3WRC - JenaLib

Title :   CRYSTAL STRUCTURE OF THE ANAEROBIC DESB-PROTOCATECHUATE (PCA) COMPLEX

Authors :   K. Sugimoto, M. Senda, D. Kasai, M. Fukuda, E. Masai, T. Senda

Date :   21 Feb 14 (Deposition) - 30 Apr 14 (Release) - 30 Apr 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Oxidoreductase, Extradiol Dioxygenase, Fe2+ Binding, Domain-Swap Dimer (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Sugimoto, M. Senda, D. Kasai, M. Fukuda, E. Masai, T. Senda
Molecular Mechanism Of Strict Substrate Specificity Of An Extradiol Dioxygenase, Desb, Derived From Sphingobium Sp. Syk-6
Plos One V. 9 92249 2014
PubMed-ID: 24657997 | Reference-DOI: 10.1371/JOURNAL.PONE.0092249

Compounds

Molecule 1 - GALLATE DIOXYGENASE
	Chains	:	A, B
	EC Number	:	1.13.11.58
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PEVK3G
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DESB
	Organism Scientific	:	SPHINGOMONAS PAUCIMOBILIS
	Organism Taxid	:	13689
	Strain	:	SYK-6
	Synonym	:	DESB, TYPE II EXTRADIOL DIOXYGENASE

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:12 , ASN A:57 , HIS A:59 , GLU A:239	BINDING SITE FOR RESIDUE FE2 A 501
2	AC2	SOFTWARE	HIS B:12 , ASN B:57 , HIS B:59 , GLU B:239 , HOH B:613 , HOH B:617	BINDING SITE FOR RESIDUE FE2 B 501
3	AC3	SOFTWARE	PHE A:374 , GLU A:377 , ASN A:387 , TYR A:391 , TYR A:412 , THR B:13 , PRO B:14 , HIS B:59 , HIS B:124 , MET B:266 , THR B:267 , HOH B:617 , HOH B:620	BINDING SITE FOR RESIDUE DHB B 502

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:399
 aligned with G2IKE5_9SPHN | G2IKE5 from UniProtKB/TrEMBL  Length:418

    Alignment length:412
                                    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       391       401       411  
         G2IKE5_9SPHN     2 AKIIGGFAVSHTPTIAFAHDANKYDDPVWAPIFQGFEPVKQWLAEQKPDVTFYVYNDHMTSFFEHYSHFALGVGEEYSPADEGGGQRDLPPIKGDPELAKHIAECLVADEFDLAYWQGMGLDHGAFSPLSVLLPHEHGWPCRIVPLQCGVLQHPIPKARRFWNFGRSLRRAIQSYPRDIKVAIAGTGGLSHQVHGERAGFNNTEWDMEFMERLANDPESLLGATVTDLAKKGGWEGAEVVMWLLMRGALSPEVKTLHQSYFLPSMTAIATMLFEDQGDAAPPAESDEALRARAKRELAGVEEIEGTYPFTIDRAVKGFRINHFLHRLIEPDFRKRFVEDPEGLFAESDLTEEEKSLIRNRDWIGMIHYGVIFFMLEKMAAVLGIGNIDVYAAFRGLSVPEFQKTRNAAITYS 413
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee...hhhhhh..---------......hhhhhhhhhhh...eeeeee.........eee.eeee...ee..............eeehhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhh........eeeeeee........hhhhhhhhhhhhhhhhh......eeee.ee...............hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh....-................eeeee....---...hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wrc A   2 AKIIGGFAVSHTPTIAFAHD---------APIFQGFEPVKQWLAEQKPDVTFYVYNDHMTSFFEHYSHFALGVGEEYSPADEGGGQRDLPPIKGDPELAKHIAECLVADEFDLAYWQGMGLDHGAFSPLSVLLPHEHGWPCRIVPLQCGVLQHPIPKARRFWNFGRSLRRAIQSYPRDIKVAIAGTGGLSHQVHGERAGFNNTEWDMEFMERLANDPESLLGATVTDLAKKGGWEGAEVVMWLLMRGALSPE-KTLHQSYFLPSMTAIATMLFEDQGD---PAESDEALRARAKRELAGVEEIEGTYPFTIDRAVKGFRINHFLHRLIEPDFRKRFVEDPEGLFAESDLTEEEKSLIRNRDWIGMIHYGVIFFMLEKMAAVLGIGNIDVYAAFRGLSVPEFQKTRNAAITYS 413
                                    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       | - |     291       301       311       321       331       341       351       361       371       381       391       401       411  
                                              21        31                                                                                                                                                                                                                           253 |                     279 283                                                                                                                                  
                                                                                                                                                                                                                                                                                       255

Chain A from PDB  Type:PROTEIN  Length:399
 aligned with Q5NTE5_SPHPI | Q5NTE5 from UniProtKB/TrEMBL  Length:418

    Alignment length:412
                                    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       391       401       411  
         Q5NTE5_SPHPI     2 AKIIGGFAVSHTPTIAFAHDANKYDDPVWAPIFQGFEPVKQWLAEQKPDVTFYVYNDHMTSFFEHYSHFALGVGEEYSPADEGGGQRDLPPIKGDPELAKHIAECLVADEFDLAYWQGMGLDHGAFSPLSVLLPHEHGWPCRIVPLQCGVLQHPIPKARRFWNFGRSLRRAIQSYPRDIKVAIAGTGGLSHQVHGERAGFNNTEWDMEFMERLANDPESLLGATVTDLAKKGGWEGAEVVMWLLMRGALSPEVKTLHQSYFLPSMTAIATMLFEDQGDAAPPAESDEALRARAKRELAGVEEIEGTYPFTIDRAVKGFRINHFLHRLIEPDFRKRFVEDPEGLFAESDLTEEEKSLIRNRDWIGMIHYGVIFFMLEKMAAVLGIGNIDVYAAFRGLSVPEFQKTRNAAITYS 413
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee...hhhhhh..---------......hhhhhhhhhhh...eeeeee.........eee.eeee...ee..............eeehhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhh........eeeeeee........hhhhhhhhhhhhhhhhh......eeee.ee...............hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh....-................eeeee....---...hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wrc A   2 AKIIGGFAVSHTPTIAFAHD---------APIFQGFEPVKQWLAEQKPDVTFYVYNDHMTSFFEHYSHFALGVGEEYSPADEGGGQRDLPPIKGDPELAKHIAECLVADEFDLAYWQGMGLDHGAFSPLSVLLPHEHGWPCRIVPLQCGVLQHPIPKARRFWNFGRSLRRAIQSYPRDIKVAIAGTGGLSHQVHGERAGFNNTEWDMEFMERLANDPESLLGATVTDLAKKGGWEGAEVVMWLLMRGALSPE-KTLHQSYFLPSMTAIATMLFEDQGD---PAESDEALRARAKRELAGVEEIEGTYPFTIDRAVKGFRINHFLHRLIEPDFRKRFVEDPEGLFAESDLTEEEKSLIRNRDWIGMIHYGVIFFMLEKMAAVLGIGNIDVYAAFRGLSVPEFQKTRNAAITYS 413
                                    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       | - |     291       301       311       321       331       341       351       361       371       381       391       401       411  
                                              21        31                                                                                                                                                                                                                           253 |                     279 283                                                                                                                                  
                                                                                                                                                                                                                                                                                       255

Chain B from PDB  Type:PROTEIN  Length:404
 aligned with G2IKE5_9SPHN | G2IKE5 from UniProtKB/TrEMBL  Length:418

    Alignment length:404
                                    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       391       401    
         G2IKE5_9SPHN     2 AKIIGGFAVSHTPTIAFAHDANKYDDPVWAPIFQGFEPVKQWLAEQKPDVTFYVYNDHMTSFFEHYSHFALGVGEEYSPADEGGGQRDLPPIKGDPELAKHIAECLVADEFDLAYWQGMGLDHGAFSPLSVLLPHEHGWPCRIVPLQCGVLQHPIPKARRFWNFGRSLRRAIQSYPRDIKVAIAGTGGLSHQVHGERAGFNNTEWDMEFMERLANDPESLLGATVTDLAKKGGWEGAEVVMWLLMRGALSPEVKTLHQSYFLPSMTAIATMLFEDQGDAAPPAESDEALRARAKRELAGVEEIEGTYPFTIDRAVKGFRINHFLHRLIEPDFRKRFVEDPEGLFAESDLTEEEKSLIRNRDWIGMIHYGVIFFMLEKMAAVLGIGNIDVYAAFRGLSVPEFQKT 405
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..eeeeee.........eee.eeee...ee..............ee.hhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhh........eeeeeee........hhhhhhhhhhhhhhhhhh.....eeeeeee...............hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee......eeeeeeee.........hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wrc B   2 AKIIGGFAVSHTPTIAFAHDANKYDDPVWAPIFQGFEPVKQWLAEQKPDVTFYVYNDHMTSFFEHYSHFALGVGEEYSPADEGGGQRDLPPIKGDPELAKHIAECLVADEFDLAYWQGMGLDHGAFSPLSVLLPHEHGWPCRIVPLQCGVLQHPIPKARRFWNFGRSLRRAIQSYPRDIKVAIAGTGGLSHQVHGERAGFNNTEWDMEFMERLANDPESLLGATVTDLAKKGGWEGAEVVMWLLMRGALSPEVKTLHQSYFLPSMTAIATMLFEDQGDAAPPAESDEALRARAKRELAGVEEIEGTYPFTIDRAVKGFRINHFLHRLIEPDFRKRFVEDPEGLFAESDLTEEEKSLIRNRDWIGMIHYGVIFFMLEKMAAVLGIGNIDVYAAFRGLSVPEFQKT 405
                                    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       391       401

Chain B from PDB  Type:PROTEIN  Length:404
 aligned with Q5NTE5_SPHPI | Q5NTE5 from UniProtKB/TrEMBL  Length:418

    Alignment length:404
                                    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       391       401    
         Q5NTE5_SPHPI     2 AKIIGGFAVSHTPTIAFAHDANKYDDPVWAPIFQGFEPVKQWLAEQKPDVTFYVYNDHMTSFFEHYSHFALGVGEEYSPADEGGGQRDLPPIKGDPELAKHIAECLVADEFDLAYWQGMGLDHGAFSPLSVLLPHEHGWPCRIVPLQCGVLQHPIPKARRFWNFGRSLRRAIQSYPRDIKVAIAGTGGLSHQVHGERAGFNNTEWDMEFMERLANDPESLLGATVTDLAKKGGWEGAEVVMWLLMRGALSPEVKTLHQSYFLPSMTAIATMLFEDQGDAAPPAESDEALRARAKRELAGVEEIEGTYPFTIDRAVKGFRINHFLHRLIEPDFRKRFVEDPEGLFAESDLTEEEKSLIRNRDWIGMIHYGVIFFMLEKMAAVLGIGNIDVYAAFRGLSVPEFQKT 405
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..eeeeee.........eee.eeee...ee..............ee.hhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhh........eeeeeee........hhhhhhhhhhhhhhhhhh.....eeeeeee...............hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee......eeeeeeee.........hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wrc B   2 AKIIGGFAVSHTPTIAFAHDANKYDDPVWAPIFQGFEPVKQWLAEQKPDVTFYVYNDHMTSFFEHYSHFALGVGEEYSPADEGGGQRDLPPIKGDPELAKHIAECLVADEFDLAYWQGMGLDHGAFSPLSVLLPHEHGWPCRIVPLQCGVLQHPIPKARRFWNFGRSLRRAIQSYPRDIKVAIAGTGGLSHQVHGERAGFNNTEWDMEFMERLANDPESLLGATVTDLAKKGGWEGAEVVMWLLMRGALSPEVKTLHQSYFLPSMTAIATMLFEDQGDAAPPAESDEALRARAKRELAGVEEIEGTYPFTIDRAVKGFRINHFLHRLIEPDFRKRFVEDPEGLFAESDLTEEEKSLIRNRDWIGMIHYGVIFFMLEKMAAVLGIGNIDVYAAFRGLSVPEFQKT 405
                                    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       391       401

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	-	→ 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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (6, 11)

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	Cis Peptide Bonds
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Description