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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BIOTIN PROTEIN LIGASE (MUTATIONS R48A AND K111A) AND BIOTIN CARBOXYL CARRIER PROTEIN COMPLEX FROM PYROCOCCUS HORIKOSHII OT3
 
Authors :  B. Bagautdinov, Y. Matsuura, S. Bagautdinova, N. Kunishima, Riken St Genomics/Proteomics Initiative (Rsgi)
Date :  16 Mar 07  (Deposition) - 18 Mar 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Biotinylation, Dimer, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Bagautdinov, Y. Matsuura, S. Bagautdinova, N. Kunishima
Protein Biotinylation Visualized By A Complex Structure Of Biotin Protein Ligase With A Substrate
J. Biol. Chem. V. 283 14739 2008
PubMed-ID: 18372281  |  Reference-DOI: 10.1074/JBC.M709116200

(-) Compounds

Molecule 1 - 235AA LONG HYPOTHETICAL BIOTIN--[ACETYL-COA-CARBOXYLASE] LIGASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: (DE3)RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BPL
    Mutation: YES
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3
    Synonym: BPL
 
Molecule 2 - 149AA LONG HYPOTHETICAL METHYLMALONYL-COA DECARBOXYLASE GAMMA CHAIN
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: (DE3)RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 77-149
    Gene: BCCP
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3
    Synonym: BCCP

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1ADN2Ligand/IonADENOSINE
2BTN3Ligand/IonBIOTIN
3GOL1Ligand/IonGLYCEROL
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1ADN1Ligand/IonADENOSINE
2BTN2Ligand/IonBIOTIN
3GOL-1Ligand/IonGLYCEROL
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1ADN1Ligand/IonADENOSINE
2BTN1Ligand/IonBIOTIN
3GOL1Ligand/IonGLYCEROL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:210 , ARG A:212 , TYR A:227 , ASP B:184 , MET C:114 , LYS C:115BINDING SITE FOR RESIDUE BTN C 1400
2AC2SOFTWARESER A:21 , THR A:22 , ASN A:23 , GLN A:42 , GLY A:45 , HIS A:46 , GLY A:47 , ALA A:48 , TRP A:53 , LEU A:62 , ASN A:103 , ASP A:104 , GLY A:114 , ILE A:128 , GLY A:129BINDING SITE FOR RESIDUE BTN A 1401
3AC3SOFTWARESER B:21 , THR B:22 , ASN B:23 , GLN B:42 , GLY B:45 , HIS B:46 , GLY B:47 , ALA B:48 , TRP B:53 , LEU B:62 , ASN B:103 , ASP B:104 , GLY B:114 , ILE B:128 , GLY B:129BINDING SITE FOR RESIDUE BTN B 1402
4AC4SOFTWAREARG A:51 , LYS A:52 , TRP A:53 , GLU A:54 , ASN A:131 , PRO A:137 , ALA A:140BINDING SITE FOR RESIDUE ADN A 2001
5AC5SOFTWAREARG B:51 , LYS B:52 , TRP B:53 , GLU B:54 , ASN B:131 , ALA B:140BINDING SITE FOR RESIDUE ADN B 2002
6AC6SOFTWAREGLN A:17 , GLU A:18 , ARG B:11 , ARG B:12 , GLU B:32BINDING SITE FOR RESIDUE GOL B 3001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Trp A:101 -Pro A:102
2Trp B:101 -Pro B:102

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2EJF)

(-) Exons   (0, 0)

(no "Exon" information available for 2EJF)

(-) 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:235
 aligned with O57883_PYRHO | O57883 from UniProtKB/TrEMBL  Length:235

    Alignment length:235
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230     
         O57883_PYRHO     1 MLGLKTSIIGRRVIYFQEITSTNEFAKTSYLEEGTVIVADKQTMGHGRLNRKWESPEGGLWLSIVLSPKVPQKDLPKIVFLGAVGVVETLKEFSIDGRIKWPNDVLVNYKKIAGVLVEGKGDKIVLGIGLNVNNKVPNGATSMKLELGSEVPLLSVFRSLITNLDRLYLNFLKNPMDILNLVRDNMILGVRVKILGDGSFEGIAEDIDDFGRLIIRLDSGEVKKVIYGDVSLRFL 235
               SCOP domains d2ejfa2 A:1-188 Biotin--[acetyl-CoA-carboxylase] ligase catalytic domain                                                                                                                    d2ejfa1 A:189-235                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeee.hhhhhhhhh......eeeeeee.................eeeeeee....hhhhhhhhhhhhhhhhhhhhhhh....eee...eeee..eeeeeeeeeee..eeeeeeee...........hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.....eeeeee....eeeeeeee.....eeee.....eeee.....eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ejf A   1 MLGLKTSIIGRRVIYFQEITSTNEFAKTSYLEEGTVIVADKQTMGHGALNRKWESPEGGLWLSIVLSPKVPQKDLPKIVFLGAVGVVETLKEFSIDGRIKWPNDVLVNYKAIAGVLVEGKGDKIVLGIGLNVNNKVPNGATSMKLELGSEVPLLSVFRSLITNLDRLYLNFLKNPMDILNLVRDNMILGVRVKILGDGSFEGIAEDIDDFGRLIIRLDSGEVKKVIYGDVSLRFL 235
                                    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:227
 aligned with O57883_PYRHO | O57883 from UniProtKB/TrEMBL  Length:235

    Alignment length:231
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230 
         O57883_PYRHO     1 MLGLKTSIIGRRVIYFQEITSTNEFAKTSYLEEGTVIVADKQTMGHGRLNRKWESPEGGLWLSIVLSPKVPQKDLPKIVFLGAVGVVETLKEFSIDGRIKWPNDVLVNYKKIAGVLVEGKGDKIVLGIGLNVNNKVPNGATSMKLELGSEVPLLSVFRSLITNLDRLYLNFLKNPMDILNLVRDNMILGVRVKILGDGSFEGIAEDIDDFGRLIIRLDSGEVKKVIYGDVS 231
               SCOP domains d2ejfb2 B:1-188 Biotin--[acetyl-CoA-carboxylase] ligase catalytic domain                                                                                                                    d2ejfb1     B:189-231                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeee.hhhhhhhhh......eeeeeee....hhhhh........eeeeeee....hhhhhhhhhhhhhhhhhhhhhhh....eee...eeee..eeeeeeeeeee..eeeeeeee...........hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh...eeee..----.eeeeeee.....eeeee...eeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ejf B   1 MLGLKTSIIGRRVIYFQEITSTNEFAKTSYLEEGTVIVADKQTMGHGALNRKWESPEGGLWLSIVLSPKVPQKDLPKIVFLGAVGVVETLKEFSIDGRIKWPNDVLVNYKAIAGVLVEGKGDKIVLGIGLNVNNKVPNGATSMKLELGSEVPLLSVFRSLITNLDRLYLNFLKNPMDILNLVRDNMILGVRVKIL----FEGIAEDIDDFGRLIIRLDSGEVKKVIYGDVS 231
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    |  200       210       220       230 
                                                                                                                                                                                                                            195  200                               


Chain C from PDB  Type:PROTEIN  Length:69
 aligned with O59021_PYRHO | O59021 from UniProtKB/TrEMBL  Length:149

    Alignment length:69
                                    90       100       110       120       130       140         
         O59021_PYRHO    81 NVVSAPMPGKVLRVLVRVGDRVRVGQGLLVLEAMKMENEIPSPRDGVVKRILVKEGEAVDTGQPLIELG 149
               SCOP domains --------------------------------------------------------------------- SCOP domains
               CATH domains 2ejfC00 C:81-149  [code=2.40.50.100, no name defined]                 CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....eeeeee......ee....eeeeee....eeeee....eeeeee......ee....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 2ejf C  81 NVVSAPMPGKVLRVLVRVGDRVRVGQGLLVLEAMKMENEIPSPRDGVVKRILVKEGEAVDTGQPLIELG 149
                                    90       100       110       120       130       140         


Chain D from PDB  Type:PROTEIN  Length:69
 aligned with O59021_PYRHO | O59021 from UniProtKB/TrEMBL  Length:149

    Alignment length:69
                                    90       100       110       120       130       140         
         O59021_PYRHO    81 NVVSAPMPGKVLRVLVRVGDRVRVGQGLLVLEAMKMENEIPSPRDGVVKRILVKEGEAVDTGQPLIELG 149
               SCOP domains --------------------------------------------------------------------- SCOP domains
               CATH domains 2ejfD00 D:81-149  [code=2.40.50.100, no name defined]                 CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....eeeeee......ee....eeeeeee..eeeeee....eeeeee......ee....eeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 2ejf D  81 NVVSAPMPGKVLRVLVRVGDRVRVGQGLLVLEAMKMENEIPSPRDGVVKRILVKEGEAVDTGQPLIELG 149
                                    90       100       110       120       130       140
   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  (2, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2EJF)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (O57883_PYRHO | O57883)
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: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: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).

Chain C,D   (O59021_PYRHO | O59021)

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 Databases and Analysis Tools

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  2ejf
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  O57883_PYRHO | O57883
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  O59021_PYRHO | O59021
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 Related Entries

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

UniProtKB/TrEMBL
        O57883_PYRHO | O57883: 1wnl 1wpy 1wq7 1wqw 1x01 2deq 2djz 2dkg 2dth 2dti 2dto 2dve 2dxt 2dxu 2dz9 2dzc 2e10 2e1h 2e41 2e64 2e65 2ejg 2fyk 2hni 2zgw
        O59021_PYRHO | O59021: 2d5d 2ejg 2evb

(-) Related Entries Specified in the PDB File

2ejg THE SAME BCCP PROTEIN AND BPL (MUTATIONS R48A) COMPLEX RELATED ID: PHO001000147.25 RELATED DB: TARGETDB