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Escherichia coli K-12 substr. MG1655 Enzyme: hybrid-cluster protein



Gene: hcp Accession Numbers: G6457 (EcoCyc), b0873, ECK0864

Synonyms: priS, ybjW, fuscoredoxin, prismane protein

Regulation Summary Diagram: ?

Summary:
The hybrid cluster protein (HCP) exhibits hydroxylamine reductase activity, possibly functioning as a scavenger of toxic by-products of nitrogen metabolism [Wolfe02]. HCP was originally suggested to be involved in nitrate-and/or nitrite respiration based on its regulation [vandenBerg00].

HCP contains iron-sulfur clusters of the [2Fe-2S] and [4Fe-2S-2O] type [Pereira99, vandenBerg00] and is reduced by the Hcr NADH oxidoreductase [vandenBerg00]. The properties of electron transfer in the Hcr-HCP system have been studied [vandenBerg00].

Related hybrid cluster proteins have been identified and, in some species, well characterized. The corresponding Salmonella enterica serovar Typhimurium protein exhibits a role in pathogenesis [Kim03a].

HCP is produced during anaerobic growth in the presence of nitrate or nitrite [vandenBerg00]. Induction of expression is dependent on NarL and NarP [Filenko05]. Expression of hcp is also upregulated by S-nitrosoglutathione, a nitrosating agent [Flatley05].

Review: [Johnson98].

Citations: [Vine11a]

Gene Citations: [Rhodius05]

Locations: cytosol

Map Position: [911,385 <- 913,037] (19.64 centisomes)
Length: 1653 bp / 550 aa

Molecular Weight of Polypeptide: 60.064 kD (from nucleotide sequence), 60 kD (experimental) [vandenBerg00 ]

Unification Links: ASAP:ABE-0002962 , DIP:DIP-9870N , EchoBASE:EB3456 , EcoGene:EG13692 , EcoliWiki:b0873 , ModBase:P75825 , OU-Microarray:b0873 , PortEco:hcp , PR:PRO_000022865 , Pride:P75825 , Protein Model Portal:P75825 , RefSeq:NP_415394 , RegulonDB:G6457 , SMR:P75825 , String:511145.b0873 , UniProt:P75825

Relationship Links: InterPro:IN-FAMILY:IPR004137 , InterPro:IN-FAMILY:IPR010048 , InterPro:IN-FAMILY:IPR011254 , InterPro:IN-FAMILY:IPR016099 , InterPro:IN-FAMILY:IPR016100 , Pfam:IN-FAMILY:PF03063

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006807 - nitrogen compound metabolic process Inferred from experiment [Wolfe02]
GO:0042542 - response to hydrogen peroxide Inferred from experiment [Almeida06]
GO:0055114 - oxidation-reduction process Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Almeida06]
Molecular Function: GO:0004601 - peroxidase activity Inferred from experiment [Almeida06]
GO:0016491 - oxidoreductase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Almeida06]
GO:0050418 - hydroxylamine reductase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, Wolfe02]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0016661 - oxidoreductase activity, acting on other nitrogenous compounds as donors Inferred by computational analysis [GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0051537 - 2 iron, 2 sulfur cluster binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06, GOA01]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism metabolism of other compounds nitrogen metabolism

Essentiality data for hcp knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Credits:
Last-Curated ? 07-Dec-2005 by Keseler I , SRI International


Enzymatic reaction of: hydroxylamine reductase (hybrid-cluster protein)

Synonyms: hydroxylamine (acceptor) reductase, ammonia:(acceptor) oxidoreductase

EC Number: 1.7.99.1

hydroxylamine + a reduced electron acceptor + H+ <=> ammonium + an oxidized electron acceptor + H2O

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

Activators (Unknown Mechanism): hydrogen cyanide [Wolfe02]

Inhibitors (Unknown Mechanism): oxygen [Wolfe02]

Kinetic Parameters:

Substrate
Km (μM)
Citations
hydroxylamine
2500.0
[Wolfe02]

pH(opt): 9 [Wolfe02]


Sequence Features

Feature Class Location Citations Comment
Metal-Binding-Site 3
[UniProt10a]
UniProt: Iron-sulfur (2Fe-2S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 6
[UniProt10a]
UniProt: Iron-sulfur (2Fe-2S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 18
[UniProt10a]
UniProt: Iron-sulfur (2Fe-2S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 25
[UniProt10a]
UniProt: Iron-sulfur (2Fe-2S); Non-Experimental Qualifier: by similarity;
Sequence-Conflict 134
[Oshima96, UniProt10]
Alternate sequence: E → V; UniProt: (in Ref. 1);
Metal-Binding-Site 249
[UniProt10a]
UniProt: Iron-oxo-sulfur (4Fe-2O-2S); via tele nitrogen; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 273
[UniProt10a]
UniProt: Iron-oxo-sulfur (4Fe-2O-2S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 317
[UniProt10a]
UniProt: Iron-oxo-sulfur (4Fe-2O-2S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 405
[UniProt10a]
UniProt: Iron-oxo-sulfur (4Fe-2O-2S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 433
[UniProt10a]
UniProt: Iron-oxo-sulfur (4Fe-2O-2S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 458
[UniProt10a]
UniProt: Iron-oxo-sulfur (4Fe-2O-2S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 492
[UniProt10a]
UniProt: Iron-oxo-sulfur (4Fe-2O-2S); Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene right-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

Almeida06: Almeida CC, Romao CV, Lindley PF, Teixeira M, Saraiva LM (2006). "The role of the hybrid cluster protein in oxidative stress defense." J Biol Chem 281(43);32445-50. PMID: 16928682

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Filenko05: Filenko NA, Browning DF, Cole JA (2005). "Transcriptional regulation of a hybrid cluster (prismane) protein." Biochem Soc Trans 33(Pt 1);195-7. PMID: 15667305

Flatley05: Flatley J, Barrett J, Pullan ST, Hughes MN, Green J, Poole RK (2005). "Transcriptional responses of Escherichia coli to S-nitrosoglutathione under defined chemostat conditions reveal major changes in methionine biosynthesis." J Biol Chem 280(11);10065-72. PMID: 15647275

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Johnson98: Johnson MK (1998). "Iron-sulfur proteins: new roles for old clusters." Curr Opin Chem Biol 2(2);173-81. PMID: 9667933

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kim03a: Kim CC, Monack D, Falkow S (2003). "Modulation of virulence by two acidified nitrite-responsive loci of Salmonella enterica serovar Typhimurium." Infect Immun 71(6);3196-205. PMID: 12761099

Oshima96: Oshima T, Aiba H, Baba T, Fujita K, Hayashi K, Honjo A, Ikemoto K, Inada T, Itoh T, Kajihara M, Kanai K, Kashimoto K, Kimura S, Kitagawa M, Makino K, Masuda S, Miki T, Mizobuchi K, Mori H, Motomura K, Nakamura Y, Nashimoto H, Nishio Y, Saito N, Horiuchi T (1996). "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map." DNA Res 3(3);137-55. PMID: 8905232

Pereira99: Pereira AS, Tavares P, Krebs C, Huynh BH, Rusnak F, Moura I, Moura JJ (1999). "Biochemical and spectroscopic characterization of overexpressed fuscoredoxin from Escherichia coli." Biochem Biophys Res Commun 260(1);209-15. PMID: 10381368

Rhodius05: Rhodius VA, Suh WC, Nonaka G, West J, Gross CA (2005). "Conserved and variable functions of the sigmaE stress response in related genomes." PLoS Biol 4(1);e2. PMID: 16336047

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

vandenBerg00: van den Berg WA, Hagen WR, van Dongen WM (2000). "The hybrid-cluster protein ('prismane protein') from Escherichia coli. Characterization of the hybrid-cluster protein, redox properties of the [2Fe-2S] and [4Fe-2S-2O] clusters and identification of an associated NADH oxidoreductase containing FAD and [2Fe-2S]." Eur J Biochem 2000;267(3);666-76. PMID: 10651802

Vine11a: Vine CE, Cole JA (2011). "Unresolved sources, sinks, and pathways for the recovery of enteric bacteria from nitrosative stress." FEMS Microbiol Lett 325(2);99-107. PMID: 22029434

Wolfe02: Wolfe MT, Heo J, Garavelli JS, Ludden PW (2002). "Hydroxylamine reductase activity of the hybrid cluster protein from Escherichia coli." J Bacteriol 184(21);5898-902. PMID: 12374823

Other References Related to Gene Regulation

Chismon10: Chismon DL, Browning DF, Farrant GK, Busby SJ (2010). "Unusual organisation, complexity and redundancy at the Escherichia coli hcp-hcr operon promoter." Biochem J. PMID: 20533909

Filenko07: Filenko N, Spiro S, Browning DF, Squire D, Overton TW, Cole J, Constantinidou C (2007). "The NsrR regulon of Escherichia coli K-12 includes genes encoding the hybrid cluster protein and the periplasmic, respiratory nitrite reductase." J Bacteriol 189(12):4410-7. PMID: 17449618

Partridge09: Partridge JD, Bodenmiller DM, Humphrys MS, Spiro S (2009). "NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility." Mol Microbiol 73(4);680-94. PMID: 19656291

Seth12: Seth D, Hausladen A, Wang YJ, Stamler JS (2012). "Endogenous protein S-Nitrosylation in E. coli: regulation by OxyR." Science 336(6080);470-3. PMID: 22539721

Vine11: Vine CE, Purewal SK, Cole JA (2011). "NsrR-dependent method for detecting nitric oxide accumulation in the Escherichia coli cytoplasm and enzymes involved in NO production." FEMS Microbiol Lett 325(2);108-14. PMID: 22092912


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Sun Dec 21, 2014, BIOCYC13A.