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(-) Description

Title :  CRYSTAL STRUCTURE OF E.COLI BIOTIN CARBOXYLASE IN COMPLEX WITH TWO ADP AND TWO CA IONS
 
Authors :  C. Y. Chou, L. Tong
Date :  05 May 11  (Deposition) - 18 May 11  (Release) - 20 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym./Biol. Unit :  A,B
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, B
    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
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: ACETYL-COA CARBOXYLASE SUBUNIT A, ACC

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1ADP4Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CA4Ligand/IonCALCIUM ION
3CL3Ligand/IonCHLORIDE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:83 , GLU A:87 , GLY A:162 , GLY A:164 , GLY A:165 , ARG A:167 , PHE A:193 , GLN A:237 , LYS A:238 , ASN A:290 , ARG A:292 , GLN A:294 , VAL A:295 , GLU A:296 , ARG A:338 , ASP A:382 , HOH A:459 , HOH A:505 , HOH A:510 , HOH A:531 , HOH A:594 , HOH A:607 , HOH A:619BINDING SITE FOR RESIDUE ADP A 1000
02AC2SOFTWARELYS 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:209 , GLN A:233 , HIS A:236 , GLU A:276 , LEU A:278 , GLU A:288 , ILE A:437 , HOH A:459 , HOH A:518 , HOH A:530 , HOH A:553 , CA A:1004BINDING SITE FOR RESIDUE ADP A 1002
03AC3SOFTWAREGLU A:276 , GLU A:288 , HOH A:530 , HOH A:619 , ADP A:1002BINDING SITE FOR RESIDUE CA A 1004
04AC4SOFTWAREGLU A:87 , GLU A:288 , ASN A:290 , HOH A:486 , HOH A:531 , HOH A:538BINDING SITE FOR RESIDUE CA A 1006
05AC5SOFTWAREARG A:10 , HIS A:370 , TYR A:375 , PRO A:378 , HOH A:863BINDING SITE FOR RESIDUE CL A 1008
06AC6SOFTWARELYS 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:209 , GLN B:233 , HIS B:236 , GLU B:276 , LEU B:278 , ILE B:287 , GLU B:288 , ILE B:437 , HOH B:536 , HOH B:545 , HOH B:609 , HOH B:623 , CA B:1005BINDING SITE FOR RESIDUE ADP B 1001
07AC7SOFTWAREGLY B:83 , GLU B:87 , GLY B:162 , GLY B:164 , GLY B:165 , GLN B:237 , LYS B:238 , ASN B:290 , ARG B:292 , GLN B:294 , VAL B:295 , GLU B:296 , ARG B:338 , ASP B:382 , HOH B:492 , HOH B:536 , HOH B:538 , HOH B:540 , HOH B:544 , HOH B:617 , HOH B:623 , HOH B:808BINDING SITE FOR RESIDUE ADP B 1003
08AC8SOFTWAREGLU B:276 , GLU B:288 , HOH B:545 , HOH B:623 , ADP B:1001BINDING SITE FOR RESIDUE CA B 1005
09AC9SOFTWAREGLU B:87 , GLU B:288 , ASN B:290 , HOH B:492 , HOH B:540 , HOH B:622BINDING SITE FOR RESIDUE CA B 1007
10BC1SOFTWAREARG B:10 , HIS B:370 , TYR B:375BINDING SITE FOR RESIDUE CL B 1009
11BC2SOFTWAREGLY B:11 , HIS B:41 , HIS B:370BINDING SITE FOR RESIDUE CL B 1011

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological 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 3RUP)

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BCPS50979 Biotin carboxylation domain profile.ACCC_ECOLI1-445
 		  2A:1-444
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

(-) Exons   (0, 0)

(no "Exon" information available for 3RUP)

(-) 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:444
 aligned with ACCC_ECOLI | P24182 from UniProtKB/Swiss-Prot  Length:449

    Alignment length:444
                                    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 MLDKIVIANRGEIALRILRACKELGIKTVAVHSSADRDLKHVLLADETVCIGPAPSVKSYLNIPAIISAAEITGAVAIHPGYGFLSENANFAEQVERSGFIFIGPKAETIRLMGDKVSAIAAMKKAGVPCVPGSDGPLGDDMDKNRAIAKRIGYPVIIKASGGGGGRGMRVVRGDAELAQSISMTRAEAKAAFSNDMVYMEKYLENPRHVEIQVLADGQGNAIYLAERDCSMQRRHQKVVEEAPAPGITPELRRYIGERCAKACVDIGYRGAGTFEFLFENGEFYFIEMNTRIQVEHPVTEMITGVDLIKEQLRIAAGQPLSIKQEEVHVRGHAVECRINAEDPNTFLPSPGKITRFHAPGGFGVRWESHIYAGYTVPPYYDSMIGKLICYGENRDVAIARMKNALQELIIDGIKTNVDLQIRIMNDENFQHGGTNIHYLEKKL 444
               SCOP domains d3rupa1 A:1-114 Biotin carboxylase (BC), N-terminal domain                                                        d3rupa2 A:115-330 Biotin carboxylase (BC), domain 2                                                                                                                                                                     d3rupa3 A:331-444 Biotin carboxylase (BC), C-domain                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..hhhhhhhhhhhhhhh..eeeeeee.....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......eeeee......ee......eeeeeeeee.hhhhhhhhhhhhhhhheee....hhhhhhhhhhhhhhhhh....hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) BC  PDB: A:1-444 UniProt: 1-445                                                                                                                                                                                                                                                                                                                                                                                                                              PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------CPSASE_1       ---------------------------------------------------------------------------------------------------------------------CPSASE_2------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3rup A   1 MLDKIVIANRGEIALRILRACKELGIKTVAVHSSADRDLKHVLLADETVCIGPAPSVKSYLNIPAIISAAEITGAVAIHPGYGFLSENANFAEQVERSGFIFIGPKAETIRLMGDKVSAIAAMKKAGVPCVPGSDGPLGDDMDKNRAIAKRIGYPVIIKASGGGGGRGMRVVRGDAELAQSISMTRAEAKAAFSNDMVYMEKYLENPRHVEIQVLADGQGNAIYLAERDCSMQRRHQKVVEEAPAPGITPELRRYIGERCAKACVDIGYRGAGTFEFLFENGEFYFIEMNTRIQVEHPVTEMITGVDLIKEQLRIAAGQPLSIKQEEVHVRGHAVECRINAEDPNTFLPSPGKITRFHAPGGFGVRWESHIYAGYTVPPYYDSMIGKLICYGENRDVAIARMKNALQELIIDGIKTNVDLQIRIMNDENFQHGGTNIHYLEKKL 444
                                    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    


Chain B 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 d3rupb1 B:1-114 Biotin carboxylase (BC), N-terminal domain                                                        d3rupb2 B:115-330 Biotin carboxylase (BC), domain 2                                                                                                                                                                     d3rupb3 B:331-446 Biotin carboxylase (BC), C-domain                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..hhhhhhhhhhhhhhh..eeeeeee.....hhhhhhh.eeeeee..hhhhh..hhhhhhhhhhhhh..eee........hhhhhhhhhhh..ee...hhhhhhhhhhhhhhhhhhhhh..............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: B:1-445 UniProt: 1-445                                                                                                                                                                                                                                                                                                                                                                                                                              - PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------CPSASE_1       ---------------------------------------------------------------------------------------------------------------------CPSASE_2--------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rup B   1 MLDKIVIANRGEIALRILRACKELGIKTVAVHSSADRDLKHVLLADETVCIGPAPSVKSYLNIPAIISAAEITGAVAIHPGYGFLSENANFAEQVERSGFIFIGPKAETIRLMGDKVSAIAAMKKAGVPCVPGSDGPLGDDMDKNRAIAKRIGYPVIIKASGGGGGRGMRVVRGDAELAQSISMTRAEAKAAFSNDMVYMEKYLENPRHVEIQVLADGQGNAIYLAERDCSMQRRHQKVVEEAPAPGITPELRRYIGERCAKACVDIGYRGAGTFEFLFENGEFYFIEMNTRIQVEHPVTEMITGVDLIKEQLRIAAGQPLSIKQEEVHVRGHAVECRINAEDPNTFLPSPGKITRFHAPGGFGVRWESHIYAGYTVPPYYDSMIGKLICYGENRDVAIARMKNALQELIIDGIKTNVDLQIRIMNDENFQHGGTNIHYLEKKLGL 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, 6)

Asymmetric/Biological 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 3RUP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3RUP)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological 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 | P24182: 1bnc 1dv1 1dv2 1k69 2gps 2gpw 2j9g 2v58 2v59 2v5a 2vr1 2w6m 2w6n 2w6o 2w6p 2w6q 2w6z 2w70 2w71 3g8c 3g8d 3jzf 3jzi 3rv3 3rv4 4hr7

(-) Related Entries Specified in the PDB File

3rv3 3rv4