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(-) Description

Title :  CRYSTAL STRUCTURE OF E.COLI BIOTIN CARBOXYLASE R16E MUTANT IN COMPLEX WITH MG-ADP AND BICARBONATE
 
Authors :  C. Y. Chou, L. Tong
Date :  05 May 11  (Deposition) - 18 May 11  (Release) - 20 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Y. Chou, L. Tong
Structural And Biochemical Studies On The Regulation Of Biotin Carboxylase By Substrate Inhibition And Dimerization
J. Biol. Chem. V. 286 24417 2011
PubMed-ID: 21592965  |  Reference-DOI: 10.1074/JBC.M111.220517

(-) Compounds

Molecule 1 - BIOTIN CARBOXYLASE
    Chains: A
    EC Number: 6.3.4.14, 6.4.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ACCC, FABG, B3256, JW3224
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: ACETYL-COA CARBOXYLASE SUBUNIT A, ACC

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 10)

Asymmetric Unit (8, 10)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2BCT1Ligand/IonBICARBONATE ION
3CL2Ligand/IonCHLORIDE ION
4CS1Ligand/IonCESIUM ION
5GOL1Ligand/IonGLYCEROL
6MG1Ligand/IonMAGNESIUM ION
7MOH1Ligand/IonMETHANOL
8NA2Ligand/IonSODIUM ION
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2BCT2Ligand/IonBICARBONATE ION
3CL-1Ligand/IonCHLORIDE ION
4CS-1Ligand/IonCESIUM ION
5GOL2Ligand/IonGLYCEROL
6MG-1Ligand/IonMAGNESIUM ION
7MOH2Ligand/IonMETHANOL
8NA-1Ligand/IonSODIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:116 , ILE A:157 , LYS A:159 , 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:209 , GLN A:233 , HIS A:236 , GLU A:276 , LEU A:278 , ILE A:287 , GLU A:288 , ILE A:437 , HOH A:551 , HOH A:813 , MG A:1004 , GOL A:1014BINDING SITE FOR RESIDUE ADP A 1000
2AC2SOFTWAREGLU A:276 , GLU A:288 , HOH A:551 , HOH A:673 , ADP A:1000BINDING SITE FOR RESIDUE MG A 1004
3AC3SOFTWARELYS A:238 , ARG A:292 , GLN A:294 , VAL A:295 , GLU A:296 , ARG A:338 , HOH A:536BINDING SITE FOR RESIDUE BCT A 1006
4AC4SOFTWAREMET A:113 , GLU A:288 , MET A:289 , HOH A:547 , HOH A:596BINDING SITE FOR RESIDUE CS A 1008
5AC5SOFTWAREASN A:345 , PHE A:347 , ASN A:429 , GLY A:433BINDING SITE FOR RESIDUE CL A 1010
6AC6SOFTWAREGLN A:407 , LEU A:409 , HOH A:470BINDING SITE FOR RESIDUE NA A 1012
7AC7SOFTWARETYR A:203 , GLN A:233 , ARG A:235 , HIS A:236 , ILE A:437 , HIS A:438 , GLU A:441 , HOH A:707 , ADP A:1000BINDING SITE FOR RESIDUE GOL A 1014
8AC8SOFTWAREVAL A:377 , PRO A:378 , ASP A:382 , HOH A:671BINDING SITE FOR RESIDUE NA A 450
9AC9SOFTWAREHIS A:79 , GLY A:81 , ILE A:293 , GLN A:312 , HOH A:478BINDING SITE FOR RESIDUE CL A 451

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RV4)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric 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 3RV4)

(-) PROSITE Motifs  (3, 3)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3RV4)

(-) 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:446
 aligned with ACCC_ECOLI | P24182 from UniProtKB/Swiss-Prot  Length:449

    Alignment length:446
                                    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_ECOLI     1 MLDKIVIANRGEIALRILRACKELGIKTVAVHSSADRDLKHVLLADETVCIGPAPSVKSYLNIPAIISAAEITGAVAIHPGYGFLSENANFAEQVERSGFIFIGPKAETIRLMGDKVSAIAAMKKAGVPCVPGSDGPLGDDMDKNRAIAKRIGYPVIIKASGGGGGRGMRVVRGDAELAQSISMTRAEAKAAFSNDMVYMEKYLENPRHVEIQVLADGQGNAIYLAERDCSMQRRHQKVVEEAPAPGITPELRRYIGERCAKACVDIGYRGAGTFEFLFENGEFYFIEMNTRIQVEHPVTEMITGVDLIKEQLRIAAGQPLSIKQEEVHVRGHAVECRINAEDPNTFLPSPGKITRFHAPGGFGVRWESHIYAGYTVPPYYDSMIGKLICYGENRDVAIARMKNALQELIIDGIKTNVDLQIRIMNDENFQHGGTNIHYLEKKLGL 446
               SCOP domains d3rv4a1 A:1-114 Biotin carboxylase (BC), N-terminal domain                                                        d3rv4a2 A:115-330 Biotin carboxylase (BC), domain 2                                                                                                                                                                     d3rv4a3 A:331-446 Biotin carboxylase (BC), C-domain                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains CPSase_L_chain-3rv4A03 A:1-110                                                                                ----CPSase_L_D2-3rv4A01 A:115-324                                                                                                                                                                                     -----------Biotin_carb_C-3rv4A02 A:336-441                                                                           ----- Pfam domains
         Sec.struct. author ...eeee..hhhhhhhhhhhhhhhh.eeeeeee.hhh.hhhhhhh.eeeeee..hhhhh..hhhhhhhhhhhhh..eee........hhhhhhhhhhh..ee...hhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhh..eeeee........eeee.hhhhhhhhhhhhhhhhhhhhh...eeeee.....eeeeeeeeee....eeeeeeeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee..eeeeeeee.....hhhhhhhhhh.hhhhhhhhhhh......hhhhh....eeeeeeee...........ee..eee......eeee.......ee......eeeeeeeee.hhhhhhhhhhhhhhhheee....hhhhhhhhhhhhhhhhh....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
                 3rv4 A   1 MLDKIVIANRGEIALEILRACKELGIKTVAVHSSADRDLKHVLLADETVCIGPAPSVKSYLNIPAIISAAEITGAVAIHPGYGFLSENANFAEQVERSGFIFIGPKAETIRLMGDKVSAIAAMKKAGVPCVPGSDGPLGDDMDKNRAIAKRIGYPVIIKASGGGGGRGMRVVRGDAELAQSISMTRAEAKAAFSNDMVYMEKYLENPRHVEIQVLADGQGNAIYLAERDCSMQRRHQKVVEEAPAPGITPELRRYIGERCAKACVDIGYRGAGTFEFLFENGEFYFIEMNTRIQVEHPVTEMITGVDLIKEQLRIAAGQPLSIKQEEVHVRGHAVECRINAEDPNTFLPSPGKITRFHAPGGFGVRWESHIYAGYTVPPYYDSMIGKLICYGENRDVAIARMKNALQELIIDGIKTNVDLQIRIMNDENFQHGGTNIHYLEKKLGL 446
                                    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)
  - → 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 Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RV4)

(-) Pfam Domains  (3, 3)

Asymmetric Unit
(-)
Clan: ATP-grasp (83)
(-)
Clan: no clan defined [family: Biotin_carb_C] (23)
(-)
Clan: no clan defined [family: CPSase_L_chain] (25)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A   (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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  3rv4
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 Related Entries

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

UniProtKB/Swiss-Prot
        ACCC_ECOLI | P24182: 1bnc 1dv1 1dv2 1k69 2gps 2gpw 2j9g 2v58 2v59 2v5a 2vr1 2w6m 2w6n 2w6o 2w6p 2w6q 2w6z 2w70 2w71 3g8c 3g8d 3jzf 3jzi 3rup 3rv3 4hr7

(-) Related Entries Specified in the PDB File

3rup 3rv3