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(-) Description

Title :  THE STRUCTURE OF BIOTIN CARBOXYLASE, MUTANT E288K, COMPLEXED WITH ATP
 
Authors :  J. B. Thoden, C. Z. Blanchard, H. M. Holden, G. L. Waldrop
Date :  19 Jan 00  (Deposition) - 09 Jun 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Atp-Grasp Biotin-Dependent Carboxylase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. B. Thoden, C. Z. Blanchard, H. M. Holden, G. L. Waldrop
Movement Of The Biotin Carboxylase B-Domain As A Result Of Atp Binding.
J. Biol. Chem. V. 275 16183 2000
PubMed-ID: 10821865  |  Reference-DOI: 10.1074/JBC.275.21.16183
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BIOTIN CARBOXYLASE
    ChainsA, B
    EC Number6.3.4.14
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentBIOTIN CARBOXYLASE
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:116 , LYS A:159 , GLY A:163 , GLY A:164 , GLY A:165 , GLY A:166 , MET A:169 , GLU A:201 , LYS A:202 , TYR A:203 , LEU A:204 , HIS A:236 , LEU A:278 , ILE A:287 , LYS A:288 , ILE A:437BINDING SITE FOR RESIDUE ATP A 1000
2AC2SOFTWARELYS B:116 , LYS B:159 , GLY B:163 , GLY B:164 , GLY B:165 , GLY B:166 , MET B:169 , GLU B:201 , LYS B:202 , TYR B:203 , LEU B:204 , HIS B:236 , GLU B:276 , ILE B:287 , LYS B:288 , ILE B:437BINDING SITE FOR RESIDUE ATP B 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1DV2)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:154 -Pro A:155
2Ala A:243 -Pro A:244
3Tyr B:154 -Pro B:155
4Ala B:243 -Pro B:244

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1DV2)

(-) PROSITE Motifs  (3, 6)

Asymmetric Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BCPS50979 Biotin carboxylation domain profile.ACCC_ECOLI1-445
 
  2A:1-445
B:1-445
2CPSASE_1PS00866 Carbamoyl-phosphate synthase subdomain signature 1.ACCC_ECOLI154-168
 
  2A:154-168
B:154-168
3CPSASE_2PS00867 Carbamoyl-phosphate synthase subdomain signature 2.ACCC_ECOLI286-293
 
  2A:286-293
B:286-293
Biological Unit 1 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BCPS50979 Biotin carboxylation domain profile.ACCC_ECOLI1-445
 
  1A:1-445
-
2CPSASE_1PS00866 Carbamoyl-phosphate synthase subdomain signature 1.ACCC_ECOLI154-168
 
  1A:154-168
-
3CPSASE_2PS00867 Carbamoyl-phosphate synthase subdomain signature 2.ACCC_ECOLI286-293
 
  1A:286-293
-
Biological Unit 2 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BCPS50979 Biotin carboxylation domain profile.ACCC_ECOLI1-445
 
  1-
B:1-445
2CPSASE_1PS00866 Carbamoyl-phosphate synthase subdomain signature 1.ACCC_ECOLI154-168
 
  1-
B:154-168
3CPSASE_2PS00867 Carbamoyl-phosphate synthase subdomain signature 2.ACCC_ECOLI286-293
 
  1-
B:286-293

(-) Exons   (0, 0)

(no "Exon" information available for 1DV2)

(-) 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:450
 aligned with ACCC_ECOLI | P24182 from UniProtKB/Swiss-Prot  Length:449

    Alignment length:450
                               1                                                                                                                                                                                                                                                                                                                                                                                                                                                              
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447
           ACCC_ECOLI     - ---MLDKIVIANRGEIALRILRACKELGIKTVAVHSSADRDLKHVLLADETVCIGPAPSVKSYLNIPAIISAAEITGAVAIHPGYGFLSENANFAEQVERSGFIFIGPKAETIRLMGDKVSAIAAMKKAGVPCVPGSDGPLGDDMDKNRAIAKRIGYPVIIKASGGGGGRGMRVVRGDAELAQSISMTRAEAKAAFSNDMVYMEKYLENPRHVEIQVLADGQGNAIYLAERDCSMQRRHQKVVEEAPAPGITPELRRYIGERCAKACVDIGYRGAGTFEFLFENGEFYFIEMNTRIQVEHPVTEMITGVDLIKEQLRIAAGQPLSIKQEEVHVRGHAVECRINAEDPNTFLPSPGKITRFHAPGGFGVRWESHIYAGYTVPPYYDSMIGKLICYGENRDVAIARMKNALQELIIDGIKTNVDLQIRIMNDENFQHGGTNIHYLEKKLGLQ 447
               SCOP domains d1dv2a2 A:1C-114 Biotin carboxylase (BC), N-terminal domain                                                          d1dv2a3 A:115-330 Biotin carboxylase (BC), domain 2                                                                                                                                                                     d1dv2a1 A:331-447 Biotin carboxylase (BC), C-domain                                                                   SCOP domains
               CATH domains ---1dv2A01 A:1-85  [code=3.40.50.20, no name defined]                                   1dv2A02 A:86-130,A:204-444                   1dv2A03 A:131-203 ATP-grasp fold, A domain                               1dv2A02 A:86-130,A:204-444 ATP-grasp fold, B domain                                                                                                                                                                                              --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeee..hhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhh.eeeeee..hhhhh..hhhhhhhhhhhhh..eee........hhhhhhhhhhh..ee...hhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhh..eeeee........eeee.hhhhhhhhhhhhhhhhhhhh....eeeee.....eeeeeeeeee....eeeeeeeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee..eeeeeeee.....hhhhhhhhhh.hhhhhhhhhhh......hhhhh....eeeeeeee...........ee..eee......eeeee......ee......eeeeeeeee.hhhhhhhhhhhhhhhheee....hhhhhhhhhhhhhhhhh....hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---BC  PDB: A:1-445 UniProt: 1-445                                                                                                                                                                                                                                                                                                                                                                                                                              -- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------CPSASE_1       ---------------------------------------------------------------------------------------------------------------------CPSASE_2---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1dv2 A  1C GSHMLDKIVIANRGEIALRILRACKELGIKTVAVHSSADRDLKHVLLADETVCIGPAPSVKSYLNIPAIISAAEITGAVAIHPGYGFLSENANFAEQVERSGFIFIGPKAETIRLMGDKVSAIAAMKKAGVPCVPGSDGPLGDDMDKNRAIAKRIGYPVIIKASGGGGGRGMRVVRGDAELAQSISMTRAEAKAAFSNDMVYMEKYLENPRHVEIQVLADGQGNAIYLAERDCSMQRRHQKVVEEAPAPGITPELRRYIGERCAKACVDIGYRGAGTFEFLFENGEFYFIKMNTRIQVEHPVTEMITGVDLIKEQLRIAAGQPLSIKQEEVHVRGHAVECRINAEDPNTFLPSPGKITRFHAPGGFGVRWESHIYAGYTVPPYYDSMIGKLICYGENRDVAIARMKNALQELIIDGIKTNVDLQIRIMNDENFQHGGTNIHYLEKKLGLQ 447
                            |||      7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447
                            |||                                                                                                                                                                                                                                                                                                                                                                                                                                                               
                           1C||                                                                                                                                                                                                                                                                                                                                                                                                                                                               
                            1B|                                                                                                                                                                                                                                                                                                                                                                                                                                                               
                             1A                                                                                                                                                                                                                                                                                                                                                                                                                                                               

Chain B from PDB  Type:PROTEIN  Length:448
 aligned with ACCC_ECOLI | P24182 from UniProtKB/Swiss-Prot  Length:449

    Alignment length:448
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439        
           ACCC_ECOLI     - -MLDKIVIANRGEIALRILRACKELGIKTVAVHSSADRDLKHVLLADETVCIGPAPSVKSYLNIPAIISAAEITGAVAIHPGYGFLSENANFAEQVERSGFIFIGPKAETIRLMGDKVSAIAAMKKAGVPCVPGSDGPLGDDMDKNRAIAKRIGYPVIIKASGGGGGRGMRVVRGDAELAQSISMTRAEAKAAFSNDMVYMEKYLENPRHVEIQVLADGQGNAIYLAERDCSMQRRHQKVVEEAPAPGITPELRRYIGERCAKACVDIGYRGAGTFEFLFENGEFYFIEMNTRIQVEHPVTEMITGVDLIKEQLRIAAGQPLSIKQEEVHVRGHAVECRINAEDPNTFLPSPGKITRFHAPGGFGVRWESHIYAGYTVPPYYDSMIGKLICYGENRDVAIARMKNALQELIIDGIKTNVDLQIRIMNDENFQHGGTNIHYLEKKLGLQ 447
               SCOP domains d1dv2b2 B:1A-114 Biotin carboxylase (BC), N-terminal domain                                                        d1dv2b3 B:115-330 Biotin carboxylase (BC), domain 2                                                                                                                                                                     d1dv2b1 B:331-447 Biotin carboxylase (BC), C-domain                                                                   SCOP domains
               CATH domains -1dv2B01 B:1-85  [code=3.40.50.20, no name defined]                                   1dv2B02 B:86-130,B:204-444                   1dv2B03 B:131-203 ATP-grasp fold, A domain                               1dv2B02 B:86-130,B:204-444 ATP-grasp fold, B domain                                                                                                                                                                                              --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..hhhhhhhhhhhhhhh..eeeeeee.....hhhhhhh.eeeeee..hhhhh..hhhhhhhhhhhh...eee........hhhhhhhhhhh..ee...hhhhhhhh.hhhhhhhhhhhhh..............hhhhhhhhhhhh..eeeee........eeee....hhhhhhhhhhhhhhhh.....eeeee.....eeeeeeeeee....eeeeeeeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee..eeeeeeee.....hhhhhhhhhh.hhhhhhhhhhh......hhhhh....eeeeeeee...........ee..eee......eeeee......ee......eeeeeeeee.hhhhhhhhhhhhhhhheee....hhhhhhhhhhhhhhhhh....hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -BC  PDB: B:1-445 UniProt: 1-445                                                                                                                                                                                                                                                                                                                                                                                                                              -- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------CPSASE_1       ---------------------------------------------------------------------------------------------------------------------CPSASE_2---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dv2 B  1A HMLDKIVIANRGEIALRILRACKELGIKTVAVHSSADRDLKHVLLADETVCIGPAPSVKSYLNIPAIISAAEITGAVAIHPGYGFLSENANFAEQVERSGFIFIGPKAETIRLMGDKVSAIAAMKKAGVPCVPGSDGPLGDDMDKNRAIAKRIGYPVIIKASGGGGGRGMRVVRGDAELAQSISMTRAEAKAAFSNDMVYMEKYLENPRHVEIQVLADGQGNAIYLAERDCSMQRRHQKVVEEAPAPGITPELRRYIGERCAKACVDIGYRGAGTFEFLFENGEFYFIKMNTRIQVEHPVTEMITGVDLIKEQLRIAAGQPLSIKQEEVHVRGHAVECRINAEDPNTFLPSPGKITRFHAPGGFGVRWESHIYAGYTVPPYYDSMIGKLICYGENRDVAIARMKNALQELIIDGIKTNVDLQIRIMNDENFQHGGTNIHYLEKKLGLQ 447
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439        
                           1A                                                                                                                                                                                                                                                                                                                                                                                                                                                               

   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  (3, 6)

Asymmetric Unit

(-) CATH Domains  (3, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DV2)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ACCC_ECOLI | P24182)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003989    acetyl-CoA carboxylase activity    Catalysis of the reaction: ATP + acetyl-CoA + HCO3- = ADP + phosphate + malonyl-CoA.
    GO:0004075    biotin carboxylase activity    Catalysis of the reaction: ATP + biotin-carboxyl-carrier protein + CO2 = ADP + phosphate + carboxybiotin-carboxyl-carrier protein.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
    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.
    GO:2001295    malonyl-CoA biosynthetic process    The chemical reactions and pathways resulting in the formation of malonyl-CoA, the S-malonyl derivative of coenzyme A.
    GO:0045717    negative regulation of fatty acid biosynthetic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of fatty acids.
cellular component
    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
        ACCC_ECOLI | P241821bnc 1dv1 1k69 2gps 2gpw 2j9g 2v58 2v59 2v5a 2vr1 2w6m 2w6n 2w6o 2w6p 2w6q 2w6z 2w70 2w71 3g8c 3g8d 3jzf 3jzi 3rup 3rv3 3rv4 4hr7

(-) Related Entries Specified in the PDB File

1dv1 STRUCTURE OF BIOTIN CARBOXYLASE (APO)