Reviewed, UniProtKB/Swiss-Prot P00437 (PCXB_PSEPU)

Names and origin

Protein names

Recommended name:
    Protocatechuate 3,4-dioxygenase beta chain
    EC=1.13.11.3
Alternative name(s):
    3,4-PCD

Gene names

Name:

pcaH

Organism

Pseudomonas putida

Taxonomic identifier

303 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Pseudomonadales › Pseudomonadaceae › Pseudomonas

Protein attributes

Sequence length	239 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Plays an essential role in the utilization of numerous aromatic and hydroaromatic compounds via the beta-ketoadipate pathway.
Catalytic activity	3,4-dihydroxybenzoate + O2 = 3-carboxy-cis,cis-muconate.
Cofactor	Binds Fe3+ ion per subunit.
Pathway	Aromatic compound metabolism; beta-ketoadipate pathway; 3-carboxy-cis,cis-muconate from 3,4-dihydroxybenzoate: step 1/1.
Subunit structure	The enzyme is an oligomer of 12 copies of the alpha and beta chains.
Sequence similarities	Belongs to the intradiol ring-cleavage dioxygenase family.
Caution	Strain ATCC 23975 was originally classified as being from Pseudomonas aeruginosa.

Ontologies

Keywords
Biological process	Aromatic hydrocarbons catabolism
Ligand	Iron Metal-binding
Molecular function	Dioxygenase Oxidoreductase
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological process	aromatic compound catabolic process Inferred from electronic annotation. Source: UniProtKB-KW oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW protocatechuate catabolic process Inferred from electronic annotation. Source: InterPro
Molecular function	ferric iron binding Inferred from electronic annotation. Source: InterPro protocatechuate 3,4-dioxygenase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.2

Chain

2 – 239

238

Protocatechuate 3,4-dioxygenase beta chain

PRO_0000085098

Sites

Metal binding

109

1

Iron; catalytic Ref.4

Metal binding

148

1

Iron; catalytic Ref.4

Metal binding

161

1

Iron; catalytic Ref.4

Metal binding

163

1

Iron; catalytic Ref.4

Experimental info

Sequence conflict

62

1

H → D AA sequence Ref.2

Sequence conflict

70

1

N → D AA sequence Ref.2

Sequence conflict

72

1

Missing AA sequence Ref.2

Sequence conflict

218

1

D → N AA sequence Ref.2

Secondary structure

1

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239

Helix Strand Turn

Details...

Beta strand

7 – 9

3

Turn

14 – 16

3

Helix

26 – 28

3

Turn

29 – 31

3

Helix

44 – 47

4

Turn

59 – 62

4

Turn

64 – 66

3

Beta strand

70 – 72

3

Beta strand

78 – 87

10

Beta strand

97 – 102

6

Beta strand

127 – 131

5

Beta strand

136 – 143

8

Beta strand

148 – 153

6

Beta strand

156 – 158

3

Beta strand

160 – 166

7

Turn

171 – 173

3

Beta strand

175 – 181

7

Helix

187 – 189

3

Turn

191 – 195

5

Helix

199 – 203

5

Beta strand

206 – 209

4

Turn

216 – 218

3

Beta strand

219 – 223

5

Beta strand

226 – 228

3

Beta strand

231 – 233

3

Sequences

	Sequence		Length	Mass (Da)
	P00437-1 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 8F8CC293B6E434CE	FASTA	239	26,793
	10 20 30 40 50 60 MPAQDNSRFV IRDRNWHPKA LTPDYKTSIA RSPRQALVSI PQSISETTGP NFSHLGFGAH 70 80 90 100 110 120 DHDLLLNFNN GGLPIGERII VAGRVVDQYG KPVPNTLVEM WQANAGGRYR HKNDRYLAPL 130 140 150 160 170 180 DPNFGGVGRC LTDSDGYYSF RTIKPGPYPW RNGPNDWRPA HIHFGISGPS IATKLITQLY 190 200 210 220 230 FEGDPLIPMC PIVKSIANPE AVQQLIAKLD MNNANPMDCL AYRFDIVLRG QRKTHFENC

References

[1]	"Cloning, sequencing, and expression of the Pseudomonas putida protocatechuate 3,4-dioxygenase genes." Frazee R.W., Livingston D.M., Laporte D.C., Lipscomb J.D. J. Bacteriol. 175:6194-6202(1993) [PubMed: 8407791] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 23975 / B-10 / NCIB 12602 / Biotype A.
[2]	"The complete amino acid sequence of the beta-subunit of protocatechuate 3,4-dioxygenase from Pseudomonas aeruginosa." Iwaki M., Kagamiyama H., Nozaki M. J. Biochem. 86:1159-1162(1979) [PubMed: 115853] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-239.
[3]	"Structure and assembly of protocatechuate 3,4-dioxygenase." Ohlendorf D.H., Lipscomb J.D., Weber P.C. Nature 336:403-405(1988) [PubMed: 3194022] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
[4]	"Structure of protocatechuate 3,4-dioxygenase from Pseudomonas aeruginosa at 2.15-A resolution." Ohlendorf D.H., Orville A.M., Lipscomb J.D. J. Mol. Biol. 244:586-608(1994) [PubMed: 7990141] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS). Strain: ATCC 23975 / B-10 / NCIB 12602 / Biotype A.
[5]	"Structures of competitive inhibitor complexes of protocatechuate 3,4-dioxygenase: multiple exogenous ligand binding orientations within the active site." Orville A.M., Elango N., Lipscomb J.D., Ohlendorf D.H. Biochemistry 36:10039-10051(1997) [PubMed: 9254599] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS). Strain: ATCC 23975 / B-10 / NCIB 12602 / Biotype A.
[6]	"Crystal structures of substrate and substrate analog complexes of protocatechuate 3,4-dioxygenase: endogenous Fe3+ ligand displacement in response to substrate binding." Orville A.M., Lipscomb J.D., Ohlendorf D.H. Biochemistry 36:10052-10066(1997) [PubMed: 9254600] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.13 ANGSTROMS). Strain: ATCC 23975 / B-10 / NCIB 12602 / Biotype A.
[7]	"Crystal structure and resonance Raman studies of protocatechuate 3,4-dioxygenase complexed with 3,4-dihydroxyphenylacetate." Elgren T.E., Orville A.M., Kelly K.A., Lipscomb J.D., Ohlendorf D.H., Que L. Jr. Biochemistry 36:11504-11513(1997) [PubMed: 9298971] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS). Strain: ATCC 23975 / B-10 / NCIB 12602 / Biotype A.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

L14836 Genomic DNA. Translation: AAB41024.1.

PIR

DAPSBA. A36930.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1YKK	X-ray	2.06	B/D/F/H/J/L	2-238	[»]
1YKL	X-ray	2.25	B/D/F/H/J/L	2-238	[»]
1YKM	X-ray	2.22	B/D/F/H/J/L	2-238	[»]
1YKN	X-ray	2.06	B/D/F/H/J/L	2-238	[»]
1YKO	X-ray	2.54	B/D/F/H/J/L	2-238	[»]
1YKP	X-ray	2.41	B/D/F/H/J/L	2-238	[»]
2PCD	X-ray	2.15	M/N/O/P/Q/R	2-239	[»]
3PCA	X-ray	2.20	M/N/O/P/Q/R	2-239	[»]
3PCB	X-ray	2.19	M/N/O/P/Q/R	2-239	[»]
3PCC	X-ray	1.98	M/N/O/P/Q/R	2-239	[»]
3PCD	X-ray	2.10	M/N/O/P/Q/R	2-238	[»]
3PCE	X-ray	2.06	M/N/O/P/Q/R	2-239	[»]
3PCF	X-ray	2.15	M/N/O/P/Q/R	2-239	[»]
3PCG	X-ray	1.96	M/N/O/P/Q/R	2-239	[»]
3PCH	X-ray	2.05	M/N/O/P/Q/R	2-239	[»]
3PCI	X-ray	2.21	M/N/O/P/Q/R	2-239	[»]
3PCJ	X-ray	2.13	M/N/O/P/Q/R	2-239	[»]
3PCK	X-ray	2.13	M/N/O/P/Q/R	2-239	[»]
3PCL	X-ray	2.15	M/N/O/P/Q/R	2-239	[»]
3PCM	X-ray	2.25	M/N/O/P/Q/R	2-239	[»]
3PCN	X-ray	2.40	M/N/O/P/Q/R	2-239	[»]

ModBase

Search...

Enzyme and pathway databases

BioCyc

MetaCyc:MON-3185.

BRENDA

1.13.11.3. 403.

Family and domain databases

InterPro

IPR000627. Intradiol_dOase_C.
IPR015889. Intradiol_dOase_core.
IPR012785. Protocat_dOase_b.
[Graphical view]

Gene3D

G3DSA:2.60.130.10. Intradiol_dOase_core. 1 hit.

Pfam

PF00775. Dioxygenase_C. 1 hit.
[Graphical view]

TIGRFAMs

TIGR02422. protocat_beta. 1 hit.

PROSITE

PS00083. INTRADIOL_DIOXYGENAS. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

PCXB_PSEPU

Accession

Primary (citable) accession number: P00437

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	January 23, 2007
Last modified:	June 16, 2009
This is version 76 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)