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(-) Description

Title :  CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE DOMAIN OF ACETYL-COENZYME A CARBOXYLASE FROM SACCHAROMYCES CEREVISIAE
 
Authors :  Y. Shen, S. L. Volrath, S. C. Weatherly, T. D. Elich, L. Tong
Date :  05 Oct 04  (Deposition) - 04 Jan 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Obesity, Diabetes, Fatty Acid Metabolism, Structure-Based Drug Design, Allosteric Inhibition, Polyketide, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Shen, S. L. Volrath, S. C. Weatherly, T. D. Elich, L. Tong
A Mechanism For The Potent Inhibition Of Eukaryotic Acetyl-Coenzyme A Carboxylase By Soraphen A, A Macrocyclic Polyketide Natural Product
Mol. Cell V. 16 881 2004
PubMed-ID: 15610732  |  Reference-DOI: 10.1016/J.MOLCEL.2004.11.034

(-) Compounds

Molecule 1 - ACETYL-COENZYME A CARBOXYLASE
    ChainsA
    EC Number6.4.1.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentBIOTIN CARBOXYLASE DOMAIN, RESIDUES 14-566
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymACC

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1W93)

(-) Sites  (0, 0)

(no "Site" information available for 1W93)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1W93)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:247 -Pro A:248
2Ala A:332 -Pro A:333

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1W93)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BCPS50979 Biotin carboxylation domain profile.ACAC_YEAST58-567  1A:58-566
2CPSASE_1PS00866 Carbamoyl-phosphate synthase subdomain signature 1.ACAC_YEAST247-261  1A:247-261
3CPSASE_2PS00867 Carbamoyl-phosphate synthase subdomain signature 2.ACAC_YEAST377-384  1A:377-384

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YNR016C1YNR016C.1XIV:661377-6546766702ACAC_YEAST1-223322331A:14-566 (gaps)553

(-) 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:549
 aligned with ACAC_YEAST | Q00955 from UniProtKB/Swiss-Prot  Length:2233

    Alignment length:553
                                    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       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563   
           ACAC_YEAST    14 MEYEITNYSERHTELPGHFIGLNTVDKLEESPLRDFVKSHGGHTVISKILIANNGIAAVKEIRSVRKWAYETFGDDRTVQFVAMATPEDLEANAEYIRMADQYIEVPGGTNNNNYANVDLIVDIAERADVDAVWAGWGHASENPLLPEKLSQSKRKVIFIGPPGNAMRSLGDKISSTIVAQSAKVPCIPWSGTGVDTVHVDEKTGLVSVDDDIYQKGCCTSPEDGLQKAKRIGFPVMIKASEGGGGKGIRQVEREEDFIALYHQAANEIPGSPIFIMKLAGRARHLEVQLLADQYGTNISLFGRDCSVQRRHQKIIEEAPVTIAKAETFHEMEKAAVRLGKLVGYVSAGTVEYLYSHDDGKFYFLELNPRLQVEHPTTEMVSGVNLPAAQLQIAMGIPMHRISDIRTLYGMNPHSASEIDFEFKTQDATKKQRRPIPKGHCTACRITSEDPNDGFKPSGGTLHELNFRSSSNVWGYFSVGNNGNIHSFSDSQFGHIFAFGENRQASRKHMVVALKELSIRGDFRTTVEYLIKLLETEDFEDNTITTGWLDDLI 566
               SCOP domains d1w93a2 A:14-183 Acetyl-CoA carboxylase, BC-N subdomain                                                                                                                   d1w93a3 A:184-450 Acetyl-CoA carboxylase, BC-M subdomain                                                                                                                                                                                                                   d1w93a1 A:451-566 Acetyl-CoA carboxylase, BC-C subdomain                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1w93A03 A:231-293 ATP-grasp fold, A domain                     --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............................hhhhhhhhhhh.......eee..hhhhhhhhhhhhhhhhhhhh........eeeehhhhhh..........eeee....hhhhh...hhhhhhhhhhhh..eee...hhhhh.hhhhhh........ee...hhhhhhh..hhhhhhhhhhhh...............ee......ee.hhhhhh.....hhhhhhhhhhhhh..eeee..........eee...hhhhhhhhhhhhhh.....eeee........eeeeeee...eeeeeeee.............ee.....hhhhhhhhhhhhhhhhhhhh..eeeeeeeee......eeeeeee......hhhhhhh...hhhhhhhhhhh......hhhhhhhhh.............................eee..............................eee...eee......eeeee...eeeee.hhhhhhhhhhhhhhhh....----.hhhhhhhhh...........hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------BC  PDB: A:58-566 UniProt: 58-567                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CPSASE_1       -------------------------------------------------------------------------------------------------------------------CPSASE_2-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:14-566 (gaps) UniProt: 1-2233 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Transcript 1
                 1w93 A  14 MEYEITNYSERHTELPGHFIGLNTVDKLEESPLRDFVKSHGGHTVISKILIANNGIAAVKEIRSVRKWAYETFGDDRTVQFVAMATPEDLEANAEYIRMADQYIEVPGGTNNNNYANVDLIVDIAERADVDAVWAGWGHASENPLLPEKLSQSKRKVIFIGPPGNAMRSLGDKISSTIVAQSAKVPCIPWSGTGVDTVHVDEKTGLVSVDDDIYQKGCCTSPEDGLQKAKRIGFPVMIKASEGGGGKGIRQVEREEDFIALYHQAANEIPGSPIFIMKLAGRARHLEVQLLADQYGTNISLFGRDCSVQRRHQKIIEEAPVTIAKAETFHEMEKAAVRLGKLVGYVSAGTVEYLYSHDDGKFYFLELNPRLQVEHPTTEMVSGVNLPAAQLQIAMGIPMHRISDIRTLYGMNPHSASEIDFEFKTQDATKKQRRPIPKGHCTACRITSEDPNDGFKPSGGTLHELNFRSSSNVWGYFSVGNNGNIHSFSDSQFGHIFAFGENRQASRKHMVVALKELSIRG----TVEYLIKLLETEDFEDNTITTGWLDDLI 566
                                    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       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533|    | 543       553       563   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  534  539                           

   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, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1W93)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ACAC_YEAST | Q00955)
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:0042759    long-chain fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of long-chain fatty acids, any fatty acid with a chain length between C13 and C22.
    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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0006998    nuclear envelope organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear envelope.
    GO:0006606    protein import into nucleus    The directed movement of a protein from the cytoplasm to the nucleus.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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    Ala A:332 - Pro A:333   [ RasMol ]  
    Phe A:247 - Pro A:248   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        ACAC_YEAST | Q009551od2 1od4 1uyr 1uys 1uyt 1uyv 1w2x 1w96 3h0j 3h0q 3h0s 3k8x 3pgq 3tv5 3tvu 3tvw 3tz3 4wyo 4wz8 5cs0 5cs4 5csa 5csk 5csl 5ctb 5ctc 5cte 5i6e 5trc

(-) Related Entries Specified in the PDB File

1od2 ACETYL-COA CARBOXYLASE CARBOXYLTRANSFERAS DOMAINE
1od4 ACETYL-COA CARBOXYLASE CARBOXYLTRANSFERASE DOMAIN
1uyr ACETYL-COA CARBOXYLASE CARBOXYLTRANSFERASE DOMAIN IN COMPLEX WITH INHIBITOR DICLOFOP
1uys ACETYL-COA CARBOXYLASE CARBOXYLTRANSFERASE DOMAIN IN COMPLEX WITH INHIBITOR HALOXYFOP
1uyt ACETYL-COA CARBOXYLASE CARBOXYLTRANSFERASE DOMAIN
1uyv ACETYL-COA CARBOXYLASE CARBOXYLTRANSFERASE DOMAIN L1705I/V1967I MUTANT
1w2x CRYSTAL STRUCTURE OF THE CARBOXYLTRANSFERASE DOMAIN OF ACETYL-COENZYME A CARBOXYLASE IN COMPLEX WITH CP-640186