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(-) Description

Title :  GEOSMIN SYNTHASE FROM STREPTOMYCES COELICOLOR N-TERMINAL DOMAIN COMPLEXED WITH THREE MG2+ IONS AND ALENDRONIC ACID
 
Authors :  G. G. Harris, P. M. Lombardi, T. A. Pemberton, T. Matsui, T. M. Weiss, K. E M. Koksal, F. V. Murphy, L. S. Vedula, W. K. W. Chou, D. E. Cane, D. W. Chri
Date :  25 Sep 15  (Deposition) - 09 Dec 15  (Release) - 23 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.11
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Terpene, Cyclase, Geosmin, Germacradienol, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. G. Harris, P. M. Lombardi, T. A. Pemberton, T. Matsui, T. M. Weiss, K. E. Cole, M. Koksal, F. V. Murphy, L. S. Vedula, W. K. Chou, D. E. Cane, D. W. Christianson
Structural Studies Of Geosmin Synthase, A Bifunctional Sesquiterpene Synthase With Alpha Alpha Domain Architecture That Catalyzes A Unique Cyclization-Fragmentation Reaction Sequence.
Biochemistry V. 54 7142 2015
PubMed-ID: 26598179  |  Reference-DOI: 10.1021/ACS.BIOCHEM.5B01143

(-) Compounds

Molecule 1 - GERMACRADIENOL/GEOSMIN SYNTHASE
    Chains: A, B
    EC Number: 4.2.3.22, 4.2.3.75, 4.1.99.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22BMV
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN (UNP RESIDUES 1-338)
    Gene: CYC2, SCO6073, SC9B1.20
    Organism Scientific: STREPTOMYCES COELICOLOR (STRAIN ATCC BAA-471 / A3(2) / M145)
    Organism Taxid: 100226
    Strain: ATCC BAA-471 / A3(2) / M145
    Synonym: SCGS

 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  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
12122Ligand/IonALENDRONATE
2MG6Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
12121Ligand/IonALENDRONATE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
12121Ligand/IonALENDRONATE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:86 , MG A:403 , 212 A:404 , HOH A:515 , HOH A:522 , HOH A:529 , HOH A:543binding site for residue MG A 401
2AC2SOFTWAREASN A:229 , SER A:233 , GLU A:237 , 212 A:404 , HOH A:508binding site for residue MG A 402
3AC3SOFTWAREASP A:86 , MG A:401 , 212 A:404 , HOH A:519 , HOH A:543 , HOH A:553binding site for residue MG A 403
4AC4SOFTWAREVAL A:82 , ASP A:86 , ARG A:184 , ASN A:229 , SER A:233 , ARG A:236 , GLU A:237 , ARG A:325 , TYR A:326 , MG A:401 , MG A:402 , MG A:403 , HOH A:508 , HOH A:519 , HOH A:522 , HOH A:528 , HOH A:529 , HOH A:543 , HOH A:551 , HOH A:553binding site for residue 212 A 404
5AC5SOFTWAREASP B:86 , MG B:403 , 212 B:404 , HOH B:513 , HOH B:517 , HOH B:533 , HOH B:541binding site for residue MG B 401
6AC6SOFTWAREASN B:229 , SER B:233 , GLU B:237 , 212 B:404 , HOH B:502binding site for residue MG B 402
7AC7SOFTWAREASP B:86 , MG B:401 , 212 B:404 , HOH B:518 , HOH B:521 , HOH B:533binding site for residue MG B 403
8AC8SOFTWAREVAL B:82 , PHE B:83 , ASP B:86 , ARG B:184 , ASN B:229 , SER B:233 , ARG B:236 , GLU B:237 , ARG B:325 , TYR B:326 , MG B:401 , MG B:402 , MG B:403 , HOH B:517 , HOH B:521 , HOH B:533 , HOH B:536 , HOH B:539 , HOH B:541binding site for residue 212 B 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DZ2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5DZ2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DZ2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DZ2)

(-) Exons   (0, 0)

(no "Exon" information available for 5DZ2)

(-) 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:322
                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dz2 A   4 QPFQLPHFYLPHPARLNPHLDEARAHSTTWAREMGMLEGSGVWEQSDLEAHDYGLLCAYTHPDCDGPALSLITDWYVWVFFFDDHFLEKYKRSQDRLAGKAHLDRLPLFMPLGMPEPRNPVEAGLADLWTRTVPAMSADWRRRFAVATEHLLNESMWELSNINEGRVANPVEYIEMRRKVGGAPWSAGLVEYATAEVPAAVAGTRPLRVLMETFSDAVHLRNDLFSYQREVEDEGELSNGVLVLETFFGCTTQEAADLVNDVLTSRLHQFEHTAFTEVPAVALEKGLTPLEVAAVGAYTKGLQDWQSGGHEWHMRSSRYMNK 329
                                    13        23        33        43        53        63        73        83        93       103       113 ||    127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327  
                                                                                                                                         115|                                                                                                                                                                                                                 
                                                                                                                                          120                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:322
                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dz2 B   4 QPFQLPHFYLPHPARLNPHLDEARAHSTTWAREMGMLEGSGVWEQSDLEAHDYGLLCAYTHPDCDGPALSLITDWYVWVFFFDDHFLEKYKRSQDRLAGKAHLDRLPLFMPLGMPEPRNPVEAGLADLWTRTVPAMSADWRRRFAVATEHLLNESMWELSNINEGRVANPVEYIEMRRKVGGAPWSAGLVEYATAEVPAAVAGTRPLRVLMETFSDAVHLRNDLFSYQREVEDEGELSNGVLVLETFFGCTTQEAADLVNDVLTSRLHQFEHTAFTEVPAVALEKGLTPLEVAAVGAYTKGLQDWQSGGHEWHMRSSRYMNK 329
                                    13        23        33        43        53        63        73        83        93       103       113 ||    127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327  
                                                                                                                                         115|                                                                                                                                                                                                                 
                                                                                                                                          120
   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  (0, 0)

(no "SCOP Domain" information available for 5DZ2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DZ2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DZ2)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        CYC2_STRCO | Q9X839: 5dw7

(-) Related Entries Specified in the PDB File

5dw7 STREPTOMYCES COELICOLOR GEOSMIN SYNTHASE IN THE UNLIGANDED STATE