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(-) Description

Title :  CRYSTAL STRUCTURE OF BIOTIN PROTEIN LIGASE FROM PYROCOCCUS HORIKOSHII OT3 IN COMPLEX WITH BIOTINYL-5'-AMP, PYROPHOSPHATE AND MG(2+)
 
Authors :  B. Bagautdinov, N. Kunishima, Riken Structural Genomics/Proteomi Initiative (Rsgi)
Date :  11 Apr 06  (Deposition) - 11 Oct 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Biotin Biosynthesis, 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, N. Kunishima
Ligand Structures Of Biotin Protein Ligase From Pyrococcus Horikoshii Ot3
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 235AA LONG HYPOTHETICAL BIOTIN-[ACETYL-COA-CARBOXYLASE] LIGASE
    Chains: A, B
    EC Number: 6.3.4.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 11A
    Expression System Strain: (DE3)RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BIRA
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3
    Synonym: BIOTIN PROTEIN LIGASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1BT52Ligand/IonBIOTINYL-5-AMP
2MG1Ligand/IonMAGNESIUM ION
3POP1Ligand/IonPYROPHOSPHATE 2-

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:103 , ASP A:104 , POP A:4001 , BT5 B:1301BINDING SITE FOR RESIDUE MG A 1001
2AC2SOFTWARESER A:21 , THR A:22 , ASN A:23 , GLN A:42 , GLY A:45 , HIS A:46 , GLY A:47 , ARG A:48 , ARG A:51 , LYS A:52 , TRP A:53 , GLU A:54 , LEU A:62 , ASN A:103 , ASP A:104 , LYS A:111 , GLY A:114 , ILE A:128 , GLY A:129 , ASN A:131 , ALA A:140 , MG A:1001 , POP A:4001BINDING SITE FOR RESIDUE BT5 B 1301
3AC3SOFTWARESER B:21 , THR B:22 , ASN B:23 , GLN B:42 , GLY B:45 , HIS B:46 , GLY B:47 , ARG B:48 , ARG B:51 , LYS B:52 , TRP B:53 , GLU B:54 , LEU B:62 , ASN B:103 , ASP B:104 , LYS B:111 , GLY B:114 , LEU B:116 , ILE B:128 , GLY B:129 , ASN B:131 , PRO B:137 , ALA B:140 , HOH B:1306 , HOH B:1430 , HOH B:1476BINDING SITE FOR RESIDUE BT5 B 1302
4AC4SOFTWAREARG A:48 , ARG A:51 , LYS A:100 , ASN A:103 , ASP A:104 , LYS A:111 , SER A:231 , LEU A:232 , MG A:1001 , HOH A:4036 , BT5 B:1301BINDING SITE FOR RESIDUE POP A 4001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological 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 2DKG)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2DKG)

(-) 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: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 d2dkga2 A:1-188 Biotin--[acetyl-CoA-carboxylase] ligase catalytic domain                                                                                                                    d2dkga1 A:189-235                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeee.hhhhhhhhh......eeeeeee.................eeeeeee.......hhhhhhhhhhhhhhhhhhhh....eee...eeee..eeeeeeeeee....eeeeeee...........hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh...eeeeee...eeeeeeeee.....eeee.....eeee.....eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dkg A   1 MLGLKTSIIGRRVIYFQEITSTNEFAKTSYLEEGTVIVADKQTMGHGRLNRKWESPEGGLWLSIVLSPKVPQKDLPKIVFLGAVGVVETLKEFSIDGRIKWPNDVLVNYKKIAGVLVEGKGDKIVLGIGLNVNNKVPNGATSMKLELGSEVPLLSVFRSLITNLDRLYLNFLKNPMDILNLVRDNMILGVRVKILGDGSFEGIAEDIDDFGRLIIRLDSGEVKKVIYGDVSLRFL 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: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 d2dkgb2 B:1-188 Biotin--[acetyl-CoA-carboxylase] ligase catalytic domain                                                                                                                    d2dkgb1 B:189-235                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee....hhhhhhhhh.....eeeee....................eeeeeee....hhhhhhhhhhhhhhhhhhhhhhh....eee...eeee..eeeeeeeeeee..eeeeeeee...........hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh...eeeee.....eeeeeeee.....eeee.....eeee......eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dkg B   1 MLGLKTSIIGRRVIYFQEITSTNEFAKTSYLEEGTVIVADKQTMGHGRLNRKWESPEGGLWLSIVLSPKVPQKDLPKIVFLGAVGVVETLKEFSIDGRIKWPNDVLVNYKKIAGVLVEGKGDKIVLGIGLNVNNKVPNGATSMKLELGSEVPLLSVFRSLITNLDRLYLNFLKNPMDILNLVRDNMILGVRVKILGDGSFEGIAEDIDDFGRLIIRLDSGEVKKVIYGDVSLRFL 235
                                    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)
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  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/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DKG)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological 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).

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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 2dth 2dti 2dto 2dve 2dxt 2dxu 2dz9 2dzc 2e10 2e1h 2e41 2e64 2e65 2ejf 2ejg 2fyk 2hni 2zgw

(-) Related Entries Specified in the PDB File

1wgw THE SAME PROTEIN COMPLEXED WITH ONLY BIOTINYL-5'-AMP RELATED ID: PHO001000147.5 RELATED DB: TARGETDB