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(-) Description

Title :  CRYSTAL STRUCTURE OF ANTD, AN N-ACYLTRANSFERASE FROM BACILLUS CEREUS IN COMPLEX WITH DTDP-4-AMINO-4,6-DIDEOXYGLUCOSE AND COENZYME A
 
Authors :  R. L. Kubiak, H. M. Holden
Date :  02 Jan 12  (Deposition) - 25 Jan 12  (Release) - 22 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,C,E
Keywords :  Anthrose, Acylated Sugar, Left-Handed Beta Helix, Sugar N-Acylation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. L. Kubiak, H. M. Holden
Structural Studies Of Antd: An N-Acyltransferase Involved I The Biosynthesis Of D-Anthrose.
Biochemistry V. 51 867 2012
PubMed-ID: 22220494  |  Reference-DOI: 10.1021/BI201650C

(-) Compounds

Molecule 1 - GALACTOSIDE O-ACETYLTRANSFERASE
    ChainsA, C, E
    EC Number2.3.1.18
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28
    Expression System StrainROSETTA2 DE3
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneANTD, BCSJ1_02085
    Organism ScientificBACILLUS CEREUS
    Organism Taxid699184
    StrainSJ1
    SynonymANTD

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ACE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
10FX3Ligand/IonDTDP-4-AMINO-4,6-DIDEOXYGLUCOSE
2BCT3Ligand/IonBICARBONATE ION
3CL1Ligand/IonCHLORIDE ION
4COA3Ligand/IonCOENZYME A

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:90 , ILE A:93 , ASP A:94 , PHE A:96 , PHE A:133 , LYS A:151 , VAL A:163 , PRO A:164 , HOH A:192 , HOH A:246 , HOH A:247 , HOH A:273 , HOH A:316 , SER E:84 , GLY E:127 , ALA E:128 , GLY E:145 , ALA E:146 , VAL E:161 , LYS E:169 , HOH E:196 , 0FX E:1500BINDING SITE FOR RESIDUE COA A 189
02AC2SOFTWAREASN A:2 , SER A:3 , ARG A:43 , ASP A:45 , ASP A:46 , HIS A:61 , HOH A:199 , HOH A:259 , HOH A:308 , BCT A:453 , TYR C:31 , SER C:51 , TYR C:69 , ALA C:92 , ASP C:94 , COA C:189 , HOH C:201BINDING SITE FOR RESIDUE 0FX A 1500
03AC3SOFTWAREHIS A:61 , ILE A:83 , 0FX A:1500 , GLY C:103 , PRO C:104BINDING SITE FOR RESIDUE BCT A 453
04AC4SOFTWARESER A:84 , GLY A:127 , ALA A:128 , GLY A:145 , ALA A:146 , VAL A:161 , LYS A:169 , HOH A:204 , HOH A:205 , HOH A:272 , 0FX A:1500 , TYR C:90 , ILE C:93 , ASP C:94 , PHE C:96 , PHE C:133 , MET C:149 , LYS C:151 , VAL C:163 , PRO C:164 , HOH C:202 , HOH C:218 , HOH C:235 , HOH C:236 , HOH C:246 , HOH C:295 , HOH C:296 , HOH C:309BINDING SITE FOR RESIDUE COA C 189
05AC5SOFTWAREMET C:1 , ASN C:2 , SER C:3 , ARG C:43 , ASP C:45 , ASP C:46 , HIS C:61 , ALA C:63 , HOH C:192 , HOH C:257 , BCT C:453 , TYR E:31 , SER E:51 , TYR E:69 , ALA E:92 , ASP E:94 , PRO E:104 , COA E:189 , HOH E:191BINDING SITE FOR RESIDUE 0FX C 1500
06AC6SOFTWAREHIS C:61 , ILE C:83 , 0FX C:1500 , GLY E:103 , PRO E:104BINDING SITE FOR RESIDUE BCT C 453
07AC7SOFTWARESER C:84 , GLY C:127 , ALA C:128 , GLY C:145 , ALA C:146 , VAL C:161 , LYS C:169 , HOH C:217 , 0FX C:1500 , TYR E:90 , ASP E:94 , PHE E:96 , PHE E:133 , MET E:149 , LYS E:151 , VAL E:163 , PRO E:164 , HOH E:209 , HOH E:236 , HOH E:241 , HOH E:276 , HOH E:278 , HOH E:299BINDING SITE FOR RESIDUE COA E 189
08AC8SOFTWAREARG A:86 , ARG C:86 , ARG E:86BINDING SITE FOR RESIDUE CL E 190
09AC9SOFTWARETYR A:31 , SER A:51 , TYR A:69 , ALA A:92 , ASP A:94 , COA A:189 , HOH A:255 , HOH A:276 , ASN E:2 , SER E:3 , ARG E:43 , ASP E:45 , ASP E:46 , HIS E:61 , HOH E:214 , HOH E:215 , HOH E:244 , BCT E:453BINDING SITE FOR RESIDUE 0FX E 1500
10BC1SOFTWAREGLY A:103 , PRO A:104 , HIS E:61 , ILE E:83 , 0FX E:1500BINDING SITE FOR RESIDUE BCT E 453

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Val A:163 -Pro A:164
2Val C:163 -Pro C:164
3Val E:163 -Pro E:164

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3VBI)

(-) 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:186
                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhh....ee...eee....eeehhh.eee...eee....eeeeeeee...eee....eeeeeeeeeee....ee....eee.ee.............hhhhh..ee..eee....ee....ee....ee....ee....ee.......eeee....eeeee..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vbi A   1 MNSFYSQEELKKIGFLSVGKNVLISKKASIYNPGVISIGNNVRIDDFCILSGKVTIGSYSHIAAYTALYGGEVGIEMYDFANISSRTIVYAAIDDFSGNALMGPTIPNQYKNVKTGKVILKKHVIIGAHSIIFPNVVIGEGVAVGAMSMVKESLDDWYIYVGVPVRKIKARKRKIVELENEFLKSM 186
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180      

Chain C from PDB  Type:PROTEIN  Length:186
                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhh....ee...eee....eeehhh.eee...eee....eeeeeeee...eee....eeeeeeeeeee....ee....eee.ee.............hhhhh..ee..eee....ee....ee....ee....ee....ee.......eeee....eeeee..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vbi C   1 MNSFYSQEELKKIGFLSVGKNVLISKKASIYNPGVISIGNNVRIDDFCILSGKVTIGSYSHIAAYTALYGGEVGIEMYDFANISSRTIVYAAIDDFSGNALMGPTIPNQYKNVKTGKVILKKHVIIGAHSIIFPNVVIGEGVAVGAMSMVKESLDDWYIYVGVPVRKIKARKRKIVELENEFLKSM 186
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180      

Chain E from PDB  Type:PROTEIN  Length:186
                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhh....ee...eee....eeehhh.eee...eee....eeeeeeee...eee....eeeeeeeeeee....ee....eee.ee.............hhhhh..ee..eee....ee....ee....ee....ee....ee.......eeee....eeeee..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vbi E   1 MNSFYSQEELKKIGFLSVGKNVLISKKASIYNPGVISIGNNVRIDDFCILSGKVTIGSYSHIAAYTALYGGEVGIEMYDFANISSRTIVYAAIDDFSGNALMGPTIPNQYKNVKTGKVILKKHVIIGAHSIIFPNVVIGEGVAVGAMSMVKESLDDWYIYVGVPVRKIKARKRKIVELENEFLKSM 186
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180      

   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 3VBI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

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(-) Related Entries Specified in the PDB File

3vbj CRYSTAL STRUCTURE OF ANTD, AN N-ACYLTRANSFERASE FROM BACILLUS CEREUS IN COMPLEX WITH DTDP AND 3-HYDROXYBUTYRYL- COA
3vbk CRYSTAL STRUCTURE OF THE S84A MUTANT OF ANTD, AN N- ACYLTRANSFERASE FROM BACILLUS CEREUS IN COMPLEX WITH DTDP- 4-AMINO-4,6-DIDEOXYGLUCOSE AND COENZYME A
3vbl CRYSTAL STRUCTURE OF THE S84C MUTANT OF ANTD, AN N- ACYLTRANSFERASE FROM BACILLUS CEREUS IN COMPLEX WITH DTDP- 4-AMINO-4,6-DIDEOXYGLUCOSE AND COENZYME A
3vbm CRYSTAL STRUCTURE OF THE S84T MUTANT OF ANTD, AN N- ACYLTRANSFERASE FROM BACILLUS CEREUS IN COMPLEX WITH DTDP AND COENZYME A
3vbn CRYSTAL STRUCTURE OF THE D94A MUTANT OF ANTD, AN N- ACYLTRANSFERASE FROM BACILLUS CEREUS IN COMPLEX WITH DTDP AND COENZYME A
3vbp CRYSTAL STRUCTURE OF THE D94N MUTANT OF ANTD, AN N- ACYLTRANSFERASE FROM BACILLUS CEREUS IN COMPLEX WITH DTDP AND COENZYME A