2WJ3 - JenaLib

Title :   CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE (HOD) FROM ARTHROBACTER NITROGUAJACOLICUS RU61A

Authors :   R. A. Steiner

Date :   20 May 09 (Deposition) - 26 Jan 10 (Release) - 26 Jan 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.09

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Alpha/Beta Hydrolase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. A. Steiner, H. J. Janssen, P. Roversi, A. J. Oakley, S. Fetzner
Structural Basis For Cofactor-Independent Dioxygenation Of N-Heteroaromatic Compounds At The {Alpha}/{Beta}-Hydrolase Fold.
Proc. Natl. Acad. Sci. Usa V. 107 657 2010
PubMed-ID: 20080731 | Reference-DOI: 10.1073/PNAS.0909033107
(for further references see the PDB file header)

Compounds

Molecule 1 - 1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
	Chains	:	A, B, C, D
	EC Number	:	1.13.11.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	M15/PREP4
	Expression System Taxid	:	562
	Expression System Vector	:	PQE30
	Mutation	:	YES
	Organism Scientific	:	ARTHROBACTER NITROGUAJACOLICUS
	Organism Taxid	:	211146
	Strain	:	RU61A

Structural Features

Chains, Units

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 10)

Asymmetric Unit (2, 10)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	SRT	8	Ligand/Ion	S,R MESO-TARTARIC ACID

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	SRT	2	Ligand/Ion	S,R MESO-TARTARIC ACID

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	SRT	2	Ligand/Ion	S,R MESO-TARTARIC ACID

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	SRT	2	Ligand/Ion	S,R MESO-TARTARIC ACID

Biological Unit 4 (1, 2)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	SRT	2	Ligand/Ion	S,R MESO-TARTARIC ACID

Sites (10, 10)

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:235 , TYR A:243 , ASP D:158	BINDING SITE FOR RESIDUE GOL A1276
02	AC2	SOFTWARE	SER B:101 , HIS B:102 , ASP B:126 , TRP B:127 , LEU B:128 , PHE B:136 , TRP B:160 , HIS B:251 , HOH B:2026	BINDING SITE FOR RESIDUE GOL B1276
03	AC3	SOFTWARE	LYS A:167 , ARG A:170 , HIS A:171 , ARG C:260 , VAL C:263	BINDING SITE FOR RESIDUE SRT A1277
04	AC4	SOFTWARE	LYS B:167 , ARG B:170 , HIS B:171 , ARG D:260 , VAL D:263	BINDING SITE FOR RESIDUE SRT B1277
05	AC5	SOFTWARE	ARG B:260 , VAL B:263 , LYS C:167 , ARG C:170 , HIS C:171	BINDING SITE FOR RESIDUE SRT C1275
06	AC6	SOFTWARE	ARG A:260 , VAL A:263 , LYS D:167 , ARG D:170 , HIS D:171	BINDING SITE FOR RESIDUE SRT D1275
07	AC7	SOFTWARE	HIS A:164 , ASP A:165 , LYS C:245 , LEU C:246 , GLY C:247 , HOH C:2086 , HOH C:2087 , HOH C:2088	BINDING SITE FOR RESIDUE SRT C1276
08	AC8	SOFTWARE	LYS B:245 , LEU B:246 , GLY B:247 , HOH B:2069 , HOH B:2070 , HOH B:2071 , GLY C:163 , HIS C:164 , ASP C:165 , GLU C:166	BINDING SITE FOR RESIDUE SRT B1278
09	AC9	SOFTWARE	HIS B:164 , ASP B:165 , HOH B:2040 , LYS D:245 , LEU D:246 , GLY D:247 , HOH D:2055 , HOH D:2056	BINDING SITE FOR RESIDUE SRT D1276
10	BC1	SOFTWARE	LYS A:245 , LEU A:246 , GLY A:247 , HOH A:2064 , HIS D:164 , ASP D:165 , GLU D:166	BINDING SITE FOR RESIDUE SRT A1278

SS Bonds (4, 4)

Cis Peptide Bonds (8, 8)

Asymmetric Unit

No.	Residues
1	Gly A:27	-	Pro A:28
2	Gln A:221	-	Pro A:222
3	Gly B:27	-	Pro B:28
4	Gln B:221	-	Pro B:222
5	Gly C:27	-	Pro C:28
6	Gln C:221	-	Pro C:222
7	Gly D:27	-	Pro D:28
8	Gln D:221	-	Pro D:222

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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
 aligned with HOD_PAENT | O31266 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:274
                                    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    
            HOD_PAENT     2 TDTYLHETLVFDNKLSYIDNQRDTDGPAILLLPGWCHDHRVYKYLIQELDADFRVIVPNWRGHGLSPCEVPDFGYQEQVKDALEILDQLGVETFLPVSHSHGGWVLVELLEQAGPERAPRGIIMDWLMWAPKPDFAKSLTLLKDPERWREGTHGLFDVWLDGHDEKRVRHHLLEEMADYGYDCWGRSGRVIEDAYGRNGSPMQMMANLTKTRPIRHIFSQPTEPEYEKINSDFAEQHPWFSYAKLGGPTHFPAIDVPDRAAVHIREFATAIRQG 275
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhh.eeeeee..eeeeeee........eeeee.....hhhhhhhhhhhhh....eeee...............hhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wj3 A   2 TDTYLHETLVFDNKLSYIDNQRDTDGPAILLLPGWCHDHRVYKYLIQELDADFRVIVPNWRGHGLSPSEVPDFGYQEQVKDALEILDQLGVETFLPVSHSHGGWVLVELLEQAGPERAPRGIIMDWLMWAPKPDFAKSLTLLKDPERWREGTHGLFDVWLDGHDEKRVRHHLLEEMADYGYDCWGRSGRVIEDAYGRNGSPMQMMANLTKTRPIRHIFSQPTEPEYEKINSDFAEQHPWFSYAKLGGPTHFPAIDVPDRAAVHIREFATAIRQG 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:273
 aligned with HOD_PAENT | O31266 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:273
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272   
            HOD_PAENT     3 DTYLHETLVFDNKLSYIDNQRDTDGPAILLLPGWCHDHRVYKYLIQELDADFRVIVPNWRGHGLSPCEVPDFGYQEQVKDALEILDQLGVETFLPVSHSHGGWVLVELLEQAGPERAPRGIIMDWLMWAPKPDFAKSLTLLKDPERWREGTHGLFDVWLDGHDEKRVRHHLLEEMADYGYDCWGRSGRVIEDAYGRNGSPMQMMANLTKTRPIRHIFSQPTEPEYEKINSDFAEQHPWFSYAKLGGPTHFPAIDVPDRAAVHIREFATAIRQG 275
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..eeeeeee........eeeee.....hhhhhhhhhhhhh....eeee...............hhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wj3 B   3 DTYLHETLVFDNKLSYIDNQRDTDGPAILLLPGWCHDHRVYKYLIQELDADFRVIVPNWRGHGLSPSEVPDFGYQEQVKDALEILDQLGVETFLPVSHSHGGWVLVELLEQAGPERAPRGIIMDWLMWAPKPDFAKSLTLLKDPERWREGTHGLFDVWLDGHDEKRVRHHLLEEMADYGYDCWGRSGRVIEDAYGRNGSPMQMMANLTKTRPIRHIFSQPTEPEYEKINSDFAEQHPWFSYAKLGGPTHFPAIDVPDRAAVHIREFATAIRQG 275
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272

Chain C from PDB  Type:PROTEIN  Length:273
 aligned with HOD_PAENT | O31266 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:273
                                    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   
            HOD_PAENT     2 TDTYLHETLVFDNKLSYIDNQRDTDGPAILLLPGWCHDHRVYKYLIQELDADFRVIVPNWRGHGLSPCEVPDFGYQEQVKDALEILDQLGVETFLPVSHSHGGWVLVELLEQAGPERAPRGIIMDWLMWAPKPDFAKSLTLLKDPERWREGTHGLFDVWLDGHDEKRVRHHLLEEMADYGYDCWGRSGRVIEDAYGRNGSPMQMMANLTKTRPIRHIFSQPTEPEYEKINSDFAEQHPWFSYAKLGGPTHFPAIDVPDRAAVHIREFATAIRQ 274
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhh.eeeeee..eeeeeee........eeeee.....hhhhhhhhhhhhh....eeee...............hhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wj3 C   2 TDTYLHETLVFDNKLSYIDNQRDTDGPAILLLPGWCHDHRVYKYLIQELDADFRVIVPNWRGHGLSPSEVPDFGYQEQVKDALEILDQLGVETFLPVSHSHGGWVLVELLEQAGPERAPRGIIMDWLMWAPKPDFAKSLTLLKDPERWREGTHGLFDVWLDGHDEKRVRHHLLEEMADYGYDCWGRSGRVIEDAYGRNGSPMQMMANLTKTRPIRHIFSQPTEPEYEKINSDFAEQHPWFSYAKLGGPTHFPAIDVPDRAAVHIREFATAIRQ 274
                                    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:273
 aligned with HOD_PAENT | O31266 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:273
                                    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   
            HOD_PAENT     2 TDTYLHETLVFDNKLSYIDNQRDTDGPAILLLPGWCHDHRVYKYLIQELDADFRVIVPNWRGHGLSPCEVPDFGYQEQVKDALEILDQLGVETFLPVSHSHGGWVLVELLEQAGPERAPRGIIMDWLMWAPKPDFAKSLTLLKDPERWREGTHGLFDVWLDGHDEKRVRHHLLEEMADYGYDCWGRSGRVIEDAYGRNGSPMQMMANLTKTRPIRHIFSQPTEPEYEKINSDFAEQHPWFSYAKLGGPTHFPAIDVPDRAAVHIREFATAIRQ 274
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee..eeeeeee........eeeee.....hhhhhhhhhhhhh....eeee...............hhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wj3 D   2 TDTYLHETLVFDNKLSYIDNQRDTDGPAILLLPGWCHDHRVYKYLIQELDADFRVIVPNWRGHGLSPSEVPDFGYQEQVKDALEILDQLGVETFLPVSHSHGGWVLVELLEQAGPERAPRGIIMDWLMWAPKPDFAKSLTLLKDPERWREGTHGLFDVWLDGHDEKRVRHHLLEEMADYGYDCWGRSGRVIEDAYGRNGSPMQMMANLTKTRPIRHIFSQPTEPEYEKINSDFAEQHPWFSYAKLGGPTHFPAIDVPDRAAVHIREFATAIRQ 274
                                    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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	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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

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Related Entries

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Related Entries Specified in the PDB File

2wj4	CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1- H-3-HYDROXY-4-OXOQUINALDINE 2,4- DIOXYGENASE (HOD) FROM ARTHROBACTER NITROGUAJACOLICUS RU61A ANAEROBICALLY COMPLEXED WITH ITS NATURAL SUBSTRATE 1-H-3-HYDROXY- 4-OXOQUINALDINE
2wj6	CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1- H-3-HYDROXY-4-OXOQUINALDINE 2,4- DIOXYGENASE (HOD) FROM ARTHROBACTER NITROGUAJACOLICUS RU61A COMPLEXED WITH ITS NATURAL SUBSTRATE N-ACETYLANTHRANILATE
2wm2	CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1- H-3-HYDROXY-4-OXOQUINALDINE 2,4- DIOXYGENASE (HOD) FROM ARTHROBACTER NITROGUAJACOLICUS RU61A IN COMPLEX WITH CHLORIDE

Description