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Information on EC 1.14.99.57 - heme oxygenase (mycobilin-producing)
for references in articles please use BRENDA:EC1.14.99.57
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EC Tree 1 Oxidoreductases
1.14 Acting on paired donors, with incorporation or reduction of molecular oxygen
1.14.99 Miscellaneous
1.14.99.57 heme oxygenase (mycobilin-producing)
IUBMB Comments
The enzyme, characterized from the bacterium Mycobacterium tuberculosis, is involved in heme degradation and iron utilization. The enzyme binds two stacked protoheme molecules per monomer. Unlike the canonical heme oxygenases, the enzyme does not release carbon monoxide or formaldehyde. Instead, it forms unique products, named mycobilins, that retain the α-meso-carbon at the ring cleavage site as an aldehyde group. EC 1.6.2.4, NADPH-hemoprotein reductase, can act as electron donor in vitro.
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
Reaction Schemes
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Synonyms
rv3592, more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
heme-degrading monooxygenase HmoB
mhuD
mycobacterial heme utilization, degrader
Rv3592
mhuD
-
-
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
protoheme + 3 reduced acceptor + 3 O2 = mycobilin a + Fe2+ + 3 acceptor + 3 H2O
(1)
-
-
-
protoheme + 3 reduced acceptor + 3 O2 = mycobilin b + Fe2+ + 3 acceptor + 3 H2O
(2)
-
-
-
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PATHWAY SOURCE
PATHWAYS
MetaCyc
heme degradation VII
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SYSTEMATIC NAME
IUBMB Comments
protoheme,donor:oxygen oxidoreductase (mycobilin-producing)
The enzyme, characterized from the bacterium Mycobacterium tuberculosis, is involved in heme degradation and iron utilization. The enzyme binds two stacked protoheme molecules per monomer. Unlike the canonical heme oxygenases, the enzyme does not release carbon monoxide or formaldehyde. Instead, it forms unique products, named mycobilins, that retain the alpha-meso-carbon at the ring cleavage site as an aldehyde group. EC 1.6.2.4, NADPH-hemoprotein reductase, can act as electron donor in vitro.
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
protoheme + 3 reduced acceptor + 3 O2
mycobilin a + Fe2+ + 3 acceptor + 3 H2O
Substrates: -
Products: -
Products: -
?
protoheme + 3 reduced acceptor + 3 O2
mycobilin a + Fe2+ + 3 acceptor + 3 H2O
Substrates: -
Products: -
Products: -
?
protoheme + 3 reduced acceptor + 3 O2
mycobilin a + Fe2+ + 3 acceptor + 3 H2O
Substrates: -
Products: -
Products: -
?
protoheme + 3 reduced acceptor + 3 O2
mycobilin b + Fe2+ + 3 acceptor + 3 H2O
Substrates: -
Products: -
Products: -
?
protoheme + 3 reduced acceptor + 3 O2
mycobilin b + Fe2+ + 3 acceptor + 3 H2O
Substrates: -
Products: -
Products: -
?
additional information
?
-
Substrates: MhuD catalysis does not generate CO. MhuD cleaves heme at the alpha-meso position but retains the meso-carbon atom at the cleavage site. The tetrapyrrole product of MhuD, mycobilin, has an aldehyde group at the cleavage site and a carbonyl group at either the beta-meso or the delta-meso position. MhuD catalysis does not involve verdoheme
Products: -
Products: -
?
additional information
?
-
Substrates: MhuD catalysis does not generate CO. MhuD cleaves heme at the alpha-meso position but retains the meso-carbon atom at the cleavage site. The tetrapyrrole product of MhuD, mycobilin, has an aldehyde group at the cleavage site and a carbonyl group at either the beta-meso or the delta-meso position. MhuD catalysis does not involve verdoheme
Products: -
Products: -
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
protoheme + 3 reduced acceptor + 3 O2
mycobilin a + Fe2+ + 3 acceptor + 3 H2O
Substrates: -
Products: -
Products: -
?
protoheme + 3 reduced acceptor + 3 O2
mycobilin a + Fe2+ + 3 acceptor + 3 H2O
Substrates: -
Products: -
Products: -
?
protoheme + 3 reduced acceptor + 3 O2
mycobilin b + Fe2+ + 3 acceptor + 3 H2O
Substrates: -
Products: -
Products: -
?
protoheme + 3 reduced acceptor + 3 O2
mycobilin b + Fe2+ + 3 acceptor + 3 H2O
Substrates: -
Products: -
Products: -
?
additional information
?
-
Substrates: MhuD catalysis does not generate CO. MhuD cleaves heme at the alpha-meso position but retains the meso-carbon atom at the cleavage site. The tetrapyrrole product of MhuD, mycobilin, has an aldehyde group at the cleavage site and a carbonyl group at either the beta-meso or the delta-meso position. MhuD catalysis does not involve verdoheme
Products: -
Products: -
?
additional information
?
-
Substrates: MhuD catalysis does not generate CO. MhuD cleaves heme at the alpha-meso position but retains the meso-carbon atom at the cleavage site. The tetrapyrrole product of MhuD, mycobilin, has an aldehyde group at the cleavage site and a carbonyl group at either the beta-meso or the delta-meso position. MhuD catalysis does not involve verdoheme
Products: -
Products: -
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
heme
MhuD can bind heme in a 1:2 protein to heme ratio, although the MhuD-diheme complex is inactive
heme
small amounts of heme ruffling have no influence on the energy of the Q-band and blue-shift the Soret band due to symmetry-allowed mixing of the Fe 3dxy and porphyrin a2u orbitals. Larger amounts of ruffling red-shift both the Q and Soret bands due to disruption of pi-bonding within the porphyrin ring
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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Tuberculosis
Unusual diheme conformation of the heme-degrading protein from Mycobacterium tuberculosis.
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
UniProt
brenda
-
UniProt
brenda
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
Highest Expressing Human Cell Lines
Cell Line LinksPlease wait a moment until the data is sorted. This message will disappear when the data is sorted.
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
metabolism
metabolism
Kd1 for heme dissociation from heme-bound MhuD is 7.6 nM and the Kd2 for heme dissocation from diheme-bound MhuD is 3.3 microM
metabolism
MhuD-diheme dissociation is far slower than monoheme dissociation at about 0.12 per min and about 0.25 per s, respectively. The strength of binding of a second heme molecule is only modestly different from that of the first heme molecule. In diheme-MhuD, the two heme molecules are tightly stacked, with the heme irons coordinated by water and imidazole nitrogen
metabolism
MhuD firstly follows a canonical monooxygenation mechanism to hydroxylate heme on the delta-meso carbon guided by residue Asn7, which experiences a 21.2 kcal/mol energy barrier in the O-O cleavage rate-limiting step. In the second degradation step, the ruffled conformation of oxoheme imposed by the hydrophobic environment of the enzyme inhibits the continuing conversion of oxoheme to biliverdin and also endows the meso-carbons with radical characteristics, the second degradation step is a dioxygenation reaction with 20.4 kcal/mol energy barrier. The ruffled structure of oxoheme is critical to the regiospecificity and even atom location selectivity, as well as the reaction mechanism of the degradation process
metabolism
a dynamic heme substrate is critical for MhuD-catalyzed heme degradation, and product depends upon the substrate conformation. The major product of the ruffled conformation is mycobilin, while the major product of the planar conformation is alpha-biliverdin
metabolism
the distal heme in the diheme MhuD active site has negligible effects on both the planarity of the His-coordinated heme macrocycle and the strength of the Fe-NHis linkage relative to the monoheme form. The process of heme binding that converts MhuD from mono- to diheme form, displays biomolecular dynamics, where the second incoming heme replaces the first as the His75-coordinated heme. Ferrous CO-ligated diheme MhuD exhibits multiple Fe-C-O conformers, one of which contains catalytically predisposed H-bonding interactions with the distal Asn7 residue identical to those in the monoheme form
metabolism
-
Kd1 for heme dissociation from heme-bound MhuD is 7.6 nM and the Kd2 for heme dissocation from diheme-bound MhuD is 3.3 microM
-
metabolism
-
MhuD-diheme dissociation is far slower than monoheme dissociation at about 0.12 per min and about 0.25 per s, respectively. The strength of binding of a second heme molecule is only modestly different from that of the first heme molecule. In diheme-MhuD, the two heme molecules are tightly stacked, with the heme irons coordinated by water and imidazole nitrogen
-
metabolism
-
MhuD firstly follows a canonical monooxygenation mechanism to hydroxylate heme on the delta-meso carbon guided by residue Asn7, which experiences a 21.2 kcal/mol energy barrier in the O-O cleavage rate-limiting step. In the second degradation step, the ruffled conformation of oxoheme imposed by the hydrophobic environment of the enzyme inhibits the continuing conversion of oxoheme to biliverdin and also endows the meso-carbons with radical characteristics, the second degradation step is a dioxygenation reaction with 20.4 kcal/mol energy barrier. The ruffled structure of oxoheme is critical to the regiospecificity and even atom location selectivity, as well as the reaction mechanism of the degradation process
-
metabolism
-
a dynamic heme substrate is critical for MhuD-catalyzed heme degradation, and product depends upon the substrate conformation. The major product of the ruffled conformation is mycobilin, while the major product of the planar conformation is alpha-biliverdin
-
metabolism
-
the distal heme in the diheme MhuD active site has negligible effects on both the planarity of the His-coordinated heme macrocycle and the strength of the Fe-NHis linkage relative to the monoheme form. The process of heme binding that converts MhuD from mono- to diheme form, displays biomolecular dynamics, where the second incoming heme replaces the first as the His75-coordinated heme. Ferrous CO-ligated diheme MhuD exhibits multiple Fe-C-O conformers, one of which contains catalytically predisposed H-bonding interactions with the distal Asn7 residue identical to those in the monoheme form
-
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). MHUD_MYCTO
Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)
105
0
11185
Swiss-Prot
-
MHUD_MYCTU
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
105
0
11185
Swiss-Prot
-
A0A0H3MBJ7_MYCBP
Mycobacterium bovis (strain BCG / Pasteur 1173P2)
105
0
11185
TrEMBL
other Location (Reliability: 1)
A0A1A2Z5J0_9MYCO
105
0
11238
TrEMBL
other Location (Reliability: 4)
A0A1R3Y4L7_MYCBO
Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97)
105
0
11185
TrEMBL
-
A0A1X1YD72_9MYCO
105
0
11265
TrEMBL
other Location (Reliability: 4)
A0A2G8BF68_9MYCO
105
0
11449
TrEMBL
other Location (Reliability: 2)
A0A498QIA2_9MYCO
105
0
11316
TrEMBL
Secretory Pathway (Reliability: 5)
A0A655ALJ6_MYCTX
105
0
11186
TrEMBL
Secretory Pathway (Reliability: 1)
A0A7I7KXD5_9MYCO
105
0
11315
TrEMBL
other Location (Reliability: 5)
A0A7I7MUI2_9MYCO
105
0
11143
TrEMBL
other Location (Reliability: 4)
A0A829C6W9_9MYCO
105
0
11185
TrEMBL
other Location (Reliability: 2)
A0A9P2M2G9_MYCTX
105
0
11185
TrEMBL
-
A0AAD1GXM1_MYCXE
105
0
11449
TrEMBL
other Location (Reliability: 2)
A0AAX1JB65_9MYCO
105
0
11256
TrEMBL
other Location (Reliability: 1)
A0AB72XQK1_MYCCP
Mycobacterium canettii (strain CIPT 140010059)
105
0
11185
TrEMBL
-
A5U8R7_MYCTA
Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra)
105
0
11185
TrEMBL
Mitochondrion (Reliability: 4)
B2HJ32_MYCMM
Mycobacterium marinum (strain ATCC BAA-535 / M)
105
0
11250
TrEMBL
-
L7VHB0_MYCL1
Mycobacterium liflandii (strain 128FXT)
105
0
11250
TrEMBL
-
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
cyanide-inhibited MhuD in complex with heme as well as detailed characterization of this species. There is no evidence for an ordered network of water molecules on the distal side of the heme substrate. The degree of heme ruffling in the crystal structure is greater than that observed for heme oxygenases and less than that observed for heme-degrading enzyme IsdI. The Fe 3dxz-, 3dyz-, and 3dxy-based molecular orbitals are very close in energy, and the room-temperature 1H NMR spectrum is consistent with population of both a 2Eg electronic state with a (dxy)2(dxz,dyz)3 electron configuration, and a 2B2g state with a (dxz,dyz)4(dxy)1 electron configuration. MhuD-heme-CN has a 2B2g electronic ground state with a low-lying 2Eg excited state
MhuD-diheme complex, to 1.75 A resolution, reveals two stacked hemes forming extensive contacts with residues in the active site. The solvent-exposed heme is axially liganded by His75 and is stacked planar upon the solvent-protected heme. The solvent-protected heme is coordinated by a chloride ion which is, in turn, stabilized by residue Asn7
mutant R26S in complex with its product biliverdin IXalpha to 2.5 A. Two biliverdin IXalpha molecules bind per active site and a alpha-helix alpha3 is found. alpha3 is stable with the proximal biliverdin IXalpha alone
the catalytically active 1:1 heme-MhuD complex has an active site structure similar to those of heme degrading enzymes IsdG and IsdI, including the nonplanarity (ruffling) of the heme group bound to the enzyme
the heme molecule in the MhuD active site is rotated about 90° about the tetrapyrrole plane with the respect to Staphylococcus aureus IsdG and IsdI active site heme molecules. In MhuD, Arg22 and Arg26 stabilize the heme propionates, and may account for heme orientation
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
F23W
mutation favors ruffled substrate conformation and leads to formation of meso-hydroxyheme, i.e. has the ability to monooxygenate heme, but subsequent oxygenation reactions may be impaired
R22S
variant does not alter the resulting chromophore product
R26S
W66A
steric bulk at residue 66 promotes MhuD-catalyzed heme oxygenation, and this reaction does not depend upon the generation of free peroxide. The protein fold is similar to wild-type
W66F
F23W
-
mutation favors ruffled substrate conformation and leads to formation of meso-hydroxyheme, i.e. has the ability to monooxygenate heme, but subsequent oxygenation reactions may be impaired
-
R22S
-
variant does not alter the resulting chromophore product
-
R26S
W66A
-
steric bulk at residue 66 promotes MhuD-catalyzed heme oxygenation, and this reaction does not depend upon the generation of free peroxide. The protein fold is similar to wild-type
-
W66F
R26S
variant alters the resulting chromophore product from mycobilin to biliverdin IXalpha and produces formaldehyde rather than carbon monoxide
R26S
variant alters the resulting chromophore product from mycobilin to biliverdin IXalpha. Biliverdin IXalpha has nanomolar affinity for MhuD and the R26S variant
W66F
steric bulk at residue 66 promotes MhuD-catalyzed heme oxygenation, and this reaction does not depend upon the generation of free peroxide. The protein fold is similar to wild-type
W66F
mutation favors planar substrate conformation, degradation product is biliverdin
R26S
-
variant alters the resulting chromophore product from mycobilin to biliverdin IXalpha and produces formaldehyde rather than carbon monoxide
-
R26S
-
variant alters the resulting chromophore product from mycobilin to biliverdin IXalpha. Biliverdin IXalpha has nanomolar affinity for MhuD and the R26S variant
-
W66F
-
steric bulk at residue 66 promotes MhuD-catalyzed heme oxygenation, and this reaction does not depend upon the generation of free peroxide. The protein fold is similar to wild-type
-
W66F
-
mutation favors planar substrate conformation, degradation product is biliverdin
-
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Graves, A.B.; Morse, R.P.; Chao, A.; Iniguez, A.; Goulding, C.W.; Liptak, M.D.
Crystallographic and spectroscopic insights into heme degradation by Mycobacterium tuberculosis MhuD
Inorg. Chem.
53
5931-5940
2014
Mycobacterium tuberculosis (P9WKH3), Mycobacterium tuberculosis ATCC 25618 (P9WKH3)
brenda
Nambu, S.; Matsui, T.; Goulding, C.W.; Takahashi, S.; Ikeda-Saito, M.
A new way to degrade heme: the Mycobacterium tuberculosis enzyme MhuD catalyzes heme degradation without generating CO
J. Biol. Chem.
288
10101-10109
2013
Mycobacterium tuberculosis (P9WKH3), Mycobacterium tuberculosis H37Rv (P9WKH3)
brenda
Chim, N.; Iniguez, A.; Nguyen, T.Q.; Goulding, C.W.
Unusual diheme conformation of the heme-degrading protein from Mycobacterium tuberculosis
J. Mol. Biol.
395
595-608
2010
Mycobacterium tuberculosis (P9WKH3), Mycobacterium tuberculosis, Mycobacterium tuberculosis ATCC 25618 (P9WKH3)
brenda
Graves, A.B.; Graves, M.T.; Liptak, M.D.
Measurement of heme ruffling changes in MhuD using UV-vis pectroscopy
J. Phys. Chem. B
120
3844-3853
2016
Mycobacterium tuberculosis (P9WKH3), Mycobacterium tuberculosis ATCC 25618 (P9WKH3)
brenda
Matthews, S.; Pacholarz, K.; France, A.; Jowitt, T.; Hay, S.; Barran, P.; Munro, A.
MhuD from Mycobacterium tuberculosis probing a dual role in heme storage and degradation
ACS Infect. Dis.
5
1855-1866
2019
Mycobacterium tuberculosis (P9WKH3), Mycobacterium tuberculosis ATCC 25618 (P9WKH3)
brenda
Chao, A.; Burley, K.; Sieminski, P.; De Miranda, R.; Chen, X.; Mobley, D.; Goulding, C.
Structure of a Mycobacterium tuberculosis heme-degrading protein, MhuD, variant in complex with its product
Biochemistry
58
4610-4620
2019
Mycobacterium tuberculosis (P9WKH3), Mycobacterium tuberculosis ATCC 25618 (P9WKH3)
brenda
Chao, A.; Goulding, C.
A Single Mutation in the Mycobacterium tuberculosis heme-degrading protein, MhuD, results in different products
Biochemistry
58
489-492
2019
Mycobacterium tuberculosis (P9WKH3), Mycobacterium tuberculosis ATCC 25618 (P9WKH3)
brenda
Thakuri, B.; ORourke, B.; Graves, A.; Liptak, M.
A Dynamic substrate is required for MhuD-catalyzed degradation of heme to mycobilin
Biochemistry
60
918-928
2021
Mycobacterium tuberculosis (P9WKH3), Mycobacterium tuberculosis ATCC 25618 (P9WKH3)
brenda
Snyder, S.; Mak, P.
Structure-function characterization of the mono- and diheme forms of MhuD, a noncanonical heme oxygenase from Mycobacterium tuberculosis
J. Biol. Chem.
298
101475
2022
Mycobacterium tuberculosis (P9WKH3), Mycobacterium tuberculosis ATCC 25618 (P9WKH3)
brenda
Thakuri, B.; Graves, A.; Chao, A.; Johansen, S.; Goulding, C.; Liptak, M.
The affinity of MhuD for heme is consistent with a heme degrading function in vivo
Metallomics
10
1560-1563
2018
Mycobacterium tuberculosis (P9WKH3), Mycobacterium tuberculosis ATCC 25618 (P9WKH3)
brenda
Yuan, C.; Zhang, Y.; Tan, H.; Li, X.; Chen, G.; Jia, Z.
ONIOM investigations of the heme degradation mechanism by MhuD The critical function of heme ruffling
Phys. Chem. Chem. Phys.
22
8817-8826
2020
Mycobacterium tuberculosis (P9WKH3), Mycobacterium tuberculosis ATCC 25618 (P9WKH3)
brenda
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