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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BACILLUS SUBTILIS N-ACETYLTRANSFERASE YLBP PROTEIN IN COMPLEX WITH COENZYME-A
 
Authors :  G. Minasov, L. Shuvalova, O. Kiryukhina, I. I. Vorontsov, F. R. Collart A. Joachimiak, W. F. Anderson, Midwest Center For Structural Gen (Mcsg)
Date :  03 May 07  (Deposition) - 15 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  N-Acetyltransferase, Yibp Protein, Coenzyme A, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Minasov, L. Shuvalova, O. Kiryukhina, I. I. Vorontsov, F. R. Collart, A. Joachimiak, W. F. Anderson
Crystal Structure Of The Bacillus Subtilis N-Acetyltransferase Ylbp Protein In Complex With Coenzyme-A
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED N-ACETYLTRANSFERASE YLBP
    Chains: A, B
    EC Number: 2.3.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: YLBP, BSU15100
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Strain: 168

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1CO2Ligand/IonCOBALT (II) ION
2COA2Ligand/IonCOENZYME A
3SO42Ligand/IonSULFATE ION
4SUC2Ligand/IonSUCROSE
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2COA2Ligand/IonCOENZYME A
3SO42Ligand/IonSULFATE ION
4SUC2Ligand/IonSUCROSE
Biological Unit 2 (3, 12)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2COA4Ligand/IonCOENZYME A
3SO44Ligand/IonSULFATE ION
4SUC4Ligand/IonSUCROSE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:5 , GLY A:53 , ASP A:54BINDING SITE FOR RESIDUE SUC A 201
2AC2SOFTWAREGLU B:5 , ASP B:54 , LYS B:108 , PRO B:148 , ASP B:149 , MET B:150 , SO4 B:204BINDING SITE FOR RESIDUE SUC B 201
3AC3SOFTWAREHIS B:147BINDING SITE FOR RESIDUE CO B 202
4AC4SOFTWARETHR B:2 , GLU B:102 , PHE B:103BINDING SITE FOR RESIDUE CO B 203
5AC5SOFTWARELYS B:105 , ASN B:127 , TRP B:146 , SUC B:201BINDING SITE FOR RESIDUE SO4 B 204
6AC6SOFTWARETYR A:63 , VAL A:65 , ASN A:66BINDING SITE FOR RESIDUE SO4 A 205
7AC7SOFTWAREGLU A:86 , VAL A:87 , GLY A:90 , GLN A:92 , ASN A:93 , ARG A:94 , GLY A:95 , GLY A:97 , ARG A:98 , LYS A:118 , SER A:119 , GLU A:121 , PHE A:122 , LYS A:125BINDING SITE FOR RESIDUE COA A 206
8AC8SOFTWAREGLU B:86 , VAL B:87 , GLY B:90 , GLN B:92 , ASN B:93 , ARG B:94 , GLY B:95 , GLY B:97 , ARG B:98 , ARG B:116 , GLU B:121 , PHE B:122 , LYS B:125BINDING SITE FOR RESIDUE COA B 206

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PR1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PR1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PR1)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GNATPS51186 Gcn5-related N-acetyltransferase (GNAT) domain profile.YLBP_BACSU7-151
 		  2A:7-151
B:7-150
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GNATPS51186 Gcn5-related N-acetyltransferase (GNAT) domain profile.YLBP_BACSU7-151
 		  2A:7-151
B:7-150
Biological Unit 2 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GNATPS51186 Gcn5-related N-acetyltransferase (GNAT) domain profile.YLBP_BACSU7-151
 		  4A:7-151
B:7-150

(-) Exons   (0, 0)

(no "Exon" information available for 2PR1)

(-) 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:152
 aligned with YLBP_BACSU | O34468 from UniProtKB/Swiss-Prot  Length:160

    Alignment length:152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  
           YLBP_BACSU     1 MTKVERLLINYKTLEEFKKFKEYGIQELSMLEELQDNIIENDSTSPFYGIYFGDKLVARMSLYQVNGKSNPYFDNRQDYLELWKLEVLPGYQNRGYGRALVEFAKSFKMPIRTNPRMKSAEFWNKMNFKTVKYDMARDKGENPLIWHPDMDR 152
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2pr1A00 A:1-152  [code=3.40.630.30, no name defined]                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeehhhhhhhhh.....hhhhhhhhhhhhhhhhhh.eeeeeeeeee..eeeeeeeeeee.......hhhhh.eeeeeeeee.......hhhhhhhhhhhh....eee..hhhhhhhhhhh..ee...hhhhhh....eee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------GNAT  PDB: A:7-151 UniProt: 7-151                                                                                                                - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pr1 A   1 MTKVERLLINYKTLEEFKKFKEYGIQELSMLEELQDNIIENDSTSPFYGIYFGDKLVARMSLYQVNGKSNPYFDNRQDYLELWKLEVLPGYQNRGYGRALVEFAKSFKMPIRTNPRMKSAEFWNKMNFKTVKYDMARDKGEDPLIWHPDMDR 152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  


Chain B from PDB  Type:PROTEIN  Length:149
 aligned with YLBP_BACSU | O34468 from UniProtKB/Swiss-Prot  Length:160

    Alignment length:149
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141         
           YLBP_BACSU     2 TKVERLLINYKTLEEFKKFKEYGIQELSMLEELQDNIIENDSTSPFYGIYFGDKLVARMSLYQVNGKSNPYFDNRQDYLELWKLEVLPGYQNRGYGRALVEFAKSFKMPIRTNPRMKSAEFWNKMNFKTVKYDMARDKGENPLIWHPDM 150
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2pr1B00 B:2-150  [code=3.40.630.30, no name defined]                                                                                                  CATH domains
           Pfam domains (1) ------------------------------------------------Acetyltransf_1-2pr1B01 B:50-129                                                 --------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------Acetyltransf_1-2pr1B02 B:50-129                                                 --------------------- Pfam domains (2)
         Sec.struct. author ...ee...hhhhhhhhh.....hhhhhhhhhhhhh..........eeeeee..eeeeeeeeeee.......hhhhh.eeeeeeeee.......hhhhhhhhhhhh....eee..hhhhhhhhhhh..ee...hhhhhh....eee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----GNAT  PDB: B:7-150 UniProt: 7-151                                                                                                                PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pr1 B   2 TKVERLLINYKTLEEFKKFKEYGIQELSMLEELQDNIIENDSTSPFYGIYFGDKLVARMSLYQVNGKSNPYFDNRQDYLELWKLEVLPGYQNRGYGRALVEFAKSFKMPIRTNPRMKSAEFWNKMNFKTVKYDMARDKGEDPLIWHPDM 150
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141
   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 2PR1)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Acetyltrans (109)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (YLBP_BACSU | O34468)
molecular function
    GO:0008080    N-acetyltransferase activity    Catalysis of the transfer of an acetyl group to a nitrogen atom on the acceptor molecule.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
    GO:0016747    transferase activity, transferring acyl groups other than amino-acyl groups    Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor).

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