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(-) Description

Title :  CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE FROM PSEUDOMONAS AERUGINOSA COMPLEXED WITH AMPCP
 
Authors :  I. Mochalkin
Date :  13 Mar 08  (Deposition) - 09 Sep 08  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.41
Chains :  Asym./Biol. Unit :  A
Keywords :  Nucleotide-Binding, Fatty Acid Biosynthesis, Lipid Synthesis, Atp- Grasp Domain, Biotin Carboxylase, Ligase, Biotin, Bacteria, Atp- Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. Mochalkin, J. R. Miller, A. Evdokimov, S. Lightle, C. Yan, C. K. Stover, G. L. Waldrop
Structural Evidence For Substrate-Induced Synergism And Half-Sites Reactivity In Biotin Carboxylase.
Protein Sci. V. 17 1706 2008
PubMed-ID: 18725455  |  Reference-DOI: 10.1110/PS.035584.108

(-) Compounds

Molecule 1 - BIOTIN CARBOXYLASE
    ChainsA
    EC Number6.3.4.14
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificPSEUDOMONAS AERUGINOSA
    Organism Taxid287
    SynonymACETYL-COA CARBOXYLASE SUBUNIT A, ACC

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1AP21Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2MG1Ligand/IonMAGNESIUM ION
3SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:116 , ILE A:157 , LYS A:159 , GLY A:163 , GLY A:164 , GLY A:165 , GLY A:166 , MET A:169 , GLU A:201 , LYS A:202 , PHE A:203 , LEU A:204 , HIS A:209 , GLN A:233 , HIS A:236 , GLU A:276 , LEU A:278 , GLU A:288 , ILE A:437 , MG A:1449 , HOH A:2092 , HOH A:2231BINDING SITE FOR RESIDUE AP2 A1448
2AC2SOFTWAREGLU A:276 , GLU A:288 , AP2 A:1448 , HOH A:2133 , HOH A:2139BINDING SITE FOR RESIDUE MG A1449
3AC3SOFTWAREGLU A:87 , MET A:113 , GLY A:114 , GLY A:163 , GLU A:288 , MET A:289 , HOH A:2140BINDING SITE FOR RESIDUE SO4 A1450

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VQD)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:154 -Pro A:155
2Ala A:243 -Pro A:244

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VQD)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BCPS50979 Biotin carboxylation domain profile.ACCC_PSEAE1-445  1A:1-445
2CPSASE_1PS00866 Carbamoyl-phosphate synthase subdomain signature 1.ACCC_PSEAE154-168  1A:154-168
3CPSASE_2PS00867 Carbamoyl-phosphate synthase subdomain signature 2.ACCC_PSEAE286-293  1A:286-293

(-) Exons   (0, 0)

(no "Exon" information available for 2VQD)

(-) 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:447
 aligned with ACCC_PSEAE | P37798 from UniProtKB/Swiss-Prot  Length:449

    Alignment length:447
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       
           ACCC_PSEAE     1 MLEKVLIANRGEIALRILRACKELGIKTVAVHSTADRELMHLSLADESVCIGPAPATQSYLQIPAIIAAAEVTGATAIHPGYGFLAENADFAEQIERSGFTFVGPTAEVIRLMGDKVSAKDAMKRAGVPTVPGSDGPLPEDEETALAIAREVGYPVIIKAAGGGGGRGMRVVYDESELIKSAKLTRTEAGAAFGNPMVYLEKFLTNPRHVEVQVLSDGQGNAIHLGDRDCSLQRRHQKVIEEAPAPGIDEKARQEVFARCVQACIEIGYRGAGTFEFLYENGRFYFIEMNTRVQVEHPVSEMVTGVDIVKEMLRIASGEKLSIRQEDVVIRGHALECRINAEDPKTFMPSPGKVKHFHAPGGNGVRVDSHLYSGYSVPPNYDSLVGKVITYGADRDEALARMRNALDELIVDGIKTNTELHKDLVRDAAFCKGGVNIHYLEKKLGMD 447
               SCOP domains d2vqda1 A:1-114 automated matches                                                                                 d2vqda2 A:115-330 automated matches                                                                                                                                                                                     d2vqda3 A:331-447 automated matches                                                                                   SCOP domains
               CATH domains 2vqdA01 A:1-85  [code=3.40.50.20, no name defined]                                   2vqdA02 A:86-130,A:204-444                   2vqdA03 A:131-203 ATP-grasp fold, A domain                               2vqdA02 A:86-130,A:204-444 ATP-grasp fold, B domain                                                                                                                                                                                              --- CATH domains
               Pfam domains CPSase_L_chain-2vqdA03 A:1-110                                                                                ----CPSase_L_D2-2vqdA01 A:115-324                                                                                                                                                                                     -----------Biotin_carb_C-2vqdA02 A:336-441                                                                           ------ Pfam domains
         Sec.struct. author ...eeee..hhhhhhhhhhhhhhh..eeeeeee.hhh.hhhhhhh.eeeeee..hhhhh..hhhhhhhhhhhhh..eee........hhhhhhhhhhh..ee...hhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhh..eeeee........eeee.hhhhhhhhhhhhhhhhhhhhh...eeeee.....eeeeeeeeee....eeeeeeee...ee..ee.eeee.....hhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee..eeeeeeee.....hhhhhhhhhh.hhhhhhhhhhh......hhhhh....eeeeeeee...........eee.eee......eeeee.....eee......eeeeeeeee.hhhhhhhhhhhhhhhheee....hhhhhhhhh.hhhhhhh....hhhhhhhh.. 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
                 2vqd A   1 MLEKVLIANRGEIALRILRACKELGIKTVAVHSTADRELMHLSLADESVCIGPAPATQSYLQIPAIIAAAEVTGATAIHPGYGFLAENADFAEQIERSGFTFVGPTAEVIRLMGDKVSAKDAMKRAGVPTVPGSDGPLPEDEETALAIAREVGYPVIIKAAGGGGGRGMRVVYDESELIKSAKLTRTEAGAAFGNPMVYLEKFLTNPRHVEVQVLSDGQGNAIHLGDRDCSLQRRHQKVIEEAPAPGIDEKARQEVFARCVQACIEIGYRGAGTFEFLYENGRFYFIEMNTRVQVEHPVSEMVTGVDIVKEMLRIASGEKLSIRQEDVVIRGHALECRINAEDPKTFMPSPGKVKHFHAPGGNGVRVDSHLYSGYSVPPNYDSLVGKVITYGADRDEALARMRNALDELIVDGIKTNTELHKDLVRDAAFCKGGVNIHYLEKKLGMD 447
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       

   Legend:   → Mismatch (orange background)
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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

(-) CATH Domains  (3, 3)

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

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ACCC_PSEAE | P37798)
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.
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ACCC_PSEAE | P377982c00

(-) Related Entries Specified in the PDB File

2c00 CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE FROM PSEUDOMONAS AERUGINOSA IN APO FORM
2j9g CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE FROM E. COLI IN COMPLEX WITH AMPPNP AND ADP
2vpq CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE FROM S. AUREUS COMPLEXED WITH AMPPNP
2vr1 CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE FROM E. COLI IN COMPLEX WITH ATP ANALOG, ADPCF2P.