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(-) Description

Title :  SYRB2 WITH FE(II), CHLORIDE, AND ALPHA-KETOGLUTARATE
 
Authors :  L. C. Blasiak, C. L. Drennan
Date :  12 Dec 05  (Deposition) - 21 Mar 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Mononuclear Iron, Cupin, Halogenase, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. C. Blasiak, F. H. Vaillancourt, C. T. Walsh, C. L. Drennan
Crystal Structure Of The Non-Haem Iron Halogenase Syrb2 In Syringomycin Biosynthesis.
Nature V. 440 368 2006
PubMed-ID: 16541079  |  Reference-DOI: 10.1038/NATURE04544

(-) Compounds

Molecule 1 - SYRINGOMYCIN BIOSYNTHESIS ENZYME 2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SYRB2
    Organism Scientific: PSEUDOMONAS SYRINGAE PV. SYRINGAE
    Organism Taxid: 321
    Strain: PV. SYRINGAE

 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, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
1AKG2Ligand/Ion2-OXOGLUTARIC ACID
2CL4Ligand/IonCHLORIDE ION
3DSU1Ligand/Ion((2R,3S,4S,5S)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)-5-((2R,3S,4S,5S,6R)-3,4,5-TRIHYDROXY-6-METHOXY-TETRAHYDRO-2H-PYRAN-2-YLOXY)-TETRAHYDROFURAN-2-YL)METHYL NONANOATE
4FE22Ligand/IonFE (II) ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1AKG1Ligand/Ion2-OXOGLUTARIC ACID
2CL-1Ligand/IonCHLORIDE ION
3DSU1Ligand/Ion((2R,3S,4S,5S)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)-5-((2R,3S,4S,5S,6R)-3,4,5-TRIHYDROXY-6-METHOXY-TETRAHYDRO-2H-PYRAN-2-YLOXY)-TETRAHYDROFURAN-2-YL)METHYL NONANOATE
4FE21Ligand/IonFE (II) ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1AKG1Ligand/Ion2-OXOGLUTARIC ACID
2CL-1Ligand/IonCHLORIDE ION
3DSU-1Ligand/Ion((2R,3S,4S,5S)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)-5-((2R,3S,4S,5S,6R)-3,4,5-TRIHYDROXY-6-METHOXY-TETRAHYDRO-2H-PYRAN-2-YLOXY)-TETRAHYDROFURAN-2-YL)METHYL NONANOATE
4FE21Ligand/IonFE (II) ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:116 , HIS B:235 , AKG B:898 , CL B:902 , HOH B:1019BINDING SITE FOR RESIDUE FE2 B 899
2AC2SOFTWAREHIS A:116 , HIS A:235 , AKG A:897 , CL A:901 , HOH A:1072BINDING SITE FOR RESIDUE FE2 A 900
3AC3SOFTWAREHIS A:116 , HIS A:235 , AKG A:897 , FE2 A:900BINDING SITE FOR RESIDUE CL A 901
4AC4SOFTWAREHIS B:116 , HIS B:235 , AKG B:898 , FE2 B:899 , HOH B:927BINDING SITE FOR RESIDUE CL B 902
5AC5SOFTWAREASP A:212BINDING SITE FOR RESIDUE CL A 903
6AC6SOFTWAREASP B:212BINDING SITE FOR RESIDUE CL B 904
7AC7SOFTWARELEU A:92 , PRO A:94 , GLU A:137 , PHE A:138 , GLY A:139 , GLN A:165 , ASN A:166 , TRP A:230 , THR A:232 , HOH A:989 , HOH A:1050 , HOH A:1100 , HOH A:1102 , HOH A:1126 , HOH A:1200BINDING SITE FOR RESIDUE DSU A 896
8AC8SOFTWAREPHE A:104 , LYS A:106 , THR A:113 , HIS A:116 , THR A:143 , TRP A:145 , LEU A:158 , HIS A:235 , SER A:237 , ARG A:248 , ARG A:254 , FE2 A:900 , CL A:901 , HOH A:915 , HOH A:1072BINDING SITE FOR RESIDUE AKG A 897
9AC9SOFTWAREPHE B:104 , THR B:113 , HIS B:116 , THR B:143 , TRP B:145 , LEU B:158 , HIS B:235 , SER B:237 , ARG B:248 , ALA B:252 , ARG B:254 , FE2 B:899 , CL B:902 , HOH B:927 , HOH B:1019BINDING SITE FOR RESIDUE AKG B 898

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2FCT)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:22 -Pro A:23
2Gly B:22 -Pro B:23

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2FCT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2FCT)

(-) Exons   (0, 0)

(no "Exon" information available for 2FCT)

(-) 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:304
 aligned with Q9RBY6_PSESY | Q9RBY6 from UniProtKB/TrEMBL  Length:310

    Alignment length:308
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302        
         Q9RBY6_PSESY     3 KKFALTAEQRASFEKNGFIGPFDAYSPEEMKETWKRTRLRLLDRSAAAYQDLDAISGGTNIANYDRHLDDDFLASHICRPEICDRVESILGPNVLCWRTEFFPKYPGDEGTDWHQADTFANASGKPQIIWPENEEFGGTITVWTAFTDANIANGCLQFIPGTQNSMNYDETKRMTYEPDANNSVVKDGVRRGFFGYDYRQLQIDENWKPDEASAVPMQMKAGQFIIFWSTLMHASYPHSGESQEMRMGFASRYVPSFVHVYPDSDHIEEYGGRISLEKYGAVQVIGDETPEYNRLVTHTTRGKKFEAV 310
               SCOP domains d2fcta1 A:3-310 Syringomycin biosynthesis enzyme 2, Sy    rB2                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhheeeeee..hhhhhhhhhhhhhhhhh............----hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh..eeeeeeeeeee.....ee................ee..........eeeeee....hhhhh.eeee.........................ee..eeee....hhhhhh.......hhhhheee.....eeeeee...eeee..........eeeeeeeeee...ee.....eeee..eeee......eeee....................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fct A   3 KKFALTAEQRASFEKNGFIGPFDAYSPEEMKETWKRTRLRLLDRSAAAYQDLDA----TNIANYDRHLDDDFLASHICRPEICDRVESILGPNVLCWRTEFFPKYPGDEGTDWHQADTFANASGKPQIIWPENEEFGGTITVWTAFTDANIANGCLQFIPGTQNSMNYDETKRMTYEPDANNSVVKDGVRRGFFGYDYRQLQIDENWKPDEASAVPMQMKAGQFIIFWSTLMHASYPHSGESQEMRMGFASRYVPSFVHVYPDSDHIEEYGGRISLEKYGAVQVIGDETPEYNRLVTHTTRGKKFEAV 310
                                    12        22        32        42        52   |    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302        
                                                                                56   61                                                                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:299
 aligned with Q9RBY6_PSESY | Q9RBY6 from UniProtKB/TrEMBL  Length:310

    Alignment length:307
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       
         Q9RBY6_PSESY     4 KFALTAEQRASFEKNGFIGPFDAYSPEEMKETWKRTRLRLLDRSAAAYQDLDAISGGTNIANYDRHLDDDFLASHICRPEICDRVESILGPNVLCWRTEFFPKYPGDEGTDWHQADTFANASGKPQIIWPENEEFGGTITVWTAFTDANIANGCLQFIPGTQNSMNYDETKRMTYEPDANNSVVKDGVRRGFFGYDYRQLQIDENWKPDEASAVPMQMKAGQFIIFWSTLMHASYPHSGESQEMRMGFASRYVPSFVHVYPDSDHIEEYGGRISLEKYGAVQVIGDETPEYNRLVTHTTRGKKFEAV 310
               SCOP domains d2fctb_ B: Syringomycin biosynthesis enzyme 2, Syr        B2                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhheeeeee..hhhhhhhhhhhhhhhh..........--------hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh..eeeeeeeeeee.....ee................ee..........eeeeee....hhhhh.eeee........................eee..eeee....hhhhhh.......hhhhheee.....eeeeee...eeee..........eeeeeeeeee...ee.....eeee..eeee......eeee....................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fct B   4 KFALTAEQRASFEKNGFIGPFDAYSPEEMKETWKRTRLRLLDRSAAAYQD--------NIANYDRHLDDDFLASHICRPEICDRVESILGPNVLCWRTEFFPKYPGDEGTDWHQADTFANASGKPQIIWPENEEFGGTITVWTAFTDANIANGCLQFIPGTQNSMNYDETKRMTYEPDANNSVVKDGVRRGFFGYDYRQLQIDENWKPDEASAVPMQMKAGQFIIFWSTLMHASYPHSGESQEMRMGFASRYVPSFVHVYPDSDHIEEYGGRISLEKYGAVQVIGDETPEYNRLVTHTTRGKKFEAV 310
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       
                                                                            53       62
   Legend:   → Mismatch (orange background)
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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  (1, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2FCT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FCT)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2FCT)

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