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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BC1960 PEPTIDOGLYCAN N-ACETYLGLUCOSAMINE DEACETYLASE FROM BACILLUS CEREUS
 
Authors :  A. Tsalafouta, V. E. Fadouloglou, M. Kokkinidis
Date :  03 Jun 13  (Deposition) - 04 Jun 14  (Release) - 05 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.34
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Tim Barrel, Hydrolase, Polysaccharide Deacetylase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. E. Fadouloglou, S. Balomenou, M. Aivaliotis, D. Kotsifaki, S. Arnaouteli, A. Tomatsidou, G. Efstathiou, N. Kountourakis, S. Miliara, M. Griniezaki, A. Tsalafouta, S. A. Pergantis, I. G. Boneca, N. M. Glykos, V. Bouriotis, M. Kokkinidis
An Unusual Alpha-Carbon Hydroxylation Of Proline Promotes Active-Site Maturation.
J. Am. Chem. Soc. 2017
PubMed-ID: 28333455  |  Reference-DOI: 10.1021/JACS.6B12209

(-) Compounds

Molecule 1 - PEPTIDOGLYCAN N-ACETYLGLUCOSAMINE DEACETYLASE
    Chains: A, B, C, D
    EC Number: 3.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26B(+)
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BC1960, BC_1960
    Organism Scientific: BACILLUS CEREUS
    Organism Taxid: 226900
    Strain: ATCC 14579

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2PXU4Mod. Amino Acid2-HYDROXY-L-PROLINE
3SO46Ligand/IonSULFATE ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2PXU1Mod. Amino Acid2-HYDROXY-L-PROLINE
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2PXU1Mod. Amino Acid2-HYDROXY-L-PROLINE
3SO41Ligand/IonSULFATE ION
Biological Unit 3 (3, 4)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2PXU1Mod. Amino Acid2-HYDROXY-L-PROLINE
3SO42Ligand/IonSULFATE ION
Biological Unit 4 (3, 4)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2PXU1Mod. Amino Acid2-HYDROXY-L-PROLINE
3SO42Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:231 , LEU A:232 , GLN A:233 , HOH A:561BINDING SITE FOR RESIDUE SO4 A 301
02AC2SOFTWAREASP A:80 , HIS A:135 , PRO A:170 , PXU A:171 , TYR A:172 , TRP A:193 , HIS A:225BINDING SITE FOR RESIDUE ACT A 302
03AC3SOFTWAREHIS B:231 , LEU B:232 , GLN B:233 , HOH B:546BINDING SITE FOR RESIDUE SO4 B 301
04AC4SOFTWAREASP B:80 , ASP B:81 , HIS B:131 , HIS B:135 , PXU B:171 , TYR B:172 , HIS B:225 , HOH B:509 , HOH B:583BINDING SITE FOR RESIDUE ACT B 302
05AC5SOFTWAREASN A:99 , LYS A:247 , HIS C:98 , PRO C:244 , LYS C:247 , HOH C:420 , HOH C:441 , HOH C:463BINDING SITE FOR RESIDUE SO4 C 301
06AC6SOFTWAREHIS C:231 , LEU C:232 , GLN C:233 , HOH C:454BINDING SITE FOR RESIDUE SO4 C 302
07AC7SOFTWAREASP C:80 , PRO C:170 , PXU C:171 , TYR C:172 , TRP C:193 , HIS C:225 , HOH C:575BINDING SITE FOR RESIDUE ACT C 303
08AC8SOFTWAREASN B:99 , LYS B:247 , HIS D:98 , ILE D:243 , PRO D:244 , LYS D:247 , HOH D:425 , HOH D:436 , HOH D:523BINDING SITE FOR RESIDUE SO4 D 301
09AC9SOFTWAREHIS D:231 , LEU D:232 , GLN D:233 , HOH D:446 , HOH D:550BINDING SITE FOR RESIDUE SO4 D 302
10BC1SOFTWAREASP D:80 , ASP D:81 , HIS D:131 , HIS D:135 , PXU D:171 , TYR D:172 , HIS D:225 , HOH D:557BINDING SITE FOR RESIDUE ACT D 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4L1G)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:82 -Pro A:83
2Gly B:82 -Pro B:83
3Gly C:82 -Pro C:83
4Gly D:82 -Pro D:83

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4L1G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4L1G)

(-) Exons   (0, 0)

(no "Exon" information available for 4L1G)

(-) 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:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh.ee........eeeeeeeee.....hhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhhhhhhhhhhh....ee.hhhhh.hhhhhhhhhhh..eee...ee.hhhhh.hhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhhh..ee.hhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l1g A  53 WTPFSWVEKYAYAFSGPYNKAEVALTFDDGPDLEFTPKILDKLKQHNVKATFFLLGENAEKFPNIVKRIANEGHVIGNHTYSHPNLAKVNEDEYRNQIIKTEEILNRLAGYAPKFIRPpYGEILENQLKWATEQNFMIVQWSVDTVDWKGVSADTITNNVLGNSFPGSVILQHSTPGGHLQGSVDALDKIIPQLKTKGARFVTLPSMFQTSKER 266
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262    
                                                                                                                                                171-PXU                                                                                           


Chain B from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh.ee........eeeeeeeee...hhhhhhhhhhhhh....eeeehhhhhh.hhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhhhhhhhhhhh....ee.hhhhh.hhhhhhhhhhh..eee...ee.hhhhh.hhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhhh..ee.hhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l1g B  53 WTPFSWVEKYAYAFSGPYNKAEVALTFDDGPDLEFTPKILDKLKQHNVKATFFLLGENAEKFPNIVKRIANEGHVIGNHTYSHPNLAKVNEDEYRNQIIKTEEILNRLAGYAPKFIRPpYGEILENQLKWATEQNFMIVQWSVDTVDWKGVSADTITNNVLGNSFPGSVILQHSTPGGHLQGSVDALDKIIPQLKTKGARFVTLPSMFQTSKER 266
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262    
                                                                                                                                                171-PXU                                                                                           


Chain C from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh.ee........eeeeeeeee...hhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhhhhhhhhhhh....ee.hhhhh.hhhhhhhhhhh..eee...ee.hhhhh.hhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhh...ee.hhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l1g C  53 WTPFSWVEKYAYAFSGPYNKAEVALTFDDGPDLEFTPKILDKLKQHNVKATFFLLGENAEKFPNIVKRIANEGHVIGNHTYSHPNLAKVNEDEYRNQIIKTEEILNRLAGYAPKFIRPpYGEILENQLKWATEQNFMIVQWSVDTVDWKGVSADTITNNVLGNSFPGSVILQHSTPGGHLQGSVDALDKIIPQLKTKGARFVTLPSMFQTSKER 266
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262    
                                                                                                                                                171-PXU                                                                                           


Chain D from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh.ee........eeeeeeeee...hhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhhhhhhhhhhh....ee.hhhhh.hhhhhhhhhhh..eee...ee.hhhhh.hhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhh...ee.hhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l1g D  54 TPFSWVEKYAYAFSGPYNKAEVALTFDDGPDLEFTPKILDKLKQHNVKATFFLLGENAEKFPNIVKRIANEGHVIGNHTYSHPNLAKVNEDEYRNQIIKTEEILNRLAGYAPKFIRPpYGEILENQLKWATEQNFMIVQWSVDTVDWKGVSADTITNNVLGNSFPGSVILQHSTPGGHLQGSVDALDKIIPQLKTKGARFVTLPSMFQTSKER 266
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263   
                                                                                                                                               171-PXU
   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 4L1G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4L1G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4L1G)

(-) Gene Ontology  (4, 4)

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