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(-) Description

Title :  STRUCTURAL CHARACTERISATION OF NANE, MANNAC6P C2 EPIMERASE, FROM CLOSTRIDIUM PERFINGENS
 
Authors :  M. C. Pelissier, C. Sebban-Kreuzer, F. Guerlesquin, J. A. Brannigan, G. J. Davies, Y. Bourne, F. Vincent
Date :  23 Jul 14  (Deposition) - 22 Oct 14  (Release) - 14 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.71
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B (1x),C (1x)
Biol. Unit 3:  B (1x),C (1x)
Keywords :  Isomerase, Sugar 2-Epimerase, Sialic Acid, Sugar Phosphate, Enzyme Mechanism, Carbohydrate, Mutagenesis, 1H Nmr Spectroscopy (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Pelissier, C. Sebban-Kreuzer, F. Guerlesquin, J. A. Brannigan, Y. Bourne, F. Vincent
Structural And Functional Characterization Of The Clostridium Perfringens N-Acetylmannosamine-6-Phosphate 2- Epimerase Essential For The Sialic Acid Salvage Pathway.
J. Biol. Chem. V. 289 35215 2014
PubMed-ID: 25320079  |  Reference-DOI: 10.1074/JBC.M114.604272

(-) Compounds

Molecule 1 - PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE
    Chains: A, B
    EC Number: 5.1.3.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-YSBLIC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA
    Expression System Vector Type: PLASMID
    Organism Scientific: CLOSTRIDIUM PERFRINGENS STR. 13
    Organism Taxid: 195102
    Other Details: 8 CHLORIDE IONS AND 4 ACTETATE MOLECULES ARE BOUND TO THE 4 MONOMERS
    Synonym: MANNAC-6-P EPIMERASE, N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE
 
Molecule 2 - PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE
    Chains: C, D
    EC Number: 5.1.3.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-YSBLIC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA
    Expression System Vector Type: PLASMID
    Organism Scientific: CLOSTRIDIUM PERFRINGENS STR. 13
    Organism Taxid: 195102
    Other Details: 8 CHLORIDE IONS AND 4 ACTETATE MOLECULES ARE BOUND TO THE 4 MONOMERS
    Synonym: MANNAC-6-P EPIMERASE, N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2CL8Ligand/IonCHLORIDE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:14 , ARG A:43 , LYS A:66 , HOH A:2056BINDING SITE FOR RESIDUE CL A1221
02AC2SOFTWAREARG A:208 , PRO A:209 , GLN A:210 , HOH A:2073 , HOH A:2074BINDING SITE FOR RESIDUE CL A1222
03AC3SOFTWARELYS A:66 , TYR A:75BINDING SITE FOR RESIDUE ACT A1223
04AC4SOFTWAREGLN B:14 , ARG B:43 , ILE B:64 , LYS B:66 , HOH B:2045BINDING SITE FOR RESIDUE CL B1221
05AC5SOFTWAREARG B:208 , PRO B:209 , GLN B:210 , HOH B:2063 , HOH B:2065BINDING SITE FOR RESIDUE CL B1222
06AC6SOFTWARELYS B:66 , TYR B:75 , THR B:147BINDING SITE FOR RESIDUE ACT B1223
07AC7SOFTWAREGLN C:14 , ARG C:43 , LYS C:66 , HOH C:2052BINDING SITE FOR RESIDUE CL C1221
08AC8SOFTWAREARG C:208 , PRO C:209 , GLN C:210 , HOH C:2068 , HOH C:2069BINDING SITE FOR RESIDUE CL C1222
09AC9SOFTWARELYS C:66 , TYR C:75BINDING SITE FOR RESIDUE ACT C1223
10BC1SOFTWAREGLN D:14 , ARG D:43 , LYS D:66BINDING SITE FOR RESIDUE CL D1221
11BC2SOFTWAREARG D:208 , PRO D:209 , GLN D:210 , HOH D:2061BINDING SITE FOR RESIDUE CL D1222
12BC3SOFTWARELYS D:66 , TYR D:75 , HOH D:2009BINDING SITE FOR RESIDUE ACT D1223

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4UTT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4UTT)

(-) 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:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhh..eeeee.........hhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhh..eeee..............hhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh...eee................hhhhhhhhhhhh...eeee....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4utt A  -8 GSHHHHHHHMLDVVKGNLIVSCQALSDEPLHSSFIMGRMAIAAKQGGAAAIRAQGVNDINEIKEVTKLPIIGIIKRNYDDSEIYITPTMKEVDELLKTDCEMIALDATKRKRPNGENVKDLVDAIHAKGRLAMADISTLEEGIEAEKLGFDCVSTTLSGYTPYSKQSNSVDFELLEELVKTVKIPVICEGRINTPEELKKALDLGAYSAVVGGAITRPQQITKRFTDIL 220
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211         


Chain B from PDB  Type:PROTEIN  Length:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhh..eeee..........hhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhh..eeee..............hhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh...eee................hhhhhhhhhh.....eeee....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4utt B  -8 GSHHHHHHHMLDVVKGNLIVSCQALSDEPLHSSFIMGRMAIAAKQGGAAAIRAQGVNDINEIKEVTKLPIIGIIKRNYDDSEIYITPTMKEVDELLKTDCEMIALDATKRKRPNGENVKDLVDAIHAKGRLAMADISTLEEGIEAEKLGFDCVSTTLSGYTPYSKQSNSVDFELLEELVKTVKIPVICEGRINTPEELKKALDLGAYSAVVGGAITRPQQITKRFTDIL 220
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211         


Chain C from PDB  Type:PROTEIN  Length:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhh..eeee..........hhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhh..eeee..............hhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh...eee................hhhhhhhhhhhh...eeee....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4utt C  -8 GSSHHHHHHMLDVVKGNLIVSCQALSDEPLHSSFIMGRMAIAAKQGGAAAIRAQGVNDINEIKEVTKLPIIGIIKRNYDDSEIYITPTMKEVDELLKTDCEMIALDATKRKRPNGENVKDLVDAIHAKGRLAMADISTLEEGIEAEKLGFDCVSTTLSGYTPYSKQSNSVDFELLEELVKTVKIPVICEGRINTPEELKKALDLGAYSAVVGGAITRPQQITKRFTDIL 220
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211         


Chain D from PDB  Type:PROTEIN  Length:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhh..eeee..........hhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhh..eeee..............hhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh...eee................hhhhhhhhhh.....eeee....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4utt D  -8 GSSHHHHHHMLDVVKGNLIVSCQALSDEPLHSSFIMGRMAIAAKQGGAAAIRAQGVNDINEIKEVTKLPIIGIIKRNYDDSEIYITPTMKEVDELLKTDCEMIALDATKRKRPNGENVKDLVDAIHAKGRLAMADISTLEEGIEAEKLGFDCVSTTLSGYTPYSKQSNSVDFELLEELVKTVKIPVICEGRINTPEELKKALDLGAYSAVVGGAITRPQQITKRFTDIL 220
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
   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 4UTT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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        NANE_CLOP1 | Q0TUP9: 4utw

(-) Related Entries Specified in the PDB File

4utu STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF THE N- ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE FROM CLOSTRIDIUM PERFRINGENS
4utw STRUCTURAL CHARACTERISATION OF NANE, MANNAC6P C2 EPIMERASE , FROM CLOSTRIDIUM PERFINGENS