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(-) Description

Title :  THE CRYSTAL STRUCTURE OF RIBOSOMAL-PROTEIN-S5-ALANINE ACETYLTRANSFERASE FROM VIBRIO FISCHERI TO 2.0A
 
Authors :  A. J. Stein, A. Sather, G. Shackelford, A. Joachimiak, Midwest Center Structural Genomics (Mcsg)
Date :  28 Jul 09  (Deposition) - 01 Sep 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (2x)
Biol. Unit 3:  B  (2x)
Keywords :  Ribosomal-Protein, Alanine, Acetyltransferase, Vibrio, Fischeri, Psi, Mcsg, Structural Genomics, Midwest Center For Structural Genomics, Protein Structure Initiative, Acyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. J. Stein, A. Sather, G. Shackelford, A. Joachimiak
The Crystal Structure Of Ribosomal-Protein-S5-Alanine Acetyltransferase From Vibrio Fischeri To 2. 0A
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RIBOSOMAL-PROTEIN-S5-ALANINE N-ACETYLTRANSFERASE
    Chains: A, B
    EC Number: 2.3.1.128
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG19
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RIMJ, VFA0750, VF_A0750
    Organism Scientific: VIBRIO FISCHERI
    Organism Taxid: 312309
    Strain: ES114

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): A 
Biological Unit 3 (2x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE8Mod. Amino AcidSELENOMETHIONINE
3NA3Ligand/IonSODIUM ION
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE8Mod. Amino AcidSELENOMETHIONINE
3NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 8)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2MSE8Mod. Amino AcidSELENOMETHIONINE
3NA-1Ligand/IonSODIUM ION
Biological Unit 3 (2, 10)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE8Mod. Amino AcidSELENOMETHIONINE
3NA-1Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:114 , ASN A:118 , ASN B:76BINDING SITE FOR RESIDUE NA A 185
2AC2SOFTWAREASN A:166 , GLY A:167 , HOH A:207 , HOH B:207BINDING SITE FOR RESIDUE NA A 186
3AC3SOFTWARETYR B:137 , ILE B:138 , ASN B:141BINDING SITE FOR RESIDUE NA B 185
4AC4SOFTWAREARG B:41 , TYR B:69 , THR B:83 , SER B:85 , GLY B:100 , TYR B:101BINDING SITE FOR RESIDUE GOL B 186

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:92 -Pro A:93
2Phe B:92 -Pro B:93

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3IGR)

(-) 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:183
 aligned with Q5DZH6_VIBF1 | Q5DZH6 from UniProtKB/TrEMBL  Length:185

    Alignment length:183
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181   
         Q5DZH6_VIBF1     2 DVSFEFEHYQVRLIKSSDAVTIANYFMRNRHHLAPWEPKRSHAFFTPEGWKQRLLQLVELHKHNLAFYFVVVDKNEHKIIGTVSYSNITRFPFHAGHVGYSLDSEYQGKGIMRRAVNVTIDWMFKAQNLHRIMAAYIPRNEKSAKVLAALGFVKEGEAKKYLYINGAWEDHILTSKINDDWKP 184
               SCOP domains d3igra_ A: automated matches                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee.hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee....eeeeeeeeeeee.....eeeeeeee.hhhh..hhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhh..eeeeeeeeeeee..eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3igr A   2 DVSFEFEHYQVRLIKSSDAVTIANYFmRNRHHLAPWEPKRSHAFFTPEGWKQRLLQLVELHKHNLAFYFVVVDKNEHKIIGTVSYSNITRFPFHAGHVGYSLDSEYQGKGImRRAVNVTIDWmFKAQNLHRImAAYIPRNEKSAKVLAALGFVKEGEAKKYLYINGAWEDHILTSKINDDWKP 184
                                    11        21      | 31        41        51        61        71        81        91       101       111 |     121  |    131  |    141       151       161       171       181   
                                                     28-MSE                                                                              113-MSE    124-MSE   134-MSE                                              


Chain B from PDB  Type:PROTEIN  Length:183
 aligned with Q5DZH6_VIBF1 | Q5DZH6 from UniProtKB/TrEMBL  Length:185

    Alignment length:183
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181   
         Q5DZH6_VIBF1     2 DVSFEFEHYQVRLIKSSDAVTIANYFMRNRHHLAPWEPKRSHAFFTPEGWKQRLLQLVELHKHNLAFYFVVVDKNEHKIIGTVSYSNITRFPFHAGHVGYSLDSEYQGKGIMRRAVNVTIDWMFKAQNLHRIMAAYIPRNEKSAKVLAALGFVKEGEAKKYLYINGAWEDHILTSKINDDWKP 184
               SCOP domains d3igrb_ B: automated matches                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee.hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee....eeeeeeeeeeee.....eeeeeeee.......hhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhh..eeeeeeeeeeee..eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3igr B   2 DVSFEFEHYQVRLIKSSDAVTIANYFmRNRHHLAPWEPKRSHAFFTPEGWKQRLLQLVELHKHNLAFYFVVVDKNEHKIIGTVSYSNITRFPFHAGHVGYSLDSEYQGKGImRRAVNVTIDWmFKAQNLHRImAAYIPRNEKSAKVLAALGFVKEGEAKKYLYINGAWEDHILTSKINDDWKP 184
                                    11        21      | 31        41        51        61        71        81        91       101       111 |     121  |    131  |    141       151       161       171       181   
                                                     28-MSE                                                                              113-MSE    124-MSE   134-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  (1, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q5DZH6_VIBF1 | Q5DZH6)
molecular function
    GO:0008080    N-acetyltransferase activity    Catalysis of the transfer of an acetyl group to a nitrogen atom on the acceptor molecule.
    GO:0008999    ribosomal-protein-alanine N-acetyltransferase activity    Catalysis of the reaction: acetyl-CoA + ribosomal-protein L-alanine = CoA + ribosomal-protein N-acetyl-L-alanine.
    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).

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