| Root |
Created: 5 June 1996
| Sirohaem-Fe4S4 centre
(overall structure) |
Iron-sulphur cluster | Formal oxidation/spin states | ||||
|---|---|---|---|---|---|---|
 |
  Cys)4 |
[Fe4S4]+ (S=1/2)|;
[Fe4S4]2+ (S=0) | Spincoupled to sirohaem |
||||
| Haem type | Haem iron coordination | Axial iron ligand(s) | Formal iron oxidation/spin states | |||
 |
 |
Cys
|
FeII (S=1 or S=2)¶;
FeIII (S=3/2 or S=5/2)¶ ¶ Spincoupled to [Fe4S4]+ |
|||
 |
Cys;
SO32-, HSO3-,
|
FeII (S=0);
FeIII (S=1/2)¶ ¶ Spincoupled to [Fe4S4]+ |
||||
Nitrite reductases (NiRs) catalyse the sixelectron reduction of nitrite
to ammonia [1,
2]:
On the basis of physiological function, two types of NiRs can be defined: the
assimilatory or ammoniaproducing (aNiRs), which are involved in
nitrate assimilation (denitrification); and the dissimilatory type (dNiRs),
which are responsible for nitrate respiration function. Higher plant aNiRs (EC
1.7.7.1)
use reduced planttype ferredoxin as the
electron donor and are monomeric. Fungal and bacterial aNiRs (EC
1.6.6.4)
use NAD(P)H as electron donor and are homodimers. All aNiRs contain
a prosthetic group termed
sirohaem
(an iron tetrahydroporphyrin of the isobacteriochlorin type, with eight
carboxylic acidcontaining peripheral sidechains), and an
[Fe4S4] cluster, while fungal and bacterial aNiRs contain
FAD as well. In contrast, bacterial dNiRs form a diverse group of enzymes that
includes Esherichia coli sirohaemcontaining reductase, hexahaem
cytochrome c552, cytochrome
cd1 and coppercontaining nitrite reductases.
NH4+ + 2H2O(1)
Similarly, there are two types of bacterial sulphite reductases (SiRs): the
assimilatory type (aSiRs), which participate in the synthesis of
sulphurcontaining compounds; and the dissimilatory type (dSiRs), which
are terminal reductases in the reduction of sulphate. aSiRs are found in
bacteria, fungi and plants and use either reduced ferredoxin (EC
1.8.7.1),
NADPH (EC
1.8.1.2)
or NADH (anaerobic sulphite reductase, EC 1.8.1.-) as electron donors. dSiRs (EC
1.8.99.3)
are found in sulphatereducing bacteria and some species of thermophilic
archaea and probably evolved before or soon after the divergence of the two
kingdoms [4 and references therein].
Phototrophic sulphur bacterium Chromatium vinosum and the
sulphuroxidising chemolithotroph Thiobacillus denitrificans
contain socalled `reverse' SiR which is related to dSiRs but is essential
for sulphur oxidation [5].
dSiRs exist as oligomers with either
2ß2
or
2ß22 structure. aSiRs can catalyse
the sixelectron reduction of sulphite to sulphide without
the formation of free intermediates (2), while dSiRs primarily form
trithionate (S3O62-) (3) and
thiosulphate (S2O32-) (4).
dSiRs also reduce NO2-, NO and NH2OH and can
form NH4+ (1).
Both types of SiR contain sirohaem and iron-sulphur clusters
[2, 3].
The E. coli assimilatory SiR is an oligomer of eight flavoprotein
(SiRFP) and four haemoprotein (SiRHP) subunits. In vivo, SiRFP transfers
electrons from reduced NADPH to SiRHP. Isolated SiRHP, when provided with
suitable electron donors, can reduce SO32- to
HS- and NO2- to NH4+
without releasing intermediates. The 3D structure of SiRHP
has been determined [6]
(see Figure 2GEP).
The sirohaem and the Fe4S4 cluster are juxtaposed at
the interface of three
HS¯ + 3H2O(2)
S3O62- + 3H2O(3)
S2O32- + 3H2O(4)
/ß
domains and bridged by a shared cysteine thiolate ligand.
A single domain is formed from subdomain 1 (residues 81-140) and subdomain 1'
(residues 347-418) which are related by a pseudotwofold axis which also
relates domains 2 (residues 155-328) and 3 (residues 426-570). A gene
duplication event apparently correlates an Nterminal repeat (subdomain 1
+ domain 2) to a Cterminal repeat (subdomain 1' + domain 3). The patterns
of conservation between the SiRHP symmetry repeats, concentrated in five
homology regions (H1-H5), are found in most other SiRs and NiRs. The
fingerprint comprising H1 to H4 is termed the sulphite/nitrite reductase
repeat (SNiRR). In both the
Nterminal and Cterminal SNiRRs, H1 regions contain residues that
interact with sirohaem. In the Nterminal SNiRR, H2 and H3 provide the
residues that interact with sirohaem and substrate bound at the active centre,
whereas in the Cterminal SNiRR, H2 and H3 each supply two of the Cys
coordinating the [Fe4S4] cluster
[2, 6].
| ENZYME | LIGAND | BRENDA | Official name | Alternative names |
|---|---|---|---|---|
| 1.6.6.4 | 1.6.6.4 | 1.6.6.4 | Nitrite reductase (NAD(P)H) | Assimilatory nitrite reductase; aNiR; NADH-nitrite oxidoreductase; NADPH-nitrite reductase |
| 1.7.7.1 | 1.7.7.1 | 1.7.7.1 | Ferredoxin-nitrite reductase | Assimilatory nitrite reductase; aNiR |
| 1.8.1.2 | 1.8.1.2 | 1.8.1.2 | Sulphite reductase (NADPH) | Assimilatory sulphite reductase; aSiR; NADPH-sulphite reductase; H2S:NADP oxidoreductase |
| 1.8.7.1 | 1.8.7.1 | 1.8.7.1 | Sulphite reductase (ferredoxin) | Ferredoxin-sulphite reductase |
| 1.8.99.3 | 1.8.99.3 | 1.8.99.3 | Hydrogensulphite reductase | Bisulphite reductase; dissimilatory sulphite reductase; dSiR; desulfoviridin; desulforubidin; desulfofuscidin; P582 |
| 1.8.1.- | 1.8.1.- | 1.8.1.- | Anaerobic sulphite reductase | ASR; NADH-sulphite reductase |
| PRINTS ID | PRINTS AC | PROSITE/BLOCKS ID | PROSITE AC | BLOCKS AC |
|---|---|---|---|---|
| SIROHAEM | PR00397 | NIR_SIR | PS00365 | BL00365 |
| Protein Family | Pfam | LPFC 3D alignment |
|---|---|---|
|
00144;
sulfite reductase (ferredoxin)
06616; ferredoxin-nitrite reductase |
| PDB | scop | BSM | RELI Base | Header | 
¹ |
|---|---|---|---|---|---|
| 1aop | 1geo | 1aop | 1geo | Sulphite reductase haemoprotein (SiRHP) (oxidised, sirohaem FeIII-PO43- complex, [Fe4S4]2+) (complex with K+); Escherichia coli (expressed in Salmonella typhimurium) | MS6MR5 |
| 2aop | 2aop | Sulphite reductase haemoprotein (SiRHP) (reduced with CrII EDTA, sirohaem FeII-PO43- complex, [Fe4S4]+) (complex with K+); Escherichia coli (expressed in Salmonella typhimurium) | |||
| 2gep | 1gep | 2gep | 1gep | Sulphite reductase haemoprotein (SiRHP) (oxidised, sirohaem FeIII-SO32- complex, [Fe4S4]2+) (complex with Na+); Escherichia coli (expressed in Salmonella typhimurium) | MS6MR5 |
| 3aop | 3aop | 3aop | Sulphite reductase haemoprotein (SiRHP) (photoreduced with proflavine EDTA, sirohaem FeII-PO43- complex, [Fe4S4]+) (complex with K+); Escherichia coli (expressed in Salmonella typhimurium) | ||
| 3geo | 3geo | 3geo | Sulphite reductase haemoprotein (SiRHP) (semireduced, sirohaem FeII-NO2¯ complex, [Fe4S4]2+) (complex with Na+); Escherichia coli (expressed in Salmonella typhimurium) | ||
| 4aop | 4aop | 4aop | Sulphite reductase haemoprotein (SiRHP) (partially photoreduced with proflavine EDTA, mixture of three oxidation states: (1) sirohaem FeIII, [Fe4S4]2+; (2) sirohaem FeII, [Fe4S4]2+; (3) sirohaem FeII, [Fe4S4]) (PO43- and H2O each coordinated to sirohaem with partial occupancy) (complex with K+); Escherichia coli (expressed in Salmonella typhimurium) | ||
| 4gep | 4gep | 4gep | Sulphite reductase haemoprotein (SiRHP) (reduced with CrII EDTA, sirohaem FeII-CN complex, [Fe4S4]+) (complex with K+); Escherichia coli (expressed in Salmonella typhimurium) | ||
| 5aop | 5aop | 5aop | Sulphite reductase haemoprotein (SiRHP) (reduced with CrII EDTA, pentacoordinate sirohaem FeII, [Fe4S4]+) (complex with K+); Escherichia coli (expressed in Salmonella typhimurium) | ||
| 5gep | 5gep | 5gep | Sulphite reductase haemoprotein (SiRHP) (reduced with CrII EDTA, sirohaem FeII-CO complex, [Fe4S4]+) (complex with K+); Escherichia coli (expressed in Salmonella typhimurium) | ||
| 6gep | 6gep | 6gep | Sulphite reductase haemoprotein (SiRHP) (partially photoreduced with proflavine EDTA, sirohaem FeII-NO complex, [Fe4S4]2+) (complex with K+); Escherichia coli (expressed in Salmonella typhimurium) | ||
| 7gep | 7gep | 7gep | Sulphite reductase haemoprotein (SiRHP) (oxidised, sirohaem FeIII-SO complex, [Fe4S4]2+) (complex with Na+); Escherichia coli (expressed in Salmonella typhimurium) | ||
| 8gep | 8gep | 8gep | Sulphite reductase haemoprotein (SiRHP) (oxidised or semireduced, sirohaem FeIII or FeII, [Fe4S4]2+) (complex with NO3¯ and K+); Escherichia coli (expressed in Salmonella typhimurium) |
¹ Macromolecular Structures abstract.
Full text is available to BioMedNet
Members
References
| Bibliography on structural studies of sirohaem-Fe4S4 enzymes |
