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Title :   STRUCTURE OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM B.FUSCUM IN COMPLEX WITH HPCA AT 1.50 ANG RESOLUTION

Authors :   E. G. Kovaleva, J. D. Lipscomb

Date :   07 Aug 12 (Deposition) - 31 Oct 12 (Release) - 12 Dec 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Dioxygenase, Oxygen Activation, Fe(Ii), 2-His-1-Carboxylate Facial Triad, Homoprotocatechuate, 4-Nitrocatechol, Oxy Complex, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. G. Kovaleva, J. D. Lipscomb
Structural Basis For The Role Of Tyrosine 257 Of Homoprotocatechuate 2, 3-Dioxygenase In Substrate And Oxygen Activation.
Biochemistry V. 51 8755 2012
PubMed-ID: 23066739 | Reference-DOI: 10.1021/BI301115C

Molecule 1 - HOMOPROTOCATECHUATE 2,3-DIOXYGENASE
	Chains	:	A, B, C, D
	EC Number	:	1.13.11.15
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PYZW204
	Expression System Strain	:	JM109
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	HPCD
	Organism Scientific	:	BREVIBACTERIUM FUSCUM
	Organism Taxid	:	47914
	Strain	:	ATCC 15993

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 16)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	CL	3	Ligand/Ion	CHLORIDE ION
3	DHY	1	Ligand/Ion	2-(3,4-DIHYDROXYPHENYL)ACETIC ACID
4	FE2	4	Ligand/Ion	FE (II) ION
5	P6G	5	Ligand/Ion	HEXAETHYLENE GLYCOL
6	PG4	2	Ligand/Ion	TETRAETHYLENE GLYCOL

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:155 , HIS A:214 , GLU A:267 , HOH A:788 , HOH A:789 , HOH A:790	BINDING SITE FOR RESIDUE FE2 A 401
02	AC2	SOFTWARE	GLU A:22 , VAL A:24 , LYS A:68 , LYS A:75 , ARG A:104 , PHE A:108 , ASP A:315 , GLY A:316 , HOH A:804	BINDING SITE FOR RESIDUE P6G A 402
03	AC3	SOFTWARE	ARG A:243 , HIS A:248 , ARG A:293	BINDING SITE FOR RESIDUE CL A 403
04	AC4	SOFTWARE	HIS B:155 , HIS B:214 , GLU B:267 , HOH B:826 , HOH B:827 , HOH B:828	BINDING SITE FOR RESIDUE FE2 B 401
05	AC5	SOFTWARE	ASP A:184 , GLU A:185 , ASP B:184 , GLU B:185 , HOH B:501	BINDING SITE FOR RESIDUE CA B 402
06	AC6	SOFTWARE	GLU B:22 , THR B:67 , LYS B:68 , LYS B:75 , ARG B:104 , PHE B:108 , ASP B:315 , GLY B:316 , HOH B:748 , HOH B:859	BINDING SITE FOR RESIDUE P6G B 403
07	AC7	SOFTWARE	ASP A:183 , THR A:284 , ALA A:344 , GLY A:345 , HOH A:659 , HOH A:863 , ASP B:183 , THR B:284 , ALA B:344 , GLY B:345 , HOH B:566 , HOH B:758 , HOH B:805	BINDING SITE FOR RESIDUE P6G B 404
08	AC8	SOFTWARE	ARG B:243 , HIS B:248 , ARG B:293	BINDING SITE FOR RESIDUE CL B 405
09	AC9	SOFTWARE	ARG A:82 , ALA B:12 , ASP B:172 , GLY B:174 , ARG B:195 , HOH B:809 , HOH B:845 , HOH B:874 , HOH B:921	BINDING SITE FOR RESIDUE PG4 B 406
10	BC1	SOFTWARE	HIS C:155 , HIS C:214 , GLU C:267 , DHY C:403 , HOH C:774	BINDING SITE FOR RESIDUE FE2 C 401
11	BC2	SOFTWARE	GLU C:22 , THR C:67 , LYS C:68 , LYS C:75 , ARG C:104 , PHE C:108 , ASP C:315 , GLY C:316 , HOH C:702 , HOH C:866	BINDING SITE FOR RESIDUE P6G C 402
12	BC3	SOFTWARE	HIS C:155 , TRP C:192 , HIS C:200 , HIS C:214 , ARG C:243 , HIS C:248 , VAL C:250 , SER C:251 , TYR C:257 , GLU C:267 , TYR C:269 , ARG C:293 , TRP C:304 , FE2 C:401	BINDING SITE FOR RESIDUE DHY C 403
13	BC4	SOFTWARE	ALA C:12 , ASP C:14 , GLY C:174 , ARG C:195 , HOH C:639 , HOH C:752 , HOH C:833 , HOH C:836	BINDING SITE FOR RESIDUE PG4 C 404
14	BC5	SOFTWARE	HIS D:155 , HIS D:214 , GLU D:267 , HOH D:791 , HOH D:858 , HOH D:861	BINDING SITE FOR RESIDUE FE2 D 401
15	BC6	SOFTWARE	GLU D:22 , THR D:67 , LYS D:68 , LYS D:75 , ARG D:104 , PHE D:108 , ASP D:315 , GLY D:316 , HOH D:719 , HOH D:789	BINDING SITE FOR RESIDUE P6G D 402
16	BC7	SOFTWARE	ARG D:243 , HIS D:248 , ARG D:293	BINDING SITE FOR RESIDUE CL D 403

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

Asymmetric/Biological Unit

No.	Residues
1	Gly A:209	-	Pro A:210
2	Gly A:244	-	Pro A:245
3	Gly B:209	-	Pro B:210
4	Gly B:244	-	Pro B:245
5	Gly C:209	-	Pro C:210
6	Gly C:244	-	Pro C:245
7	Gly D:209	-	Pro D:210
8	Gly D:244	-	Pro D:245

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

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

(no "Exon" information available for 4GHG)

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:356
                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4ghga1 A:3-147 Homoprotocatechuate 2,3-dioxygenase                                                                                              d4ghga2 A:148-358 Homoprotocatechuate 2,3-dioxygenase                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeeeeee.hhhhhhhhhh.....eeeee...eeeee.........eeeee....eeeeeeeee.hhhhhhhhhhhhhhh...eeee..........eeeee.....eeeee......................eeeeeeeee.hhhhhhhhhhhh..eeeeeee.....eeeeeee.......eeeee....eeeeeeee..hhhhhhhhhhhhhhh.hhh.eeeeeee......eeeeee.....eeeeee............eeee..............hhhhhhh....................hhhhhhh....ee..........ee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ghg A   3 NEIPKPVAPAPDILRCAYAELVVTDLAKSRNFYVDVLGLHVSYEDENQIYLRSFEEFIHHNLVLTKGPVAALKAMAFRVRTPEDVDKAEAYYQELGCRTERRKDGFVKGIGDALRVEDPLGFPYEFFFETTHVERLHMRYDLYSAGELVRLDHFNQVTPDVPRGRKYLEDLGFRVTEDIQDDEGTTYAAWMHRKGTVHDTALTGGNGPRLHHVAFSTHEKHNIIQICDKMGALRISDRIERGPGRHGVSNAFYLYILDPDNHRIEIYTQDYYTGDPDNPTITWNVHDNQRRDWWGNPVVPSWYTEASKVLDLDGNVQEIIERTDDSELEVTIGADGFSFTRAGDEDGSYHGQASKG 358
                                    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       282       292       302       312       322       332       342       352

Chain B from PDB  Type:PROTEIN  Length:360
                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4ghgb1 B:3-147 Homoprotocatechuate 2,3-dioxygenase                                                                                              d4ghgb2 B:148-362 Homoprotocatechuate 2,3-dioxygenase                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............eeeeeeeeeee.hhhhhhhhhh.....eeeee...eeeee.........eeeee....eeeeeeeee.hhhhhhhhhhhhhhh...eeee..........eeeee.....eeeee......................eeeeeeeee.hhhhhhhhhhhh..eeeeeee.....eeeeeee.......eeeee....eeeeeeee..hhhhhhhhhhhhhhh.hhh.eeeeeee......eeeeee.....eeeeee............eeee..............hhhhhhh.ee.................hhhhhhhh...ee..........ee......eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ghg B   3 NEIPKPVAPAPDILRCAYAELVVTDLAKSRNFYVDVLGLHVSYEDENQIYLRSFEEFIHHNLVLTKGPVAALKAMAFRVRTPEDVDKAEAYYQELGCRTERRKDGFVKGIGDALRVEDPLGFPYEFFFETTHVERLHMRYDLYSAGELVRLDHFNQVTPDVPRGRKYLEDLGFRVTEDIQDDEGTTYAAWMHRKGTVHDTALTGGNGPRLHHVAFSTHEKHNIIQICDKMGALRISDRIERGPGRHGVSNAFYLYILDPDNHRIEIYTQDYYTGDPDNPTITWNVHDNQRRDWWGNPVVPSWYTEASKVLDLDGNVQEIIERTDDSELEVTIGADGFSFTRAGDEDGSYHGQASKGFKLG 362
                                    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       282       292       302       312       322       332       342       352       362

Chain C from PDB  Type:PROTEIN  Length:356
                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4ghgc1 C:2-147 Homoprotocatechuate 2,3-dioxygenase                                                                                               d4ghgc2 C:148-357 Homoprotocatechuate 2,3-dioxygenase                                                                                                                                                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeeeeeee.hhhhhhhhhhh....eeeee...eeeee.........eeeee....eeeeeeeee..hhhhhhhhhhhhhh...eeee..........eeeee.....eeeee......................eeeeeeeee.hhhhhhhhhhhh..eeeeeee.....eeeeeee.......eeeee....eeeeeeee..hhhhhhhhhhhhhhh.hhh.eeeeeee......eeeeee.....eeeeee............eeee..............hhhhhhh.ee.................hhhhhhhh...ee..........ee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ghg C   2 SNEIPKPVAPAPDILRCAYAELVVTDLAKSRNFYVDVLGLHVSYEDENQIYLRSFEEFIHHNLVLTKGPVAALKAMAFRVRTPEDVDKAEAYYQELGCRTERRKDGFVKGIGDALRVEDPLGFPYEFFFETTHVERLHMRYDLYSAGELVRLDHFNQVTPDVPRGRKYLEDLGFRVTEDIQDDEGTTYAAWMHRKGTVHDTALTGGNGPRLHHVAFSTHEKHNIIQICDKMGALRISDRIERGPGRHGVSNAFYLYILDPDNHRIEIYTQDYYTGDPDNPTITWNVHDNQRRDWWGNPVVPSWYTEASKVLDLDGNVQEIIERTDDSELEVTIGADGFSFTRAGDEDGSYHGQASK 357
                                    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

Chain D from PDB  Type:PROTEIN  Length:360
                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4ghgd1 D:3-147 Homoprotocatechuate 2,3-dioxygenase                                                                                              d4ghgd2 D:148-362 Homoprotocatechuate 2,3-dioxygenase                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............eeeeeeeeeee.hhhhhhhhhh.....eeeee...eeeee.........eeeee....eeeeeeeee.hhhhhhhhhhhhhhh...eeee..........eeeee.....eeeee......................eeeeeeeee.hhhhhhhhhhhh..eeeeeee.....eeeeeee.......eeeee....eeeeeeee..hhhhhhhhhhhhhhh.hhh.eeeeeee......eeeeee.....eeeeee............eeee..............hhhhhhh....................hhhhhhh....ee..........ee..hhh.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ghg D   3 NEIPKPVAPAPDILRCAYAELVVTDLAKSRNFYVDVLGLHVSYEDENQIYLRSFEEFIHHNLVLTKGPVAALKAMAFRVRTPEDVDKAEAYYQELGCRTERRKDGFVKGIGDALRVEDPLGFPYEFFFETTHVERLHMRYDLYSAGELVRLDHFNQVTPDVPRGRKYLEDLGFRVTEDIQDDEGTTYAAWMHRKGTVHDTALTGGNGPRLHHVAFSTHEKHNIIQICDKMGALRISDRIERGPGRHGVSNAFYLYILDPDNHRIEIYTQDYYTGDPDNPTITWNVHDNQRRDWWGNPVVPSWYTEASKVLDLDGNVQEIIERTDDSELEVTIGADGFSFTRAGDEDGSYHGQASKGFKLG 362
                                    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       282       292       302       312       322       332       342       352       362

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase (136)

Superfamily: Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase (136)

Family: Extradiol dioxygenases (43)

Protein domain: Homoprotocatechuate 2,3-dioxygenase (17)

Brevibacterium fuscum [TaxId: 47914] (14)

1a	d4ghga1	A:3-147
1b	d4ghga2	A:148-358
1c	d4ghgb1	B:3-147
1d	d4ghgb2	B:148-362
1e	d4ghgc1	C:2-147
1f	d4ghgc2	C:148-357
1g	d4ghgd1	D:3-147
1h	d4ghgd2	D:148-362

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:209 - Pro A:210	[ RasMol ]
		Gly A:244 - Pro A:245	[ RasMol ]
		Gly B:209 - Pro B:210	[ RasMol ]
		Gly B:244 - Pro B:245	[ RasMol ]
		Gly C:209 - Pro C:210	[ RasMol ]
		Gly C:244 - Pro C:245	[ RasMol ]
		Gly D:209 - Pro D:210	[ RasMol ]
		Gly D:244 - Pro D:245	[ RasMol ]

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	4ghg
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4ghc	STRUCTURE OF Y257F VARIANT OF HOMOPROTOCATECHUATE 2,3- DIOXYGENASE FROM B.FUSCUM AT 1.55 ANG RESOLUTION
4ghd	STRUCTURE OF Y257F VARIANT OF HOMOPROTOCATECHUATE 2,3- DIOXYGENASE FROM B.FUSCUM IN COMPLEX WITH HPCA AT 1.85 ANG RESOLUTION
4ghe	STRUCTURE OF Y257F VARIANT OF HOMOPROTOCATECHUATE 2,3- DIOXYGENASE FROM B.FUSCUM IN COMPLEX WITH 4-NITROCATECHOL AT 1.60 ANG RESOLUTION
4ghf	STRUCTURE OF Y257F VARIANT OF HOMOPROTOCATECHUATE 2,3- DIOXYGENASE FROM B.FUSCUM IN COMPLEX WITH 4-NITROCATECHOL AND DIOXYGEN AT 1.67 ANG RESOLUTION
4ghh	STRUCTURE OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM B.FUSCUM IN COMPLEX WITH 4-NITROCATECHOL AT 1.55 ANG RESOLUTION

Description

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Ligands, Modified Residues, Ions (6, 16)

Sites (16, 16)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

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Exons (0, 0)

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Gene Ontology (3, 3)

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