4Z6R - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURE OF H200E VARIANT OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM B.FUSCUM IN COMPLEX WITH 4-SULFONYL CATECHOL AT 1.70 ANG RESOLUTION

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

Date :   06 Apr 15 (Deposition) - 26 Aug 15 (Release) - 16 Sep 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Dioxygenase, 2-His-1-Carboxylate Facial Triad, Oxygen Activation, Acid-Base Catalysis, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. G. Kovaleva, M. S. Rogers, J. D. Lipscomb
Structural Basis For Substrate And Oxygen Activation In Homoprotocatechuate 2, 3-Dioxygenase: Roles Of Conserved Active Site Histidine 200.
Biochemistry V. 54 5329 2015
PubMed-ID: 26267790 | Reference-DOI: 10.1021/ACS.BIOCHEM.5B00709

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

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (7, 18)

No.	Name	Count	Type	Full Name
1	4SX	1	Ligand/Ion	3,4-DIHYDROXYBENZENESULFONIC ACID
2	CA	1	Ligand/Ion	CALCIUM ION
3	CL	4	Ligand/Ion	CHLORIDE ION
4	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
5	FE2	4	Ligand/Ion	FE (II) ION
6	P6G	5	Ligand/Ion	HEXAETHYLENE GLYCOL
7	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:155 , HIS A:214 , GLU A:267 , HOH A:503 , HOH A:551 , HOH A:569	binding site for residue FE2 A 401
02	AC2	SOFTWARE	GLU A:22 , LYS A:68 , LYS A:75 , ARG A:104 , PHE A:108 , ASP A:315 , GLY A:316 , HOH A:575	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:503 , HOH B:546 , HOH B:681	binding site for residue FE2 B 401
05	AC5	SOFTWARE	ASP A:184 , GLU A:185 , HOH A:686 , ASP B:184 , GLU B:185 , HOH B:711	binding site for residue CA B 402
06	AC6	SOFTWARE	GLU B:22 , LYS B:68 , LYS B:75 , ARG B:104 , PHE B:108 , ASP B:315 , GLY B:316 , HOH B:640	binding site for residue P6G B 403
07	AC7	SOFTWARE	ASP A:183 , ALA A:344 , GLY A:345 , HOH A:671 , ASP B:183 , ALA B:344 , GLY B:345 , HOH B:501 , HOH B:504 , HOH B:653 , HOH B:684 , HOH B:712	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 B:195 , HOH B:570	binding site for residue EDO B 406
10	AD1	SOFTWARE	THR B:133	binding site for residue EDO B 407
11	AD2	SOFTWARE	HIS C:155 , HIS C:214 , GLU C:267 , 4SX C:403 , HOH C:609	binding site for residue FE2 C 401
12	AD3	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:579 , HOH C:662	binding site for residue P6G C 402
13	AD4	SOFTWARE	HIS C:155 , TRP C:192 , GLU 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:292 , ARG C:293 , FE2 C:401 , CL C:404 , HOH C:609	binding site for residue 4SX C 403
14	AD5	SOFTWARE	ARG C:243 , HIS C:248 , ARG C:293 , 4SX C:403	binding site for residue CL C 404
15	AD6	SOFTWARE	ASP C:172 , GLY C:174 , ARG C:195 , HOH C:719	binding site for residue PEG C 405
16	AD7	SOFTWARE	HIS D:155 , HIS D:214 , GLU D:267 , HOH D:504 , HOH D:507 , HOH D:644	binding site for residue FE2 D 401
17	AD8	SOFTWARE	GLU D:22 , LYS D:68 , LYS D:75 , ARG D:104 , PHE D:108 , ASP D:315 , GLY D:316 , HOH D:648	binding site for residue P6G D 402
18	AD9	SOFTWARE	ARG D:243 , HIS D:248 , ARG D:293	binding site for residue CL D 403

(no "SS Bond" information available for 4Z6R)

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 4Z6R)

(no "PROSITE Motif" information available for 4Z6R)

(no "Exon" information available for 4Z6R)

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:355
                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 4z6r A   4 EIPKPVAPAPDILRCAYAELVVTDLAKSRNFYVDVLGLHVSYEDENQIYLRSFEEFIHHNLVLTKGPVAALKAMAFRVRTPEDVDKAEAYYQELGCRTERRKDGFVKGIGDALRVEDPLGFPYEFFFETTHVERLHMRYDLYSAGELVRLDHFNQVTPDVPRGRKYLEDLGFRVTEDIQDDEGTTYAAWMHRKGTVEDTALTGGNGPRLHHVAFSTHEKHNIIQICDKMGALRISDRIERGPGRHGVSNAFYLYILDPDNHRIEIYTQDYYTGDPDNPTITWNVHDNQRRDWWGNPVVPSWYTEASKVLDLDGNVQEIIERTDDSELEVTIGADGFSFTRAGDEDGSYHGQASKG 358
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353

Chain B from PDB  Type:PROTEIN  Length:359
                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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.................hhhhhhh....ee..........ee..hhh.eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z6r B   4 EIPKPVAPAPDILRCAYAELVVTDLAKSRNFYVDVLGLHVSYEDENQIYLRSFEEFIHHNLVLTKGPVAALKAMAFRVRTPEDVDKAEAYYQELGCRTERRKDGFVKGIGDALRVEDPLGFPYEFFFETTHVERLHMRYDLYSAGELVRLDHFNQVTPDVPRGRKYLEDLGFRVTEDIQDDEGTTYAAWMHRKGTVEDTALTGGNGPRLHHVAFSTHEKHNIIQICDKMGALRISDRIERGPGRHGVSNAFYLYILDPDNHRIEIYTQDYYTGDPDNPTITWNVHDNQRRDWWGNPVVPSWYTEASKVLDLDGNVQEIIERTDDSELEVTIGADGFSFTRAGDEDGSYHGQASKGFKLG 362
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353

Chain C from PDB  Type:PROTEIN  Length:354
                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eeeeeeeeeee.hhhhhhhhhh.....eeeee...eeeee.........eeeee....eeeeeeeee..hhhhhhhhhhhhhh...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
                 4z6r C   4 EIPKPVAPAPDILRCAYAELVVTDLAKSRNFYVDVLGLHVSYEDENQIYLRSFEEFIHHNLVLTKGPVAALKAMAFRVRTPEDVDKAEAYYQELGCRTERRKDGFVKGIGDALRVEDPLGFPYEFFFETTHVERLHMRYDLYSAGELVRLDHFNQVTPDVPRGRKYLEDLGFRVTEDIQDDEGTTYAAWMHRKGTVEDTALTGGNGPRLHHVAFSTHEKHNIIQICDKMGALRISDRIERGPGRHGVSNAFYLYILDPDNHRIEIYTQDYYTGDPDNPTITWNVHDNQRRDWWGNPVVPSWYTEASKVLDLDGNVQEIIERTDDSELEVTIGADGFSFTRAGDEDGSYHGQASK 357
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353

Chain D from PDB  Type:PROTEIN  Length:359
                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeeeeee.hhhhhhhhhh.....eeeee...eeeee.........eeeee....eeeeeeeee..hhhhhhhhhhhhhh...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
                 4z6r D   4 EIPKPVAPAPDILRCAYAELVVTDLAKSRNFYVDVLGLHVSYEDENQIYLRSFEEFIHHNLVLTKGPVAALKAMAFRVRTPEDVDKAEAYYQELGCRTERRKDGFVKGIGDALRVEDPLGFPYEFFFETTHVERLHMRYDLYSAGELVRLDHFNQVTPDVPRGRKYLEDLGFRVTEDIQDDEGTTYAAWMHRKGTVEDTALTGGNGPRLHHVAFSTHEKHNIIQICDKMGALRISDRIERGPGRHGVSNAFYLYILDPDNHRIEIYTQDYYTGDPDNPTITWNVHDNQRRDWWGNPVVPSWYTEASKVLDLDGNVQEIIERTDDSELEVTIGADGFSFTRAGDEDGSYHGQASKGFKLG 362
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353

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 '\|'

(no "SCOP Domain" information available for 4Z6R)

(no "CATH Domain" information available for 4Z6R)

(no "Pfam Domain" information available for 4Z6R)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
		4SX	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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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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	4z6r
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4z6l	STRUCTURE OF H200E VARIANT OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM B.FUSCUM AT 1.65 ANG RESOLUTION
4z6m	STRUCTURE OF H200Q VARIANT OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM B.FUSCUM AT 1.35 ANG RESOLUTION
4z6n	STRUCTURE OF H200N VARIANT OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM B.FUSCUM AT 1.52 ANG RESOLUTION
4z6o	STRUCTURE OF H200E VARIANT OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM B.FUSCUM IN COMPLEX WITH HPCA AT 1.63 ANG RESOLUTION
4z6p	STRUCTURE OF H200Q VARIANT OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM B.FUSCUM IN COMPLEX WITH HPCA AT 1.75 ANG RESOLUTION
4z6q	STRUCTURE OF H200N VARIANT OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM B.FUSCUM IN COMPLEX WITH HPCA AT 1.57 ANG RESOLUTION
4z6s	STRUCTURE OF H200Q VARIANT OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM B.FUSCUM IN COMPLEX WITH 4-SULFONYL CATECHOL AT 1.42 ANG RESOLUTION
4z6t	STRUCTURE OF H200N VARIANT OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM B.FUSCUM IN COMPLEX WITH 4-SULFONYL CATECHOL AT 1.50 ANG RESOLUTION
4z6u	STRUCTURE OF H200E VARIANT OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM B.FUSCUM IN COMPLEX WITH 4-NITROCATECHOL AT 1.48 ANG RESOLUTION
4z6v	STRUCTURE OF H200Q VARIANT OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM B.FUSCUM IN COMPLEX WITH 4-NITROCATECHOL AT 1.37 ANG RESOLUTION
4z6w	STRUCTURE OF H200N VARIANT OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM B.FUSCUM IN COMPLEX WITH 4-NITROCATECHOL AT 1.57 ANG RESOLUTION
4z6z	STRUCTURE OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM B.FUSCUM IN COMPLEX WITH 4-SULFONYL CATECHOL AT 1.52 ANG RESOLUTION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 18)

Sites (18, 18)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Gene Ontology (3, 3)

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