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Title :   CRYSTAL STRUCTURE OF QUEE FROM BURKHOLDERIA MULTIVORANS IN COMPLEX WITH ADOMET, 7-CARBOXY-7-DEAZAGUANINE, AND MG2+

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) - 05 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.91

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

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

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 11)

No.	Name	Count	Type	Full Name
1	2KA	2	Ligand/Ion	2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDINE-5-CARBOXYLIC ACID
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	NA	1	Ligand/Ion	SODIUM ION
4	PO4	2	Ligand/Ion	PHOSPHATE ION
5	SAM	2	Ligand/Ion	S-ADENOSYLMETHIONINE
6	SF4	2	Ligand/Ion	IRON/SULFUR CLUSTER

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:31 , CYS A:46 , CYS A:49 , GLY A:92 , ASN A:118 , LYS A:135 , SAM A:302	BINDING SITE FOR RESIDUE SF4 A 301
02	AC2	SOFTWARE	PHE A:48 , CYS A:49 , ASP A:50 , THR A:51 , THR A:90 , GLY A:91 , 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 , 2KA A:303 , HOH A:414 , HOH A:422	BINDING SITE FOR RESIDUE SAM A 302
03	AC3	SOFTWARE	LEU A:12 , GLN A:13 , GLY A:14 , PHE A:25 , ARG A:27 , THR A:90 , HIS A:204 , PRO A:210 , SAM A:302 , MG A:304 , HOH A:516	BINDING SITE FOR RESIDUE 2KA A 303
04	AC4	SOFTWARE	ARG A:27 , ASP A:50 , THR A:51 , 2KA A:303 , HOH A:414 , HOH A:441 , HOH A:601	BINDING SITE FOR RESIDUE MG A 304
05	AC5	SOFTWARE	ARG A:21 , HIS A:84 , HOH A:487 , HOH A:526 , HOH B:580	BINDING SITE FOR RESIDUE PO4 A 305
06	AC6	SOFTWARE	CYS B:31 , CYS B:46 , CYS B:49 , GLY B:92 , ASN B:118 , LYS B:135 , SAM B:302	BINDING SITE FOR RESIDUE SF4 B 301
07	AC7	SOFTWARE	PHE B:48 , CYS B:49 , ASP B:50 , THR B:51 , THR B:90 , GLY B:91 , 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 , 2KA B:303 , HOH B:405 , HOH B:413	BINDING SITE FOR RESIDUE SAM B 302
08	AC8	SOFTWARE	LEU B:12 , GLN B:13 , GLY B:14 , PHE B:25 , ARG B:27 , THR B:90 , HIS B:204 , PRO B:210 , SAM B:302 , MG B:304	BINDING SITE FOR RESIDUE 2KA B 303
09	AC9	SOFTWARE	ARG B:27 , THR B:51 , 2KA B:303 , HOH B:413 , HOH B:442	BINDING SITE FOR RESIDUE MG B 304
10	BC1	SOFTWARE	ARG B:21 , HIS B:84 , HOH B:511 , HOH B:535 , HOH B:579	BINDING SITE FOR RESIDUE PO4 B 305
11	BC2	SOFTWARE	HOH A:416 , HOH A:420 , GLN B:154 , HOH B:444 , HOH B:545	BINDING SITE FOR RESIDUE NA B 306

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

Asymmetric/Biological Unit

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

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

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

(no "Exon" information available for 4NJK)

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
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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........hhhhhh...................eee.hhhhhhhhhhhh........eeeee..hhhhh.hhhhhhhhhhh..eeeeee...........eeee...........eeeeeeeee.....hhhhhh..eeeeeeeee....hhhhhhhhhhhhhhhh..eee..hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4njk 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.hhhhhhhhhhhh........eeeee..hhhhh.hhhhhhhhhhh..eeeeee...........eeee...........eeeeeeeee.....hhhhhh..eeeeeeeee....hhhhhhhhhhhhhhhh..eee..hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4njk 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 '\|'

(no "SCOP Domain" information available for 4NJK)

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

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

Asymmetric/Biological Unit(hide GO term definitions)

(no "Gene Ontology" information available for 4NJK)

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Gly A:91 - Gly A:92	[ RasMol ]
		Gly B:91 - Gly B:92	[ RasMol ]
		Ile A:152 - Pro A:153	[ RasMol ]
		Ile B:152 - Pro B:153	[ RasMol ]

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	4njk
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	QUEE_BURM1 \| A0A0H3KB22
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	4.3.99.3
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	QUEE_BURM1 \| A0A0H3KB22
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UniProtKB/Swiss-Prot
	QUEE_BURM1 \| A0A0H3KB22	:	4njg 4njh 4nji 4njj

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+
4njj	QUEE FROM BURKHOLDERIA MULTIVORANS IN COMPLEX WITH ADOMET, 6-CARBOXY-5,6,7,8-TETRAHYDROPTERIN, AND MN2+

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 11)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (0, 0)

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Gene Ontology (0, 0)

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