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(-) Description

Title :  CRYSTAL STRUCTURE OF QUEE FROM BURKHOLDERIA MULTIVORANS IN COMPLEX WITH ADOMET, 6-CARBOXY-5,6,7,8-TETRAHYDROPTERIN, AND MANGANESE(II)
 
Authors :  D. P. Dowling, N. A. Bruender, A. P. Young, R. M. Mccarty, V. Bandarian, C. L. Drennan
Date :  10 Nov 13  (Deposition) - 25 Dec 13  (Release) - 02 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Adomet Radical Enzyme, Modified Partial Tim Barrel-Like Structure, Radical Sam Fold, Radical Adomet Fold, Synthase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. P. Dowling, N. A. Bruender, A. P. Young, R. M. Mccarty, V. Bandarian, C. L. Drennan
Radical Sam Enzyme Quee Defines A New Minimal Core Fold And Metal-Dependent Mechanism.
Nat. Chem. Biol. V. 10 106 2014
PubMed-ID: 24362703  |  Reference-DOI: 10.1038/NCHEMBIO.1426

(-) Compounds

Molecule 1 - 7-CARBOXY-7-DEAZAGUANINE SYNTHASE
    Chains: A, B
    EC Number: 4.3.99.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: QUEE, BMUL_3115, BMULJ_00116
    Organism Scientific: BURKHOLDERIA MULTIVORANS
    Organism Taxid: 395019
    Strain: ATCC 17616 / 249
    Synonym: CDG SYNTHASE, QUEUOSINE BIOSYNTHESIS PROTEIN QUEE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
12K82Ligand/Ion(6R)-2-AMINO-4-OXO-3,4,5,6,7,8-HEXAHYDROPTERIDINE-6-CARBOXYLIC ACID
2MN4Ligand/IonMANGANESE (II) ION
3SAM2Ligand/IonS-ADENOSYLMETHIONINE
4SF42Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:31 , CYS A:46 , CYS A:49 , GLY A:92 , ASN A:118 , LYS A:135 , SAM A:302BINDING SITE FOR RESIDUE SF4 A 301
02AC2SOFTWAREPHE A:48 , CYS A:49 , ASP A:50 , THR A:51 , THR A:90 , GLY A:92 , GLU A:93 , GLU A:116 , THR A:117 , ASN A:118 , SER A:133 , LYS A:135 , LYS A:149 , VAL A:151 , GLN A:173 , PRO A:174 , MET A:175 , ASP A:176 , GLN A:202 , SF4 A:301 , 2K8 A:303 , HOH A:434BINDING SITE FOR RESIDUE SAM A 302
03AC3SOFTWARELEU A:12 , GLN A:13 , GLY A:14 , GLU A:15 , PHE A:25 , ARG A:27 , THR A:90 , GLU A:116 , HIS A:204 , PRO A:210 , SAM A:302 , MN A:304 , HOH A:416 , HOH A:417BINDING SITE FOR RESIDUE 2K8 A 303
04AC4SOFTWARETHR A:51 , 2K8 A:303 , HOH A:416 , HOH A:417BINDING SITE FOR RESIDUE MN A 304
05AC5SOFTWAREASP A:52BINDING SITE FOR RESIDUE MN A 305
06AC6SOFTWARECYS B:31 , CYS B:46 , CYS B:49 , GLY B:92 , ASN B:118 , LYS B:135 , SAM B:302BINDING SITE FOR RESIDUE SF4 B 301
07AC7SOFTWAREPHE B:48 , CYS B:49 , ASP B:50 , THR B:51 , THR B:90 , GLY B:92 , GLU B:93 , GLU B:116 , THR B:117 , ASN B:118 , SER B:133 , LYS B:135 , LYS B:149 , VAL B:151 , GLN B:173 , PRO B:174 , MET B:175 , ASP B:176 , GLN B:202 , SF4 B:301 , 2K8 B:303 , HOH B:430BINDING SITE FOR RESIDUE SAM B 302
08AC8SOFTWARELEU B:12 , GLN B:13 , GLY B:14 , GLU B:15 , PHE B:25 , ARG B:27 , THR B:90 , GLU B:116 , HIS B:204 , PRO B:210 , SAM B:302 , MN B:304 , HOH B:419BINDING SITE FOR RESIDUE 2K8 B 303
09AC9SOFTWARETHR B:51 , 2K8 B:303 , HOH B:418 , HOH B:419BINDING SITE FOR RESIDUE MN B 304
10BC1SOFTWAREASP B:52BINDING SITE FOR RESIDUE MN B 305

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:91 -Gly A:92
2Ile A:152 -Pro A:153
3Gly B:91 -Gly B:92
4Ile B:152 -Pro B:153

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NJJ)

(-) 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:209
                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee.........eeeeeee...........hhhhh.................eee.hhhhhhhhhhh.........eeeee..hhhhh.hhhhhhhhhhh..eeeeee...........eeee...........eeeeeeeee.....hhhhhh..eeeeeeeee....hhhhhhhhhhhhhhhh...ee...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4njj A   2 TYAVKEIFYTLQGEGANAGRPAVFCRFAGCNLWSGREEDRAQAVCRFCDTDFVGTDGENGGKFKDADALVATIAGLWPAGEAHRFVVCTGGEPMLQLDQPLVDALHAAGFGIAIETNGSLPVLESIDWICVSPKADAPLVVTKGNELKVVIPQDNQRLADYAKLDFEYFLVQPMDGPSRDLNTKLAIDWCKRHPQWRLSMQTHKYLNIP 210
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201         


Chain B from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee.........eeeeeee........hhhhhh...................eee.hhhhhhhhhhh.........eeeee..hhhhh.hhhhhhhhhhh..eeeeee...........eeee..............eeeeee.....hhhhhh.....eeeeee....hhhhhhhhhhhhhhhh..eee..hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4njj B   2 TYAVKEIFYTLQGEGANAGRPAVFCRFAGCNLWSGREEDRAQAVCRFCDTDFVGTDGENGGKFKDADALVATIAGLWPAGEAHRFVVCTGGEPMLQLDQPLVDALHAAGFGIAIETNGSLPVLESIDWICVSPKADAPLVVTKGNELKVVIPQDNQRLADYAKLDFEYFLVQPMDGPSRDLNTKLAIDWCKRHPQWRLSMQTHKYLNIP 210
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201
   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 4NJJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4NJJ)

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  Cis Peptide Bonds
    Gly A:91 - Gly A:92   [ RasMol ]  
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    Ile A:152 - Pro A:153   [ RasMol ]  
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  4njj
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  QUEE_BURM1 | A0A0H3KB22
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  4.3.99.3
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        QUEE_BURM1 | A0A0H3KB22: 4njg 4njh 4nji 4njk

(-) Related Entries Specified in the PDB File

4njg QUEE FROM BURKHOLDERIA MULTIVORANS IN COMPLEX WITH ADOMET AND 6-CARBOXYPTERIN
4njh QUEE FROM BURKHOLDERIA MULTIVORANS IN COMPLEX WITH ADOMET AND 6-CARBOXY-5,6,7,8-TETRAHYDROPTERIN
4nji QUEE FROM BURKHOLDERIA MULTIVORANS IN COMPLEX WITH ADOMET, 6-CARBOXY-5,6,7,8-TETRAHYDROPTERIN, AND MG2+
4njk QUEE FROM BURKHOLDERIA MULTIVORANS IN COMPLEX WITH ADOMET, 7-CARBOXY-7-DEAZAGUANINE, AND MG2+