DB code: D00282

RLCP classification 8.113.594730.651 : Isomerization
4.1034.769660.650 : Addition
CATH domain 3.30.390.10 : Enolase-like; domain 1
3.20.20.120 : TIM Barrel Catalytic domain
E.C. 5.5.1.1
CSA 1muc
M-CSA 1muc
MACiE M0269

CATH domain Related DB codes (homologues)
3.30.390.10 : Enolase-like; domain 1 D00261 D00273 D00283
3.20.20.120 : TIM Barrel D00261 D00273 D00283

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P08310 Muconate cycloisomerase 1
EC 5.5.1.1
Cis,cis-muconate lactonizing enzyme I
MLE
Muconate cycloisomerase I
PF02746 (MR_MLE_N)
[Graphical View]
Q51958
Muconate lactonizing enzyme
PF02746 (MR_MLE_N)
[Graphical View]

KEGG enzyme name
muconate cycloisomerase
muconate cycloisomerase I
cis,cis-muconate-lactonizing enzyme
cis,cis-muconate cycloisomerase
muconate lactonizing enzyme
4-carboxymethyl-4-hydroxyisocrotonolactone lyase (decyclizing)

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q51958 Q51958_PSEPU
P08310 CATB_PSEPU 2,5-dihydro-5-oxofuran-2-acetate = cis,cis- hexadienedioate. Homooctamer. Manganese.

KEGG Pathways
Map code Pathways E.C.
MAP00362 Benzoate degradation via hydroxylation
MAP00364 Fluorobenzoate degradation
MAP00622 Toluene and xylene degradation
MAP00627 1,4-Dichlorobenzene degradation

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00034 C02480 C04105 I00069
E.C.
Compound Manganese cis,cis-Muconate 2,5-Dihydro-5-oxofuran-2-acetate 2,5-Dihydro-5-oxofuran-2-enolate
Type heavy metal carboxyl group carboxyl group,aromatic ring (with hetero atoms other than nitrogen atoms)
ChEBI 35154
18291
16508
18080
PubChem 23930
5280518
542
1bkhA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1bkhB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1bkhC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1f9cA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1f9cB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1mucA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1mucB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2mucA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2mucB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
3mucA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
3mucB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1bkhA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1bkhB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1bkhC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1f9cA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MN Unbound Unbound
1f9cB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MN Unbound Unbound
1mucA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MN Unbound Unbound
1mucB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MN Unbound Unbound
2mucA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MN Unbound Unbound
2mucB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MN Unbound Unbound
3mucA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MN Unbound Unbound
3mucB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MN Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [11], [15]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1bkhA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1bkhB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1bkhC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1f9cA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1f9cB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1mucA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1mucB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2mucA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2mucB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3mucA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain mutant I54V
3mucB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain mutant I54V
1bkhA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 167;LYS 169;GLU 327 ASP 198;GLU 224;ASP 249(Manganese binding)
1bkhB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 167;LYS 169;GLU 327 ASP 198;GLU 224;ASP 249(Manganese binding)
1bkhC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 167;LYS 169;GLU 327 ASP 198;GLU 224;ASP 249(Manganese binding)
1f9cA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 167;LYS 169;GLU 327 ASP 198;GLU 224;ASP 249(Manganese binding) mutant D178N
1f9cB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 167;LYS 169;GLU 327 ASP 198;GLU 224;ASP 249(Manganese binding) mutant D178N
1mucA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 167;LYS 169;GLU 327 ASP 198;GLU 224;ASP 249(Manganese binding)
1mucB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 167;LYS 169;GLU 327 ASP 198;GLU 224;ASP 249(Manganese binding)
2mucA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 167;LYS 169;GLU 327 ASP 198;GLU 224;ASP 249(Manganese binding) mutant F329I
2mucB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 167;LYS 169;GLU 327 ASP 198;GLU 224;ASP 249(Manganese binding) mutant F329I
3mucA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 167;LYS 169;GLU 327 ASP 198;GLU 224;ASP 249(Manganese binding)
3mucB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 167;LYS 169;GLU 327 ASP 198;GLU 224;ASP 249(Manganese binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[3]
p.151-152
[6]
Fig.3, p.693-694
[10]
Fig.3
[11]
Scheme 1, p.937
[12]
Fig.1, p.1159
[14]
FIG.1, p.10400-10401
[15]
Fig.1, p.132-135
[18]
Fig.7
[21]

References
[1]
Resource
Comments
Medline ID
PubMed ID 6652062
Journal Biochemistry
Year 1983
Volume 22
Pages 5223-30
Authors Ngai KL, Ornston LN, Kallen RG
Title Enzymes of the beta-ketoadipate pathway in Pseudomonas putida: kinetic and magnetic resonance studies of the cis,cis-muconate cycloisomerase catalyzed reaction.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 3999146
Journal J Mol Biol
Year 1985
Volume 182
Pages 353-5
Authors Goldman A, Ollis D, Ngai KL, Steitz TA
Title Crystal structure of muconate lactonizing enzyme at 6.5 A resolution.
Related PDB
Related UniProtKB
[3]
Resource
Comments X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
Medline ID 87283908
PubMed ID 3612800
Journal J Mol Biol
Year 1987
Volume 194
Pages 143-53
Authors Goldman A, Ollis DL, Steitz TA
Title Crystal structure of muconate lactonizing enzyme at 3 A resolution.
Related PDB
Related UniProtKB P08310
[4]
Resource
Comments
Medline ID
PubMed ID 2099737
Journal Biochem Soc Symp
Year 1990
Volume 57
Pages 135-41
Authors Neidhart DC, Howell PL, Petsko GA, Gerlt JA, Kozarich JW, Powers VM, Kenyon GL
Title Restructuring catalysis in the mandelate pathway.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 2394680
Journal J Bacteriol
Year 1990
Volume 172
Pages 5119-29
Authors Schlomann M, Fischer P, Schmidt E, Knackmuss HJ
Title Enzymatic formation, stability, and spontaneous reactions of 4-fluoromuconolactone, a metabolite of the bacterial degradation of 4-fluorobenzoate.
Related PDB
Related UniProtKB
[6]
Resource
Comments SIMILARITY TO MR.
Medline ID 91015392
PubMed ID 2215699
Journal Nature
Year 1990
Volume 347
Pages 692-4
Authors Neidhart DJ, Kenyon GL, Gerlt JA, Petsko GA
Title Mandelate racemase and muconate lactonizing enzyme are mechanistically distinct and structurally homologous.
Related PDB
Related UniProtKB P08310
[7]
Resource
Comments
Medline ID
PubMed ID 1708883
Journal Proteins
Year 1990
Volume 8
Pages 334-40
Authors Rice PA, Goldman A, Steitz TA
Title A helix-turn-strand structural motif common in alpha-beta proteins.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 8110801
Journal Biochemistry
Year 1994
Volume 33
Pages 1961-70
Authors Mazur P, Pieken WA, Budihas SR, Williams SE, Wong S, Kozarich JW
Title Cis,cis-muconate lactonizing enzyme from Trichosporon cutaneum: evidence for a novel class of cycloisomerases in eucaryotes.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 8021223
Journal J Bacteriol
Year 1994
Volume 176
Pages 4366-75
Authors Vollmer MD, Fischer P, Knackmuss HJ, Schlomann M
Title Inability of muconate cycloisomerases to cause dehalogenation during conversion of 2-chloro-cis,cis-muconate.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 7493952
Journal J Biol Chem
Year 1995
Volume 270
Pages 29229-35
Authors Blasco R, Wittich RM, Mallavarapu M, Timmis KN, Pieper DH
Title From xenobiotic to antibiotic, formation of protoanemonin from 4-chlorocatechol by enzymes of the 3-oxoadipate pathway.
Related PDB
Related UniProtKB
[11]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS).
Medline ID 96107379
PubMed ID 7500361
Journal J Mol Biol
Year 1995
Volume 254
Pages 918-41
Authors Helin S, Kahn PC, Guha BL, Mallows DG, Goldman A
Title The refined X-ray structure of muconate lactonizing enzyme from Pseudomonas putida PRS2000 at 1.85 A resolution.
Related PDB 1muc
Related UniProtKB P08310
[12]
Resource
Comments
Medline ID
PubMed ID 7855594
Journal Science
Year 1995
Volume 267
Pages 1159-61
Authors Babbitt PC, Mrachko GT, Hasson MS, Huisman GW, Kolter R, Ringe D, Petsko GA, Kenyon GL, Gerlt JA
Title A functionally diverse enzyme superfamily that abstracts the alpha protons of carboxylic acids.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 8987982
Journal Biochemistry
Year 1996
Volume 35
Pages 16489-501
Authors Babbitt PC, Hasson MS, Wedekind JE, Palmer DR, Barrett WC, Reed GH, Rayment I, Ringe D, Kenyon GL, Gerlt JA
Title The enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids.
Related PDB
Related UniProtKB
[14]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 9724714
Journal Proc Natl Acad Sci U S A
Year 1998
Volume 95
Pages 10396-401
Authors Hasson MS, Schlichting I, Moulai J, Taylor K, Barrett W, Kenyon GL, Babbitt PC, Gerlt JA, Petsko GA, Ringe D
Title Evolution of an enzyme active site: the structure of a new crystal form of muconate lactonizing enzyme compared with mandelate racemase and enolase.
Related PDB 1bkh
Related UniProtKB
[15]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10336378
Journal Proteins
Year 1999
Volume 34
Pages 125-36
Authors Schell U, Helin S, Kajander T, Schlomann M, Goldman A
Title Structural basis for the activity of two muconate cycloisomerase variants toward substituted muconates.
Related PDB 2muc 3muc
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 11092867
Journal J Bacteriol
Year 2000
Volume 182
Pages 7044-52
Authors Cosper NJ, Collier LS, Clark TJ, Scott RA, Neidle EL
Title Mutations in catB, the gene encoding muconate cycloisomerase, activate transcription of the distal ben genes and contribute to a complex regulatory circuit in Acinetobacter sp. strain ADP1.
Related PDB
Related UniProtKB
[17]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 11080642
Journal Structure Fold Des
Year 2000
Volume 8
Pages 1203-14
Authors Kajander T, Kahn PC, Passila SH, Cohen DC, Lehtio L, Adolfsen W, Warwicker J, Schell U, Goldman A
Title Buried charged surface in proteins.
Related PDB 1f9c
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 11443090
Journal J Bacteriol
Year 2001
Volume 183
Pages 4551-61
Authors Kaulmann U, Kaschabek SR, Schlomann M
Title Mechanism of chloride elimination from 3-chloro- and 2,4-dichloro-cis,cis-muconate: new insight obtained from analysis of muconate cycloisomerase variant CatB-K169A.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 12218027
Journal J Bacteriol
Year 2002
Volume 184
Pages 5402-9
Authors Skiba A, Hecht V, Pieper DH
Title Formation of protoanemonin from 2-chloro-cis,cis-muconate by the combined action of muconate cycloisomerase and muconolactone isomerase.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 12855164
Journal FEMS Microbiol Lett
Year 2003
Volume 224
Pages 29-34
Authors Cha CJ, Bruce NC
Title Stereo- and regiospecific cis,cis-muconate cycloisomerization by Rhodococcus rhodochrous N75.
Related PDB
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 12930985
Journal Protein Sci
Year 2003
Volume 12
Pages 1855-64
Authors Kajander T, Lehtio L, Schlomann M, Goldman A
Title The structure of Pseudomonas P51 Cl-muconate lactonizing enzyme: co-evolution of structure and dynamics with the dehalogenation function.
Related PDB
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID 15697231
Journal Biochemistry
Year 2005
Volume 44
Pages 2059-71
Authors Kalyanaraman C, Bernacki K, Jacobson MP
Title Virtual screening against highly charged active sites: identifying substrates of alpha-beta barrel enzymes.
Related PDB
Related UniProtKB

Comments
This enzyme is homologous to chloromuconate cycloisomerase (E.C. 5.5.1.7; D00283 in EzCatDB), sharing the same reactions, although the homologous enzyme further catalyzes dehalogenation.
According to the literature [11], [14] and [15], this enzyme catalyzes an addition of the C1 carboxylate oxygen in substrate, muconate, to the C4 double-bonded carbon, and an isomerization, through an enolate intermediate as follows:
(A) Addition of carboxylate oxygen to the C4 double-bonded carbon, forming an enolate intermediate:
(A1) The C1 carboxylate oxygen makes a nucleophilic attack on the C4 (sp2) carbon, whereas Glu327 acts as a general acid to protonate the C6 carboxylate. The reactions lead to the formation of an enolate intermediate.
(A2) The negative charge on the enolate intermediate is stabilized by Lys167 and the Mn2+ cofactor, which is bound to Asp198, Glu224 and Asp249.
(B) Isomerization; Shift of double-bond position (from C=C-O to C-C=O):
(B1) The negative charge on the enolate oxygen is stabilized by Lys167 and the Mn2+ cofactor, which is bound to Asp198, Glu224 and Asp249.
(B2) Lys169 acts as a general acid to protonate the C5 carbon, whereas Glu327 acts as a general base to deprotonate the C6 enolate oxygen.
According to the literature in S00852 of EzCatDB, the muconate lactonizing enzymes (MLEs) convert cis,cis-muconates into muconolactones, as a part of the beta-ketoadipate pathway. This pathway consists of two branches, catechol (MLEs; E.C. 5.5.1.1) and protocatechuate (3-carboxy-cis,cis-MLEs or CMLEs; E.C. 5.5.1.2). Moreover, MLEs can be classified into three evolutionarily distinct classes. Firstly, bacterial MLEs catalyze a syn addition, using a Mn2+ cofactor with a TIM barrel fold as the catalitic domain (this entry in EzCatDB). Secondly, bacterial CMLEs (PDB;1q5n) catalyze an anti addition, without metal cofactor on a fold, which is related to class II fumarase (T00086) family (CATH 1.20.200.10). Thirdly, both eukaryotic MLEs and CMLEs catalyze a syn addition, without metal cofactor.

Created Updated
2005-05-20 2010-08-10