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(-) Description

Title :  SUBSTRATE-BOUND STRUCTURE OF A UBIA HOMOLOG FROM AEROPYRUM PERNIX K1
 
Authors :  W. Li, W. Cheng
Date :  10 Jan 14  (Deposition) - 19 Mar 14  (Release) - 19 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.56
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Keywords :  All Alpha Helical, Intramembrane Aromatic Prenyltransferase, Membrane, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Cheng, W. Li
Structural Insights Into Ubiquinone Biosynthesis In Membranes.
Science V. 343 878 2014
PubMed-ID: 24558159  |  Reference-DOI: 10.1126/SCIENCE.1246774

(-) Compounds

Molecule 1 - 4-HYDROXYBENZOATE OCTAPRENYLTRANSFERASE
    Chains: A, B, C, D, E, F
    EC Number: 2.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: C43
    Expression System Taxid: 562
    Expression System Vector Type: PET
    Gene: UBIA, APE_1570
    Organism Scientific: AEROPYRUM PERNIX
    Organism Taxid: 272557
    Strain: K1

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A     
Biological Unit 2 (1x):  B    
Biological Unit 3 (1x):   C   
Biological Unit 4 (1x):    D  
Biological Unit 5 (1x):     E 
Biological Unit 6 (1x):      F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 24)

Asymmetric Unit (3, 24)
No.NameCountTypeFull Name
1GST6Ligand/IonGERANYL S-THIOLODIPHOSPHATE
2MG12Ligand/IonMAGNESIUM ION
3PHB6Ligand/IonP-HYDROXYBENZOIC ACID
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1GST1Ligand/IonGERANYL S-THIOLODIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3PHB1Ligand/IonP-HYDROXYBENZOIC ACID
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1GST1Ligand/IonGERANYL S-THIOLODIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3PHB1Ligand/IonP-HYDROXYBENZOIC ACID
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1GST1Ligand/IonGERANYL S-THIOLODIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3PHB1Ligand/IonP-HYDROXYBENZOIC ACID
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
1GST1Ligand/IonGERANYL S-THIOLODIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3PHB1Ligand/IonP-HYDROXYBENZOIC ACID
Biological Unit 5 (2, 2)
No.NameCountTypeFull Name
1GST1Ligand/IonGERANYL S-THIOLODIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3PHB1Ligand/IonP-HYDROXYBENZOIC ACID
Biological Unit 6 (2, 2)
No.NameCountTypeFull Name
1GST1Ligand/IonGERANYL S-THIOLODIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3PHB1Ligand/IonP-HYDROXYBENZOIC ACID

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:43 , ARG A:63 , ARG A:67 , TYR A:115 , LEU A:133 , PHB A:302 , MG A:303 , MG A:304 , HOH A:401BINDING SITE FOR RESIDUE GST A 301
02AC2SOFTWARELEU A:42 , ARG A:43 , GLY A:46 , MET A:47 , ASN A:50 , VAL A:132 , GST A:301BINDING SITE FOR RESIDUE PHB A 302
03AC3SOFTWAREASP A:58 , GST A:301BINDING SITE FOR RESIDUE MG A 303
04AC4SOFTWAREGST A:301 , HOH A:401BINDING SITE FOR RESIDUE MG A 304
05AC5SOFTWAREARG B:43 , ASP B:54 , ASP B:58 , ARG B:63 , ARG B:67 , TYR B:115 , LEU B:129 , LEU B:133 , PHB B:302 , MG B:303 , MG B:304 , HOH B:401BINDING SITE FOR RESIDUE GST B 301
06AC6SOFTWARELEU B:42 , ARG B:43 , MET B:47 , ASN B:50 , VAL B:132 , GST B:301BINDING SITE FOR RESIDUE PHB B 302
07AC7SOFTWAREASP B:54 , ASP B:58 , LYS B:119 , GST B:301BINDING SITE FOR RESIDUE MG B 303
08AC8SOFTWAREGST B:301 , HOH B:401BINDING SITE FOR RESIDUE MG B 304
09AC9SOFTWAREARG C:43 , ASP C:58 , ARG C:63 , ARG C:67 , TYR C:115 , LYS C:119 , LEU C:129 , LEU C:133 , ASP C:175 , PHB C:302 , MG C:303 , MG C:304 , HOH C:401BINDING SITE FOR RESIDUE GST C 301
10BC1SOFTWARELEU C:42 , ARG C:43 , GLY C:46 , MET C:47 , ASN C:50 , VAL C:132 , GST C:301BINDING SITE FOR RESIDUE PHB C 302
11BC2SOFTWAREASP C:58 , LYS C:119 , GST C:301BINDING SITE FOR RESIDUE MG C 303
12BC3SOFTWAREGST C:301 , HOH C:401BINDING SITE FOR RESIDUE MG C 304
13BC4SOFTWAREASP D:58 , ARG D:63 , ARG D:67 , TYR D:115 , LEU D:133 , PHB D:302 , MG D:303 , MG D:304 , HOH D:401BINDING SITE FOR RESIDUE GST D 301
14BC5SOFTWAREARG D:43 , MET D:47 , ASN D:50 , GST D:301BINDING SITE FOR RESIDUE PHB D 302
15BC6SOFTWAREASP D:58 , LYS D:119 , GST D:301BINDING SITE FOR RESIDUE MG D 303
16BC7SOFTWAREGST D:301 , HOH D:401BINDING SITE FOR RESIDUE MG D 304
17BC8SOFTWAREARG E:43 , ASN E:50 , ASP E:54 , ASP E:58 , ARG E:63 , ARG E:67 , TYR E:115 , LYS E:119 , LEU E:133 , PHB E:302 , MG E:303 , MG E:304 , HOH E:401BINDING SITE FOR RESIDUE GST E 301
18BC9SOFTWARELEU E:42 , ARG E:43 , GLY E:46 , MET E:47 , ASN E:50 , ALA E:112 , VAL E:132 , GST E:301BINDING SITE FOR RESIDUE PHB E 302
19CC1SOFTWAREASP E:54 , ASP E:58 , LYS E:119 , GST E:301BINDING SITE FOR RESIDUE MG E 303
20CC2SOFTWAREGST E:301 , HOH E:401BINDING SITE FOR RESIDUE MG E 304
21CC3SOFTWAREASP F:58 , ARG F:63 , ARG F:67 , TYR F:115 , LEU F:133 , PHB F:302 , MG F:303 , MG F:304 , HOH F:401BINDING SITE FOR RESIDUE GST F 301
22CC4SOFTWAREARG F:43 , GLY F:46 , MET F:47 , ASN F:50 , GST F:301BINDING SITE FOR RESIDUE PHB F 302
23CC5SOFTWAREILE F:57 , ASP F:58 , GST F:301BINDING SITE FOR RESIDUE MG F 303
24CC6SOFTWAREGST F:301 , HOH F:401BINDING SITE FOR RESIDUE MG F 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4OD5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4OD5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4OD5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OD5)

(-) Exons   (0, 0)

(no "Exon" information available for 4OD5)

(-) 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:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.....hhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4od5 A   2 RLVRIEHTIFSLPFAYVGALLSRYPFTLADAILMAAAVVGLRMAGMAYNNIADLDIDRLNPRTAKRPLVVGAVSLREAWALVAAGSAIYFASAALLNTYALLLSPLVLAIALTYPHAKRLHPLPHLHLGIVLGSVVFGGAVAASGDEASSLGEVLRSVPWLYVAAVSLWVAGFDTIYSIMDIDFDRSHGLGSIPALLGPKGALAASLAMHAAAVALFIAGVEAYGLGAIATVSTALTALVIILVQAMAWLGRVKESFNLNLAVPIIIGAGIIVD 275
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    


Chain B from PDB  Type:PROTEIN  Length:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.....hhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4od5 B   2 RLVRIEHTIFSLPFAYVGALLSRYPFTLADAILMAAAVVGLRMAGMAYNNIADLDIDRLNPRTAKRPLVVGAVSLREAWALVAAGSAIYFASAALLNTYALLLSPLVLAIALTYPHAKRLHPLPHLHLGIVLGSVVFGGAVAASGDEASSLGEVLRSVPWLYVAAVSLWVAGFDTIYSIMDIDFDRSHGLGSIPALLGPKGALAASLAMHAAAVALFIAGVEAYGLGAIATVSTALTALVIILVQAMAWLGRVKESFNLNLAVPIIIGAGIIVD 275
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    


Chain C from PDB  Type:PROTEIN  Length:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.....hhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4od5 C   2 RLVRIEHTIFSLPFAYVGALLSRYPFTLADAILMAAAVVGLRMAGMAYNNIADLDIDRLNPRTAKRPLVVGAVSLREAWALVAAGSAIYFASAALLNTYALLLSPLVLAIALTYPHAKRLHPLPHLHLGIVLGSVVFGGAVAASGDEASSLGEVLRSVPWLYVAAVSLWVAGFDTIYSIMDIDFDRSHGLGSIPALLGPKGALAASLAMHAAAVALFIAGVEAYGLGAIATVSTALTALVIILVQAMAWLGRVKESFNLNLAVPIIIGAGIIVD 275
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    


Chain D from PDB  Type:PROTEIN  Length:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.....hhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4od5 D   2 RLVRIEHTIFSLPFAYVGALLSRYPFTLADAILMAAAVVGLRMAGMAYNNIADLDIDRLNPRTAKRPLVVGAVSLREAWALVAAGSAIYFASAALLNTYALLLSPLVLAIALTYPHAKRLHPLPHLHLGIVLGSVVFGGAVAASGDEASSLGEVLRSVPWLYVAAVSLWVAGFDTIYSIMDIDFDRSHGLGSIPALLGPKGALAASLAMHAAAVALFIAGVEAYGLGAIATVSTALTALVIILVQAMAWLGRVKESFNLNLAVPIIIGAGIIVD 275
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    


Chain E from PDB  Type:PROTEIN  Length:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.....hhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4od5 E   2 RLVRIEHTIFSLPFAYVGALLSRYPFTLADAILMAAAVVGLRMAGMAYNNIADLDIDRLNPRTAKRPLVVGAVSLREAWALVAAGSAIYFASAALLNTYALLLSPLVLAIALTYPHAKRLHPLPHLHLGIVLGSVVFGGAVAASGDEASSLGEVLRSVPWLYVAAVSLWVAGFDTIYSIMDIDFDRSHGLGSIPALLGPKGALAASLAMHAAAVALFIAGVEAYGLGAIATVSTALTALVIILVQAMAWLGRVKESFNLNLAVPIIIGAGIIVD 275
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    


Chain F from PDB  Type:PROTEIN  Length:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.....hhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4od5 F   2 RLVRIEHTIFSLPFAYVGALLSRYPFTLADAILMAAAVVGLRMAGMAYNNIADLDIDRLNPRTAKRPLVVGAVSLREAWALVAAGSAIYFASAALLNTYALLLSPLVLAIALTYPHAKRLHPLPHLHLGIVLGSVVFGGAVAASGDEASSLGEVLRSVPWLYVAAVSLWVAGFDTIYSIMDIDFDRSHGLGSIPALLGPKGALAASLAMHAAAVALFIAGVEAYGLGAIATVSTALTALVIILVQAMAWLGRVKESFNLNLAVPIIIGAGIIVD 275
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271
   Legend:   → Mismatch (orange background)
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  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 4OD5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OD5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OD5)

(-) Gene Ontology  (4, 4)

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        Q9YBM8_AERPE | Q9YBM8: 4od4

(-) Related Entries Specified in the PDB File

4od4 APO STRUCTURE OF A UBIA HOMOLOG FROM AEROPYRUM PERNIX K1