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(-) Description

Title :  CRYSTAL STRUCTURE OF MYXOCOCCUS XANTHUS GLUTAMINYL CYCLASE
 
Authors :  C. Parthier, D. R. Carrillo, M. T. Stubbs
Date :  25 Jun 10  (Deposition) - 03 Nov 10  (Release) - 26 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta-Propeller, Glutaminyl Cyclase, Cyclotransferase, Pyroglutamate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. R. Carrillo, C. Parthier, N. Janckel, J. Grandke, M. Stelter, S. Schilling, M. Boehme, P. Neumann, R. Wolf, H. U. Demuth, M. T. Stubbs J. U. Rahfeld
Kinetic And Structural Characterization Of Bacterial Glutaminyl Cyclases From Zymomonas Mobilis And Myxococcus Xanthus
Biol. Chem. V. 391 1419 2010
PubMed-ID: 20868223  |  Reference-DOI: 10.1515/BC.2010.130

(-) Compounds

Molecule 1 - GLUTAMINYL CYCLASE
    Chains: A, B
    EC Number: 2.3.2.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: MYXOCOCCUS XANTHUS
    Organism Taxid: 34
    Strain: DSM 16526

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2DDQ2Ligand/IonDECYLAMINE-N,N-DIMETHYL-N-OXIDE
3GOL1Ligand/IonGLYCEROL
4MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2DDQ1Ligand/IonDECYLAMINE-N,N-DIMETHYL-N-OXIDE
3GOL-1Ligand/IonGLYCEROL
4MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2DDQ1Ligand/IonDECYLAMINE-N,N-DIMETHYL-N-OXIDE
3GOL1Ligand/IonGLYCEROL
4MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:48 , GLU A:173 , LEU A:174 , GLU A:175 , ILE A:228 , HOH A:311BINDING SITE FOR RESIDUE CA A 257
2AC2SOFTWARELEU B:48 , GLU B:173 , LEU B:174 , GLU B:175 , ILE B:228 , HOH B:275BINDING SITE FOR RESIDUE CA B 257
3AC3SOFTWAREPRO A:232 , GLY A:233 , SER A:234 , GLY A:235 , VAL B:49 , ALA B:90 , SER B:91 , CYS B:130 , TYR B:131 , GLU B:175 , CYS B:176 , GOL B:259 , HOH B:275 , HOH B:349BINDING SITE FOR RESIDUE MES B 258
4AC4SOFTWAREVAL A:49 , ALA A:90 , SER A:91 , CYS A:130 , TYR A:131 , GLU A:175 , CYS A:176 , VAL A:230 , PRO A:232 , HOH A:298 , HOH A:311 , GOL B:259BINDING SITE FOR RESIDUE MES A 258
5AC5SOFTWAREALA A:177 , ASN A:178 , VAL A:230 , PRO A:232 , MES A:258 , HOH A:391 , PRO B:232 , MES B:258 , HOH B:350BINDING SITE FOR RESIDUE GOL B 259
6AC6SOFTWARETRP A:186 , DDQ A:2745 , GLN B:46 , GLU B:87 , TRP B:127 , ASN B:172 , LYS B:242BINDING SITE FOR RESIDUE DDQ B 2745
7AC7SOFTWAREGLN A:46 , GLU A:87 , TRP A:101 , TRP A:127 , TRP A:186 , ASN A:220 , LYS A:242 , TRP B:186 , DDQ B:2745BINDING SITE FOR RESIDUE DDQ A 2745

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:130 -A:176
2B:130 -B:176

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1His A:61 -Gln A:62
2Met A:112 -Pro A:113
3His B:61 -Gln B:62
4Met B:112 -Pro B:113

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NOK)

(-) 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:234
 aligned with E7FH78_MYXXA | E7FH78 from UniProtKB/TrEMBL  Length:248

    Alignment length:234
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244    
         E7FH78_MYXXA    15 VQEPVRRVAHIIREYPHATNAFTQGLVFHQGHFFESTGHQGTLRQLSLESAQPVWMERLGNIFAEGLASDGERLYQLTWTEGLLFTWSGMPPQRERTTRYSGEGWGLCYWNGKLVRSDGGTMLTFHEPDGFALVGAVQVKLRGQPVELINELECANGVIYANIWHSSDVLEIDPATGTVVGVIDASALTRAVAGQVTNPEAVLNGIAVEPGSGRIFMTGKLWPRLFEVRLDVVD 248
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeeeeee......eeeeeee..eeeeee....eeee.........eeee.....eeeeee....eeeee....eeeeee....eeeeeee.......eeee..eeeee....eeeee......eeeeee.ee..ee...eeeeeee..eeeeee....eeeee......eeeeeehhhhhhhhh.........eeeeee......eeeee....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3nok A  23 VQEPVRRVAHIIREYPHATNAFTQGLVFHQGHFFESTGHQGTLRQLSLESAQPVWMERLGNIFAEGLASDGERLYQLTWTEGLLFTWSGMPPQRERTTRYSGEGWGLCYWNGKLVRSDGGTMLTFHEPDGFALVGAVQVKLRGQPVELINELECANGVIYANIWHSSDVLEIDPATGTVVGVIDASALTRAVAGQVTNPEAVLNGIAVEPGSGRIFMTGKLWPRLFEVRLDVVD 256
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252    


Chain B from PDB  Type:PROTEIN  Length:232
 aligned with E7FH78_MYXXA | E7FH78 from UniProtKB/TrEMBL  Length:248

    Alignment length:232
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246  
         E7FH78_MYXXA    17 EPVRRVAHIIREYPHATNAFTQGLVFHQGHFFESTGHQGTLRQLSLESAQPVWMERLGNIFAEGLASDGERLYQLTWTEGLLFTWSGMPPQRERTTRYSGEGWGLCYWNGKLVRSDGGTMLTFHEPDGFALVGAVQVKLRGQPVELINELECANGVIYANIWHSSDVLEIDPATGTVVGVIDASALTRAVAGQVTNPEAVLNGIAVEPGSGRIFMTGKLWPRLFEVRLDVVD 248
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee......eeeeeee..eeeeee....eeee.........eeee.....eeeeee....eeeee....eeeeee....eeeeeee.......eeee..eeee.....eeeee......eeeeee.ee..ee...eeeeeee..eeeeee....eeeee......eeeeeehhhhhhhhh.........eeeeee......eeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nok B  25 EPVRRVAHIIREYPHATNAFTQGLVFHQGHFFESTGHQGTLRQLSLESAQPVWMERLGNIFAEGLASDGERLYQLTWTEGLLFTWSGMPPQRERTTRYSGEGWGLCYWNGKLVRSDGGTMLTFHEPDGFALVGAVQVKLRGQPVELINELECANGVIYANIWHSSDVLEIDPATGTVVGVIDASALTRAVAGQVTNPEAVLNGIAVEPGSGRIFMTGKLWPRLFEVRLDVVD 256
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 3NOK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (E7FH78_MYXXA | E7FH78)
molecular function
    GO:0016603    glutaminyl-peptide cyclotransferase activity    Catalysis of the reaction: L-glutaminyl-peptide = 5-oxoprolyl-peptide + NH3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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