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(-) Description

Title :  BIOTIN PROTEIN LIGASE R40G MUTANT FROM AQUIFEX AEOLICUS IN COMPLEX WITH BIOTIN
 
Authors :  C. M. Tron, I. W. Mcnae, M. D. Walkinshaw, R. L. Baxter, D. J. Campopiano
Date :  10 Sep 08  (Deposition) - 09 Jun 09  (Release) - 09 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Protein Biotin Complex, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. M. Tron, I. W. Mcnae, M. Nutley, D. J. Clarke, A. Cooper, M. D. Walkinshaw, R. L. Baxter, D. J. Campopiano
Structural And Functional Studies Of The Biotin Protein Ligase From Aquifex Aeolicus Reveal A Critical Role For A Conserved Residue In Target Specificity
J. Mol. Biol. V. 387 129 2009
PubMed-ID: 19385043
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BIOTIN [ACETYL-COA-CARBOXYLASE] LIGASE
    Chains: A, B
    EC Number: 6.3.4.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Synonym: BIOTIN PROTEIN LIGASE

 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  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1BTN2Ligand/IonBIOTIN
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1BTN1Ligand/IonBIOTIN
2SO43Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1BTN1Ligand/IonBIOTIN
2SO41Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:13 , THR A:14 , GLN A:15 , GLN A:34 , GLY A:37 , ARG A:38 , GLY A:40 , LEU A:46 , PHE A:54 , SER A:55 , ASP A:96 , LYS A:103 , GLY A:106 , VAL A:107 , LEU A:108 , ILE A:120 , HOH A:1036BINDING SITE FOR RESIDUE BTN A 1001
2AC2SOFTWARELYS A:92 , ASP A:96 , SER A:229 , LEU A:230 , ARG A:231 , LYS B:192BINDING SITE FOR RESIDUE SO4 A 1002
3AC3SOFTWAREGLU A:222 , ILE A:223 , LEU A:224 , SER A:225 , PHE A:228 , HOH A:1018BINDING SITE FOR RESIDUE SO4 A 1003
4AC4SOFTWARELYS A:113 , ASN A:125 , ASP A:149 , ARG A:150 , HOH A:1014BINDING SITE FOR RESIDUE SO4 A 1004
5AC5SOFTWARESER B:13 , THR B:14 , GLN B:15 , GLN B:34 , GLY B:37 , ARG B:38 , GLY B:40 , LEU B:46 , SER B:55 , ASP B:96 , LYS B:103 , GLY B:106 , ILE B:120 , GLY B:121BINDING SITE FOR RESIDUE BTN B 1001
6AC6SOFTWARELYS B:61 , ASN B:125 , TRP B:148 , ARG B:150 , HOH B:1012 , HOH B:1034BINDING SITE FOR RESIDUE SO4 B 1002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Trp A:93 -Pro A:94
2Trp B:93 -Pro B:94

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EFR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3EFR)

(-) Exons   (0, 0)

(no "Exon" information available for 3EFR)

(-) 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:233
 aligned with O66837_AQUAE | O66837 from UniProtKB/TrEMBL  Length:233

    Alignment length:233
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230   
         O66837_AQUAE     1 MFKNLIWLKEVDSTQERLKEWNVSYGTALVADRQTKGRGRLGRKWLSQEGGLYFSFLLNPKEFENLLQLPLVLGLSVSEALEEITEIPFSLKWPNDVYFQEKKVSGVLCELSKDKLIVGIGINVNQREIPEEIKDRATTLYEITGKDWDRKEVLLKVLKRISENLKKFKEKSFKEFKGKIESKMLYLGEEVKLLGEGKITGKLVGLSEKGGALILTEEGIKEILSGEFSLRRS 233
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....hhhhhhhhh.....eeeee............hhhhh..eeeeeeee........hhhhhhhhhhhhhhhhhhhh...eee...eeee..eeeeeeeeeee..eeeeeeeee...............hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.......eeeee...eeeeeeeee.....eeeee..eeeee.....eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3efr A   1 MFKNLIWLKEVDSTQERLKEWNVSYGTALVADRQTKGRGGLGRKWLSQEGGLYFSFLLNPKEFENLLQLPLVLGLSVSEALEEITEIPFSLKWPNDVYFQEKKVSGVLRELSKDKLIVGIGINVNQREIPEEIKDRATTLYEITGKDWDRKEVLLKVLKRISENLKKFKEKSFKEFKGKIESKMLYLGEEVKLLGEGKITGKLVGLSEKGGALILTEEGIKEILSGEFSLRRS 233
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230   


Chain B from PDB  Type:PROTEIN  Length:233
 aligned with O66837_AQUAE | O66837 from UniProtKB/TrEMBL  Length:233

    Alignment length:233
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230   
         O66837_AQUAE     1 MFKNLIWLKEVDSTQERLKEWNVSYGTALVADRQTKGRGRLGRKWLSQEGGLYFSFLLNPKEFENLLQLPLVLGLSVSEALEEITEIPFSLKWPNDVYFQEKKVSGVLCELSKDKLIVGIGINVNQREIPEEIKDRATTLYEITGKDWDRKEVLLKVLKRISENLKKFKEKSFKEFKGKIESKMLYLGEEVKLLGEGKITGKLVGLSEKGGALILTEEGIKEILSGEFSLRRS 233
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....hhhhhhhhh......eeee............hhhhh..eeeeeeeehhhhh...hhhhhhhhhhhhhhhhhhhh...eee...eeee..eeeeeeeeeee..eeeeeeeee......hhhhh....hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.......eeeee...eeeeeeeee.....eeeee..eeeee.....eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3efr B   1 MFKNLIWLKEVDSTQERLKEWNVSYGTALVADRQTKGRGGLGRKWLSQEGGLYFSFLLNPKEFENLLQLPLVLGLSVSEALEEITEIPFSLKWPNDVYFQEKKVSGVLRELSKDKLIVGIGINVNQREIPEEIKDRATTLYEITGKDWDRKEVLLKVLKRISENLKKFKEKSFKEFKGKIESKMLYLGEEVKLLGEGKITGKLVGLSEKGGALILTEEGIKEILSGEFSLRRS 233
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
   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  (0, 0)

(no "SCOP Domain" information available for 3EFR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (O66837_AQUAE | O66837)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004077    biotin-[acetyl-CoA-carboxylase] ligase activity    Catalysis of the reaction: ATP + biotin + apo-(acetyl-CoA:carbon-dioxide ligase (ADP forming)) = AMP + diphosphate + (acetyl-CoA:carbon-dioxide ligase (ADP forming)).
    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: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:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).

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 Related Entries

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

UniProtKB/TrEMBL
        O66837_AQUAE | O66837: 2eay 3efs 3fjp

(-) Related Entries Specified in the PDB File

1wpy 2dto 2eay 3efs