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(-) Description

Title :  CRYSTAL STRUCTURE OF BIOTIN PROTEIN LIGASE FROM PYROCOCCUS HORIKOSHII OT3 IN COMPLEX WITH ADP AND BIOTIN
 
Authors :  B. Bagautdinov, N. Kunishima, Riken Structural Genomics/Proteomi Initiative (Rsgi)
Date :  08 Feb 06  (Deposition) - 08 Aug 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
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 - BIOTIN--PROTEIN 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

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric/Biological Unit (3, 14)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2BTN2Ligand/IonBIOTIN
3MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:48 , ARG A:51 , LYS A:52 , TRP A:53 , GLU A:54 , ASP A:104 , LYS A:111 , ASN A:131 , ALA A:140 , BTN A:1401 , HOH A:1439 , HOH A:1526 , HOH A:1639 , HOH A:1645 , HOH A:1653 , HOH A:1678 , HOH A:1685 , HOH A:1686BINDING SITE FOR RESIDUE ADP A 1301
2AC2SOFTWAREARG B:48 , ARG B:51 , LYS B:52 , TRP B:53 , GLU B:54 , ASN B:103 , ASP B:104 , LYS B:111 , ASN B:131 , ALA B:140 , BTN B:1402 , HOH B:1464 , HOH B:1476 , HOH B:1576 , HOH B:1589BINDING SITE FOR RESIDUE ADP B 1302
3AC3SOFTWARESER A:21 , THR A:22 , ASN A:23 , GLN A:42 , GLY A:45 , HIS A:46 , TRP A:53 , LEU A:62 , ASN A:103 , ASP A:104 , LYS A:111 , GLY A:114 , VAL A:115 , ILE A:128 , GLY A:129 , ADP A:1301BINDING SITE FOR RESIDUE BTN A 1401
4AC4SOFTWARESER B:21 , THR B:22 , ASN B:23 , GLN B:42 , GLY B:45 , HIS B:46 , GLY B:47 , ARG B:48 , TRP B:53 , LEU B:62 , ASN B:103 , ASP B:104 , LYS B:111 , GLY B:114 , VAL B:115 , ILE B:128 , GLY B:129 , ADP B:1302BINDING SITE FOR RESIDUE BTN B 1402

(-) SS Bonds  (0, 0)

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

(-) 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 2FYK)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2FYK)

(-) 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 d2fyka2 A:1-188 Biotin--[acetyl-CoA-carboxylase] ligase catalytic domain                                                                                                                    d2fyka1 A:189-235                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee....hhhhhhhhh......eeee.......hhhhh........eeeeeee....hhhhhhhhhhhhhhhhhhhhhhh....eee...eeee..eeeeeeeeee....eeeeeee...........hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh....eeeee...eeeeeeeee.....eeee.....eeee.....eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fyk 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     
                            |                                         44-MSE                                                                                            143-MSE                          176-MSE   186-MSE                                             
                            1-MSE                                                                                                                                                                                                                                      


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 d2fykb2 B:1-188 Biotin--[acetyl-CoA-carboxylase] ligase catalytic domain                                                                                                                    d2fykb1 B:189-235                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeee.hhhhhhhhh......eeeeeee....hhhhh........eeeeeee.......hhhhhhhhhhhhhhhhhhhh....eee...eeee..eeeeeeeeeee..eeeeeeee...........hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.....eeeee.....eeeeeeee.....eeee.....eeee......eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fyk 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     
                            1-MSE                                     44-MSE                                                                                            143-MSE                          176-MSE   186-MSE
   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/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 2FYK)

(-) Pfam Domains  (0, 0)

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

(-) 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 2dkg 2dth 2dti 2dto 2dve 2dxt 2dxu 2dz9 2dzc 2e10 2e1h 2e41 2e64 2e65 2ejf 2ejg 2hni 2zgw

(-) Related Entries Specified in the PDB File

1wnl THE SAME PROTEIN IN COMPLEX WITH ADP
1wpy THE SAME PROTEIN IN COMPLEX WITH BIOTIN
1wq7 THE SAME PROTEIN
1wqw THE SAME PROTEIN IN COMPLEX WITH BIOTINYL-5'-AMP RELATED ID: PHO001000147.2 RELATED DB: TARGETDB
1x01 THE SAME PROTEIN IN COMPLEX WITH ATP