4WHP - JenaLib

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Title :   RESTING PROTOCATECHUATE 3,4-DIOXYGENASE (PSEUDOMONAS PUTIDA) AT PH 6.5

Authors :   C. J. Knoot, J. D. Lipscomb

Date :   23 Sep 14 (Deposition) - 31 Dec 14 (Release) - 28 Jan 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.54

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

Keywords :   Dioxygen Activation, Non-Heme Iron, Intradiol Dioxygenase, Aromatic Ring Cleavage, Catalytic Intermediates, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. J. Knoot, V. M. Purpero, J. D. Lipscomb
Crystal Structures Of Alkylperoxo And Anhydride Intermediates In An Intradiol Ring-Cleaving Dioxygenase.
Proc. Natl. Acad. Sci. Usa V. 112 388 2015
PubMed-ID: 25548185 | Reference-DOI: 10.1073/PNAS.1419118112

Molecule 1 - PROTOCATECHUATE 3,4-DIOXYGENASE ALPHA CHAIN
	Chains	:	A, E, C
	EC Number	:	1.13.11.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PCE120K
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PCAG
	Organism Scientific	:	PSEUDOMONAS PUTIDA
	Organism Taxid	:	303
	Synonym	:	3,4-PCD

Molecule 2 - PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAIN
	Chains	:	F, D
	EC Number	:	1.13.11.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PCE120K
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PCAH
	Organism Scientific	:	PSEUDOMONAS PUTIDA
	Organism Taxid	:	303
	Synonym	:	3,4-PCD

Molecule 3 - PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAIN
	Chains	:	B
	EC Number	:	1.13.11.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PCE120K
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PCAH
	Organism Scientific	:	PSEUDOMONAS PUTIDA
	Organism Taxid	:	303
	Synonym	:	3,4-PCD

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (4x)	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 9)

No.	Name	Count	Type	Full Name
1	BCT	1	Ligand/Ion	BICARBONATE ION
2	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
3	FE	3	Ligand/Ion	FE (III) ION
4	MHO	1	Mod. Amino Acid	S-OXYMETHIONINE
5	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 24)

No.	Name	Count	Type	Full Name
1	BCT	4	Ligand/Ion	BICARBONATE ION
2	BME	4	Ligand/Ion	BETA-MERCAPTOETHANOL
3	FE	-1	Ligand/Ion	FE (III) ION
4	MHO	4	Mod. Amino Acid	S-OXYMETHIONINE
5	SO4	12	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR F:408 , TYR F:447 , HIS F:460 , HIS F:462 , HOH F:872	binding site for residue FE F 601
2	AC2	SOFTWARE	ARG E:133 , TYR F:324 , THR F:326 , TRP F:449 , HOH F:779 , HOH F:880 , HOH F:881 , HOH F:887	binding site for residue SO4 F 602
3	AC3	SOFTWARE	ASN C:37 , ARG C:38 , THR C:105 , HIS C:107 , HOH C:487	binding site for residue BCT C 301
4	AC4	SOFTWARE	TYR D:408 , TYR D:447 , HIS D:460 , HIS D:462 , HOH D:894	binding site for residue FE D 601
5	AC5	SOFTWARE	ARG C:133 , TYR D:324 , THR D:326 , TRP D:449 , HOH D:806 , HOH D:892 , HOH D:897 , HOH D:901	binding site for residue SO4 D 602
6	AC6	SOFTWARE	GLN D:503 , ARG D:522 , PHE D:523 , ASP D:524	binding site for residue BME D 603
7	AC7	SOFTWARE	ARG A:133 , TYR B:324 , THR B:326 , TRP B:449 , HOH B:793 , HOH B:891 , HOH B:892 , HOH B:893 , HOH B:894	binding site for residue SO4 B 601
8	AC8	SOFTWARE	TYR B:408 , TYR B:447 , HIS B:460 , HIS B:462 , HOH B:887	binding site for residue FE B 602

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

(no "Cis Peptide Bond" information available for 4WHP)

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

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

(no "Exon" information available for 4WHP)

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:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhh.........................eeeeee.ee..........eeeee....................eeeee.......eeeeee....ee.....ee...eeeeee.......eeeeeee..hhhhhhh..hhhhh.hhhhhh..eeeeeee..eeeee..ee.........ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4whp A   1 PIELLPETPSQTAGPYVHIGLALEAAGNPTRDQEIWNRLAKPDAPGEHILLLGQVYDGNGHLVRDSFLEVWQADANGEYQDAYNLENAFNSFGRTATTFDAGEWTLHTVKPGVVNNAAGVPMAPHINISLFARGINIHLHTRLYFDDEAQANAKCPVLNLIEQPQRRETLIAKRCEVDGKTAYRFDIRIQGEGETVFFDF 200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain B from PDB  Type:PROTEIN  Length:238
                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee...............hhhhh........ee...hhhhhh.............................eeeeeeeeee.........eeeee.........................eeeee.....eeeeeee....eee.....eee..eeeeee........eeeeeee....hhhhh.hhhhh.hhhhhhh.eeee.hhhh.....eeee..eee..eee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4whp B 301 PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRYRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPYPWRNGPNDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPmCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFENC 538
                                   310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530        
                                                                                                                                                                                                                     488-MHO

Chain C from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhh.........................eeeeee.ee..........eeeee....................eeeee.......eeeeee................eeeeee.......eeeeeee..hhhhhhh..hhhhh.hhhhhh..eeeeeee..eeeee..ee.........ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4whp C   1 PIELLPETPSQTAGPYVHIGLALEAAGNPTRDQEIWNRLAKPDAPGEHILLLGQVYDGNGHLVRDSFLEVWQADANGEYQDAYNLENAFNSFGRTATTFDAGEWTLHTVKPGVVNNAAGVPMAPHINISLFARGINIHLHTRLYFDDEAQANAKCPVLNLIEQPQRRETLIAKRCEVDGKTAYRFDIRIQGEGETVFFDF 200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain D from PDB  Type:PROTEIN  Length:238
                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee...............hhhhh........ee...hhhhhh.............................eeeeeeeeee.........eeeee.........................eeeee.....eeeeeee....eee.....eee..eeeeee........eeeeeee....hhhhh.hhhhh.hhhhhhh.eeee.hhhh.....eeee..eee..eee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4whp D 301 PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRYRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPYPWRNGPNDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFENC 538
                                   310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530

Chain E from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhh.........................eeeeee.ee..........eeeee....................eeeee.......eeeeee....ee.....ee...eeeeee.......eeeeeee..hhhhhhh..hhhhh.hhhhhh..eeeeeee..eeeee..ee.........ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4whp E   1 PIELLPETPSQTAGPYVHIGLALEAAGNPTRDQEIWNRLAKPDAPGEHILLLGQVYDGNGHLVRDSFLEVWQADANGEYQDAYNLENAFNSFGRTATTFDAGEWTLHTVKPGVVNNAAGVPMAPHINISLFARGINIHLHTRLYFDDEAQANAKCPVLNLIEQPQRRETLIAKRCEVDGKTAYRFDIRIQGEGETVFFDF 200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain F from PDB  Type:PROTEIN  Length:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee...............hhhhh........ee...hhhhhh.............................eeeeeeeeee.........eeeee.........................eeeee.....eeeeeee....eee.....eee..eeeeee........eeeeeee....hhhhh.hhhhh.hhhhhhh.eeee.hhhh.....eeee..eee..eee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4whp F 301 PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRYRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPYPWRNGPNDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFEN 537
                                   310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530

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 4WHP)

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4whp)

Biological Unit
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		Biological Unit 1	[ Jena3D ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 9)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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Gene Ontology (13, 24)

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