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(-) Description

Title :  QUED FROM E. COLI
 
Authors :  V. Bandarian, S. A. Roberts, Z. D. Miles
Date :  02 Dec 13  (Deposition) - 16 Jul 14  (Release) - 10 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  T-Fold, 6-Ptps, Queuosine Biosynthesis Enzyme, Sepiapterin, C27A, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. D. Miles, S. A. Roberts, R. M. Mccarty, V. Bandarian
Biochemical And Structural Studies Of 6-Carboxy-5, 6, 7, 8-Tetrahydropterin Synthase Reveal The Molecular Basis Of Catalytic Promiscuity Within The Tunnel-Fold Superfamily.
J. Biol. Chem. V. 289 23641 2014
PubMed-ID: 24990950  |  Reference-DOI: 10.1074/JBC.M114.555680

(-) Compounds

Molecule 1 - 6-CARBOXY-5,6,7,8-TETRAHYDROPTERIN SYNTHASE
    Chains: A, B, C, D, E, F
    EC Number: 4.1.2.50
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PET29A
    Gene: B2765, JW2735, QUED, YGCM
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: CPH4 SYNTHASE, QUEUOSINE BIOSYNTHESIS PROTEIN QUED

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric/Biological Unit (3, 17)
No.NameCountTypeFull Name
1ACT5Ligand/IonACETATE ION
2ZN6Ligand/IonZINC ION
3ZSP6Ligand/Ion2-AMINO-6-[(1Z)-1,2-DIHYDROXYPROP-1-EN-1-YL]-7,8-DIHYDROPTERIDIN-4(3H)-ONE

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:16 , HIS A:31 , HIS A:33 , ZSP A:202BINDING SITE FOR RESIDUE ZN A 201
02AC2SOFTWAREHIS A:16 , HIS A:31 , HIS A:33 , THR A:84 , SER A:85 , GLU A:86 , GLU A:110 , ZN A:201 , HIS C:71 , LEU E:6 , TRP E:51 , ILE E:53 , ASP E:54 , PHE E:55BINDING SITE FOR RESIDUE ZSP A 202
03AC3SOFTWARELYS A:8 , LYS A:59 , HOH A:371BINDING SITE FOR RESIDUE ACT A 203
04AC4SOFTWAREHIS B:16 , HIS B:31 , HIS B:33 , ZSP B:202BINDING SITE FOR RESIDUE ZN B 201
05AC5SOFTWARELEU A:6 , TRP A:51 , ILE A:53 , ASP A:54 , PHE A:55 , HIS B:16 , LEU B:18 , LYS B:26 , HIS B:31 , HIS B:33 , THR B:84 , SER B:85 , GLU B:86 , GLU B:110 , ZN B:201 , HIS D:71BINDING SITE FOR RESIDUE ZSP B 202
06AC6SOFTWARELYS B:8 , LYS B:59 , HOH B:371 , LYS E:26BINDING SITE FOR RESIDUE ACT B 203
07AC7SOFTWAREHIS C:16 , HIS C:31 , HIS C:33 , ZSP C:202BINDING SITE FOR RESIDUE ZN C 201
08AC8SOFTWAREHIS A:71 , HIS C:16 , LEU C:18 , LYS C:26 , ALA C:27 , HIS C:31 , HIS C:33 , THR C:84 , SER C:85 , GLU C:86 , GLU C:110 , ZN C:201 , LEU D:6 , TRP D:51 , ILE D:53 , ASP D:54 , PHE D:55BINDING SITE FOR RESIDUE ZSP C 202
09AC9SOFTWARELYS C:8 , LYS C:59 , HOH C:371BINDING SITE FOR RESIDUE ACT C 203
10BC1SOFTWAREHIS D:16 , HIS D:31 , HIS D:33 , ZSP D:202BINDING SITE FOR RESIDUE ZN D 201
11BC2SOFTWAREHIS B:71 , HIS D:16 , LYS D:26 , ALA D:27 , HIS D:31 , HIS D:33 , THR D:84 , SER D:85 , GLU D:86 , GLU D:110 , ZN D:201 , LEU F:6 , TRP F:51 , ILE F:53 , ASP F:54 , PHE F:55BINDING SITE FOR RESIDUE ZSP D 202
12BC3SOFTWARELYS D:8 , LYS D:59 , HOH D:360BINDING SITE FOR RESIDUE ACT D 203
13BC4SOFTWAREHIS E:16 , HIS E:31 , HIS E:33 , ZSP E:202BINDING SITE FOR RESIDUE ZN E 201
14BC5SOFTWARELEU B:6 , TRP B:51 , ILE B:53 , ASP B:54 , PHE B:55 , HOH B:359 , HIS E:16 , ALA E:27 , HIS E:31 , HIS E:33 , THR E:84 , SER E:85 , GLU E:86 , GLU E:110 , ZN E:201 , HIS F:71BINDING SITE FOR RESIDUE ZSP E 202
15BC6SOFTWARELYS E:8 , LYS E:59 , HOH E:367 , HOH E:373BINDING SITE FOR RESIDUE ACT E 203
16BC7SOFTWAREHIS F:16 , HIS F:31 , HIS F:33 , ZSP F:202BINDING SITE FOR RESIDUE ZN F 201
17BC8SOFTWARELEU C:6 , TRP C:51 , ILE C:53 , ASP C:54 , PHE C:55 , HIS E:71 , HIS F:16 , LYS F:26 , ALA F:27 , HIS F:31 , HIS F:33 , THR F:84 , SER F:85 , GLU F:86 , GLU F:110 , ZN F:201BINDING SITE FOR RESIDUE ZSP F 202

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NTK)

(-) Sequences/Alignments

Asymmetric/Biological 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:121
                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeee........hhhhh.eeeeeeeeeeee...........hhhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhh.....eeeeeeeee..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ntk A   1 MMSTTLFKDFTFEAAHRLPHVPEGHKAGRLHGHSFMVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVMVKETCTAGCIYRGE 121
                                    10        20        30        40        50        60        70        80        90       100       110       120 


Chain B from PDB  Type:PROTEIN  Length:118
                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee........hhhhh.eeeeeeeeeeeee..........hhhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhh.....eeeeeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 4ntk B   3 STTLFKDFTFEAAHRLPHVPEGHKAGRLHGHSFMVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVMVKETCTAGCIYRG 120
                                    12        22        32        42        52        62        72        82        92       102       112        


Chain C from PDB  Type:PROTEIN  Length:119
                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee........hhhhh.eeeeeeeeeeee...........hhhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhh.....eeeeeeeee..eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 4ntk C   2 MSTTLFKDFTFEAAHRLPHVPEGHKAGRLHGHSFMVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVMVKETCTAGCIYRG 120
                                    11        21        31        41        51        61        71        81        91       101       111         


Chain D from PDB  Type:PROTEIN  Length:119
                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee........hhhhh.eeeeeeeeeeeee..........hhhhhhhhhhhhhhhhh.ee.hhh......hhhhhhhhhhhhhh.....eeeeeeeee..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 4ntk D   3 STTLFKDFTFEAAHRLPHVPEGHKAGRLHGHSFMVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVMVKETCTAGCIYRGE 121
                                    12        22        32        42        52        62        72        82        92       102       112         


Chain E from PDB  Type:PROTEIN  Length:120
                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee........hhhhh.eeeeeeeeeeee...........hhhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhh.....eeeeeeeee..eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ntk E   2 MSTTLFKDFTFEAAHRLPHVPEGHKAGRLHGHSFMVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVMVKETCTAGCIYRGE 121
                                    11        21        31        41        51        61        71        81        91       101       111       121


Chain F from PDB  Type:PROTEIN  Length:120
                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeee........hhhhh.eeeeeeeeeeee...........hhhhhhhhhhhhhhhhh.ee.hhh......hhhhhhhhhhhhhh.....eeeeeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ntk F   1 MMSTTLFKDFTFEAAHRLPHVPEGHKAGRLHGHSFMVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVMVKETCTAGCIYRG 120
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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 4NTK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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        QUED_ECOLI | P65870: 3qn0 3qn9 3qna 4ntm 4ntn

(-) Related Entries Specified in the PDB File

4ntm 4ntn