting selectively and non-covalently with biotin (cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid), the (+) enantiomer of which is very widely distributed in cells and serves as a carrier in a number of enzymatic beta-carboxylation reactions.
    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:0006633    fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
    GO:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
cellular component
    GO:0009317    acetyl-CoA carboxylase complex    A protein complex that catalyzes the first step in long-chain fatty acid biosynthesis. For example, in E. coli the complex is heterohexameric and composed of biotin carbonyl carrier protein, biotin carboxylase and the acetate CoA-transferase complex.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BCCP_ECO57 | P0ABE0: 1k69
        BCCP_ECOL6 | P0ABD9: 1k69
        BCCP_ECOLI | P0ABD8: 1a6x 1bdo 1k69 2bdo 3bdo 4hr7
        BCCP_SHIFL | P0ABE1: 1k69
        BIRA_ECOLI | P06709: 1bia 1bib 1hxd 2ewn 4wf2

(-) Related Entries Specified in the PDB File

1bdo STRUCTURE OF THE BIOTINYL DOMAIN OF ACETYL-COENZYME A CARBOXYLASE DETERMINED BY MAD PHASING
1hxd CRYSTAL STRUCTURE OF E. COLI BIOTIN REPRESSOR WITH BOUND BIOTIN
1k69 MODEL INTERACTION BETWEEN BCCP AND ATP-BOUND CARBOXYLASE SUBUNIT OF ACETYL COA CARBOXYLASE