5D08 - JenaLib

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Title :   CRYSTAL STRUCTURE OF SELENOMETHIONINE-LABELED EPOXYQUEUOSINE REDUCTASE

Authors :   D. P. Dowling, Z. D. Miles, C. Kohrer, V. Bandarian, C. L. Drennan

Date :   02 Aug 15 (Deposition) - 28 Sep 16 (Release) - 14 Dec 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   B12, Trna Modification, Heat-Domain, Queuosine, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. P. Dowling, Z. D. Miles, C. Kohrer, S. J. Maiocco, S. J. Elliott, V. Bandarian, C. L. Drennan
Molecular Basis Of Cobalamin-Dependent Rna Modification.
Nucleic Acids Res. V. 44 9965 2016
PubMed-ID: 27638883 | Reference-DOI: 10.1093/NAR/GKW806

Molecule 1 - EPOXYQUEUOSINE REDUCTASE
	Chains	:	A, B
	EC Number	:	1.17.99.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PASK-IBA43PLUS
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	QUEG, YGAP, YHBA, BSU08910
	Organism Scientific	:	BACILLUS SUBTILIS (STRAIN 168)
	Organism Taxid	:	224308
	Strain	:	168
	Synonym	:	QUEUOSINE BIOSYNTHESIS PROTEIN QUEG

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 27)

No.	Name	Count	Type	Full Name
1	B12	2	Ligand/Ion	COBALAMIN
2	CL	2	Ligand/Ion	CHLORIDE ION
3	GOL	2	Ligand/Ion	GLYCEROL
4	MSE	15	Mod. Amino Acid	SELENOMETHIONINE
5	PO4	2	Ligand/Ion	PHOSPHATE ION
6	SF4	4	Ligand/Ion	IRON/SULFUR CLUSTER

Biological Unit 1 (5, 14)

No.	Name	Count	Type	Full Name
1	B12	1	Ligand/Ion	COBALAMIN
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	1	Ligand/Ion	GLYCEROL
4	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
5	PO4	2	Ligand/Ion	PHOSPHATE ION
6	SF4	2	Ligand/Ion	IRON/SULFUR CLUSTER

Biological Unit 2 (4, 11)

No.	Name	Count	Type	Full Name
1	B12	1	Ligand/Ion	COBALAMIN
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	1	Ligand/Ion	GLYCEROL
4	MSE	7	Mod. Amino Acid	SELENOMETHIONINE
5	PO4	-1	Ligand/Ion	PHOSPHATE ION
6	SF4	2	Ligand/Ion	IRON/SULFUR CLUSTER

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:153 , LYS A:154 , ASN A:155 , CYS A:188 , CYS A:191 , CYS A:194 , CYS A:247 , PRO A:248 , LEU A:249	binding site for residue SF4 A 501
02	AC2	SOFTWARE	CYS A:198 , LEU A:209 , CYS A:214 , ILE A:215 , CYS A:240 , CYS A:243	binding site for residue SF4 A 502
03	AC3	SOFTWARE	SER A:32 , LEU A:33 , ARG A:36 , SER A:47 , GLU A:50 , ARG A:57 , CYS A:97 , ASP A:134 , LEU A:138 , SER A:139 , ASP A:140 , ARG A:141 , ALA A:142 , SER A:152 , ASN A:155 , CYS A:156 , MSE A:157 , ILE A:158 , SER A:165 , VAL A:167 , LEU A:169 , PRO A:206 , GLY A:207 , LEU A:209 , SER A:216 , GLY A:239 , CYS A:240 , ASP A:241 , CYS A:243 , GLN A:244 , HOH A:643 , HOH A:693 , HOH A:731 , HOH A:744 , HOH A:758 , HOH A:770 , HOH A:779 , HOH A:832 , HOH A:844	binding site for residue B12 A 503
04	AC4	SOFTWARE	PHE A:49 , ASP A:134 , GLN A:220 , TYR A:238 , TRP A:294 , HOH A:606 , HOH A:660 , HOH A:770	binding site for residue GOL A 504
05	AC5	SOFTWARE	LYS A:112 , HIS A:258 , PRO A:259 , GLU A:260 , HOH A:673 , HOH A:735 , LYS B:354 , LYS B:358	binding site for residue PO4 A 505
06	AC6	SOFTWARE	LYS A:354 , LYS A:358 , HOH A:679 , HOH A:689 , LYS B:112 , HIS B:258 , PRO B:259 , GLU B:260	binding site for residue PO4 A 506
07	AC7	SOFTWARE	ALA B:153 , LYS B:154 , ASN B:155 , CYS B:188 , CYS B:191 , CYS B:194 , CYS B:247	binding site for residue SF4 B 501
08	AC8	SOFTWARE	CYS B:198 , LEU B:203 , LEU B:209 , CYS B:214 , ILE B:215 , CYS B:240 , THR B:242 , CYS B:243	binding site for residue SF4 B 502
09	AC9	SOFTWARE	SER B:32 , LEU B:33 , ARG B:36 , SER B:47 , GLU B:50 , ARG B:57 , CYS B:97 , ASP B:134 , LEU B:138 , SER B:139 , ASP B:140 , ARG B:141 , ALA B:142 , SER B:152 , ASN B:155 , CYS B:156 , MSE B:157 , ILE B:158 , SER B:165 , VAL B:167 , LEU B:169 , PRO B:206 , LEU B:209 , SER B:216 , GLY B:239 , CYS B:240 , ASP B:241 , CYS B:243 , GLN B:244 , HOH B:641 , HOH B:658 , HOH B:659 , HOH B:684 , HOH B:688 , HOH B:710 , HOH B:777	binding site for residue B12 B 503
10	AD1	SOFTWARE	ASP B:134 , GLN B:220 , TYR B:238 , TRP B:294 , HOH B:606 , HOH B:659 , HOH B:716	binding site for residue GOL B 504

(no "SS Bond" information available for 5D08)

(no "Cis Peptide Bond" information available for 5D08)

(no "SAP(SNP)/Variant" information available for 5D08)

(no "PROSITE Motif" information available for 5D08)

(no "Exon" information available for 5D08)

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:384
                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhh........hhhhhhhhhhhh....eeeeeeee..................ee.hhhh..hhhhhhhhhhhhhhhhhhh......eeee......hhhhhhhhh...ee.....ee.......eeeeeeee.................hhhhhhh....eee..ee.hhhhhhhhhh.....hhhhhh....eee..hhhhhhhhhhh......hhhhh.hhhhhh.hhhhhh..hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5d08 A   2 NVYQLKEELIEYAKSIGVDKIGFTTADTFDSLKDRLILQESLGYLSGFEEPDIEKRVTPKLLLPKAKSIVAIALAYPSRmKDAPRSTRTERRGIFCRASWGKDYHDVLREKLDLLEDFLKSKHEDIRTKSmVDTGELSDRAVAERAGIGFSAKNCmITTPEYGSYVYLAEmITNIPFEPDVPIEDmCGSCTKCLDACPTGALVNPGQLNAQRCISFLTQTKGFLPDEFRTKIGNRLYGCDTCQTVCPLNKGKDFHLHPEmEPDPEIAKPLLKPLLAISNREFKEKFGHVSGSWRGKKPIQRNAILALAHFKDASALPELTELmHKDPRPVIRGTAAWAIGKIGDPAYAEELEKALEKEKDEEAKLEIEKGIELLKASGmTKQGL 385
                                    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       281       291       301       311       321  |    331       341       351       361       371       381    
                                                                                                          81-MSE                                            132-MSE                  157-MSE        172-MSE        187-MSE                                                                   261-MSE                                                        324-MSE                                                 380-MSE

Chain B from PDB  Type:PROTEIN  Length:375
                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhh........hhhhhhhhhhhh....eeeeeeee..................ee.hhhh..hhhhhhhhhhhhhhhhhhh......eeee......hhhhhhhhh...ee.....ee.......eeeeeeee.................hhhhhhh....eee..ee.hhhhhhhhhh.....hhhhhh....eee..hhhhhhhhhhh......hhhhh.hhhhhh.hhhhhh..hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d08 B   2 NVYQLKEELIEYAKSIGVDKIGFTTADTFDSLKDRLILQESLGYLSGFEEPDIEKRVTPKLLLPKAKSIVAIALAYPSRmKDAPRSTRTERRGIFCRASWGKDYHDVLREKLDLLEDFLKSKHEDIRTKSmVDTGELSDRAVAERAGIGFSAKNCmITTPEYGSYVYLAEmITNIPFEPDVPIEDmCGSCTKCLDACPTGALVNPGQLNAQRCISFLTQTKGFLPDEFRTKIGNRLYGCDTCQTVCPLNKGKDFHLHPEmEPDPEIAKPLLKPLLAISNREFKEKFGHVSGSWRGKKPIQRNAILALAHFKDASALPELTELmHKDPRPVIRGTAAWAIGKIGDPAYAEELEKALEKEKDEEAKLEIEKGIELLK 376
                                    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       281       291       301       311       321  |    331       341       351       361       371     
                                                                                                          81-MSE                                            132-MSE                  157-MSE        172-MSE        187-MSE                                                                   261-MSE                                                        324-MSE

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 5D08)

(no "CATH Domain" information available for 5D08)

(no "Pfam Domain" information available for 5D08)

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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
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	5d08
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		Orientation in Membranes	:	OPM
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	QUEG_BACSU \| P97030
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	1.17.99.6
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	QUEG_BACSU \| P97030	:	5d0a 5d0b 5t8y

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 27)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Gene Ontology (9, 9)

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