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11  structures 4345  species 0  interactions 9607  sequences 23  architectures

Family: CbiQ (PF02361)

Summary: Cobalt transport protein

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Cobalamin biosynthesis". More...

Cobalamin biosynthesis Edit Wikipedia article

CobD_Cbib
Identifiers
SymbolCobD_Cbib
PfamPF03186
InterProIPR004485
CobS
Identifiers
SymbolCobS
PfamPF02654
InterProIPR003805
CobT
Identifiers
SymbolCobT
PfamPF06213
InterProIPR006538
CobU
PDB 1cbu EBI.jpg
adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase (cobu) from salmonella typhimurium
Identifiers
SymbolCobU
PfamPF02283
Pfam clanCL0023
InterProIPR003203
SCOPe1cbu / SUPFAM
CDDcd00544
cobW
PDB 1nij EBI.jpg
yjia protein
Identifiers
SymbolcobW
PfamPF02492
Pfam clanCL0023
InterProIPR003495
SCOPe1nij / SUPFAM
CobW C terminal
PDB 1nij EBI.jpg
yjia protein
Identifiers
SymbolCobW_C
PfamPF07683
InterProIPR011629
SCOPe1nij / SUPFAM
CbiA
PDB 1dah EBI.jpg
dethiobiotin synthetase complexed with 7,8-diamino-nonanoic acid, 5'-adenosyl-methylene-triphosphate, and manganese
Identifiers
SymbolCbiA
PfamPF01656
Pfam clanCL0023
InterProIPR002586
SCOPe1dts / SUPFAM
CbiD
PDB 1sr8 EBI.jpg
structural genomics, 1.9a crystal structure of cobalamin biosynthesis protein (cbid) from archaeoglobus fulgidus
Identifiers
SymbolCbiD
PfamPF01888
InterProIPR002748
CbiG N terminus
Identifiers
SymbolCbiG_N
PfamPF11760
InterProIPR021744
CbiG central region
Identifiers
SymbolCbiG_mid
PfamPF11761
InterProIPR021745
CbiG C terminus
Identifiers
SymbolCbiG_C
PfamPF01890
InterProIPR002750
CbiJ
Identifiers
SymbolCbiJ
PfamPF02571
InterProIPR003723
CbiM
Identifiers
SymbolCbiM
PfamPF01891
Pfam clanCL0315
InterProIPR002751
TCDB3.A.1.23
OPM superfamily134
OPM protein4m58
CbiN
Identifiers
SymbolCbiN
PfamPF02553
InterProIPR003705
TCDB3.A.1
CbiQ
Identifiers
SymbolCbiQ
PfamPF02361
InterProIPR003339
TCDB3.A.1
CbiX
PDB 1tjn EBI.jpg
crystal structure of hypothetical protein af0721 from archaeoglobus fulgidus
Identifiers
SymbolCbiX
PfamPF01903
Pfam clanCL0043
InterProIPR002762
CbiZ
Identifiers
SymbolCbiZ
PfamPF01955
InterProIPR002808

In molecular biology, cobalamin biosynthesis is the synthesis of cobalamin (vitamin B12).

Cobalamin

Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adenosylcobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these enzymes include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia-lyase, and diol dehydratase.[1] In certain mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase.[2]

Pathways of cobalamin biosynthesis

There are at least two distinct cobalamin biosynthetic pathways in bacteria:[3]

Either pathway can be divided into two parts:

  • Corrin ring synthesis (differs in aerobic and anaerobic pathways)
  • Adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways).[7]

Proteins involved in cobalamin biosynthesis

There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans.

CbiB/CobD

The CbiB or CobD protein converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group. It is part of the cob operon.[8]

CobT/CobN/CobS

Aerobic cobalt chelatase consists of three subunits, CobT, CobN and CobS. Cobalamin (vitamin B12) can be complexed with metal via the ATP-dependent reactions (aerobic pathway) (e.g., in P. denitrificans) or via ATP-independent reactions (anaerobic pathway) (e.g., in Salmonella typhimurium).[9][10] The corresponding cobalt chelatases are not homologous. However, aerobic cobalt chelatase subunits CobN and CobS are homologous to Mg-chelatase subunits BchH and BchI, respectively.[10] CobT, too, has been found to be remotely related to the third subunit of Mg-chelatase, BchD (involved in bacteriochlorophyll synthesis, e.g., in Rhodobacter capsulatus).[10]

The CobS protein is a cobalamin-5-phosphate synthase that catyalzes the reactions:

  • Adenosylcobinamide-GDP + alpha-ribazole-5'-P = adenosylcobalamin-5'-phosphate + GMP
  • Adenosylcobinamide-GDP + alpha-ribazole = adenosylcobalamin + GMP

The protein product from these catalyses is associated with a large complex of proteins and is induced by cobinamide. CobS is involved in part III of cobalamin biosynthesis, one of the late steps in adenosylcobalamin synthesis that, together with CobU, CobT, and CobC proteins, defines the nucleotide loop assembly pathway.[11][12]

CobU

CobU proteins are bifunctional cobalbumin biosynthesis enzymes which display cobinamide kinase and cobinamide phosphate guanyltransferase activity. The crystal structure of the enzyme reveals the molecule to be a trimer with a propeller-like shape.[13]

CobW

CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis.[1] They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids. CobW-like proteins include P47K, a Pseudomonas chlororaphis protein needed for nitrile hydratase expression,[14] and urease accessory protein UreG, which acts as a chaperone in the activation of urease upon insertion of nickel into the active site.[15]

CbiA

The CbiA family of proteins consists of various cobyrinic acid a,c-diamide synthases. These include CbiA and CbiP from Salmonella typhimurium.,[16] and CobQ from Rhodobacter capsulatus.[17] These amidases catalyse amidations to various side chains of hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis of cobalamin (vitamin B12) from uroporphyrinogen III.[16]

CbiD

CbiD is an essential protein for cobalamin biosynthesis in both Salmonella typhimurium and Bacillus megaterium. A deletion mutant of CbiD suggests that this enzyme is involved in C-1 methylation and deacylation reactions required during the ring contraction process in the anaerobic pathway to cobalamin (similar role as CobF).[18] The CbiD protein has a putative S-AdoMet binding site.[19] CbiD has no counterpart in the aerobic pathway.

CbiG

CbiG proteins are specific for anaerobic cobalamin biosynthesis. CbiG, which shows homology with CobE of the aerobic pathway, participates in the conversion of cobalt-precorrin 5 into cobalt-precorrin 6.[20] CbiG is responsible for the opening of the delta-lactone ring and extrusion of the C2-unit.[21] The aerobic pathway uses molecular oxygen to trigger the events at C-20 leading to contraction and expulsion of the C2-unit as acetic acid from a metal-free intermediate, whereas the anaerobic route involves the internal delivery of oxygen from a carboxylic acid terminus to C-20 followed by extrusion of the C2-unit as acetaldehyde, using cobalt complexes as substrates.[21]

CbiJ

The CbiJ family of proteins includes the CobK and CbiJ precorrin-6x reductases EC 1.3.1.54. In the aerobic pathway, CobK catalyses the reduction of the macrocycle of precorrin-6X to produce precorrin-6Y; while in the anaerobic pathway CbiJ catalyses the reduction of the macrocycle of cobalt-precorrin-6X into cobalt-precorrin-6Y.[22][23]

CbiM

CbiM is a transmembrane cobalamin transporter.

CbiN

The cobalt transport protein CbiN is part of the active cobalt transport system involved in uptake of cobalt into the cell involved with cobalamin biosynthesis (vitamin B12). It has been suggested that CbiN may function as the periplasmic binding protein component of the active cobalt transport system.[17]

CbiQ

The CbiQ family consists of various cobalt transport proteins Most of which are found in Cobalamin (Vitamin B12) biosynthesis operons. In Salmonella the cbiN cbiQ (product CbiQ in this family) and cbiO are likely to form an active cobalt transport system.[24]

CbiX

The CbiX protein functions as a cobalt-chelatase in the anaerobic biosynthesis of cobalamin. It catalyses the insertion of cobalt into sirohydrochlorin. The structure of CbiX from Archaeoglobus fulgidus consists of a central mixed beta-sheet flanked by four alpha-helices, although it is about half the size of other Class II tetrapyrrole chelatases.[25] The CbiX proteins found in archaea appear to be shorter than those found in eubacteria.[26]

CbiZ

The CbiZ family of proteins includes CbiZ, which is involved in the salvage pathway of cobinamide in archaea. Archaea convert adenosylcobinamide (AdoCbi) into adenosylcobinamide phosphate (AdoCbi-P) in two steps. First, the amidohydrolase activity of CbiZ cleaves off the aminopropanol moiety of AdoCbi yielding adenosylcobyric acid (AdoCby); second, AdoCby is converted into AdoCbi-P by the action of adenosylcobinamide-phosphate synthase (CbiB). Adenosylcobyric acid is an intermediate of the de novo coenzyme B12 biosynthetic route.[27]

References

  1. ^ a b Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS (October 2003). "Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes". J. Biol. Chem. 278 (42): 41148–59. doi:10.1074/jbc.M305837200. PMID 12869542.
  2. ^ Banerjee R (April 2006). "B12 trafficking in mammals: A for coenzyme escort service". ACS Chem. Biol. 1 (3): 149–59. doi:10.1021/cb6001174. PMID 17163662.
  3. ^ Roessner CA, Santander PJ, Scott AI (2001). Multiple biosynthetic pathways for vitamin B12: variations on a central theme. Vitam. Horm. Vitamins & Hormones. 61. pp. 267–97. doi:10.1016/s0083-6729(01)61009-4. ISBN 9780127098616. PMID 11153269.
  4. ^ Heldt D, Lawrence AD, Lindenmeyer M, Deery E, Heathcote P, Rigby SE, Warren MJ (August 2005). "Aerobic synthesis of vitamin B12: ring contraction and cobalt chelation". Biochem. Soc. Trans. 33 (Pt 4): 815–9. doi:10.1042/BST0330815. PMID 16042605.
  5. ^ Roessner CA, Huang KX, Warren MJ, Raux E, Scott AI (June 2002). "Isolation and characterization of 14 additional genes specifying the anaerobic biosynthesis of cobalamin (vitamin B12) in Propionibacterium freudenreichii (P. shermanii)". Microbiology. 148 (Pt 6): 1845–53. doi:10.1099/00221287-148-6-1845. PMID 12055304.
  6. ^ Moore, Simon J.; Lawrence, Andrew D.; Biedendieck, Rebekka; Deery, Evelyne; Frank, Stefanie; Howard, Mark J.; Rigby, Stephen E. J.; Warren, Martin J. (2013-09-10). "Elucidation of the anaerobic pathway for the corrin component of cobalamin (vitamin B12)". Proceedings of the National Academy of Sciences. 110 (37): 14906–14911. doi:10.1073/pnas.1308098110. ISSN 0027-8424. PMC 3773766. PMID 23922391.
  7. ^ Raux E, Schubert HL, Warren MJ (December 2000). "Biosynthesis of cobalamin (vitamin B12): a bacterial conundrum". Cell. Mol. Life Sci. 57 (13–14): 1880–93. doi:10.1007/PL00000670. PMID 11215515.
  8. ^ Woodson JD, Zayas CL, Escalante-Semerena JC (December 2003). "A new pathway for salvaging the coenzyme B12 precursor cobinamide in archaea requires cobinamide-phosphate synthase (CbiB) enzyme activity". J. Bacteriol. 185 (24): 7193–201. doi:10.1128/jb.185.24.7193-7201.2003. PMC 296239. PMID 14645280.
  9. ^ Roth JR, Lawrence JG, Bobik TA (1996). "Cobalamin (coenzyme B12): synthesis and biological significance". Annu. Rev. Microbiol. 50: 137–81. doi:10.1146/annurev.micro.50.1.137. PMID 8905078.
  10. ^ a b c Fodje MN, Hansson A, Hansson M, Olsen JG, Gough S, Willows RD, Al-Karadaghi S (August 2001). "Interplay between an AAA module and an integrin I domain may regulate the function of magnesium chelatase". J. Mol. Biol. 311 (1): 111–22. doi:10.1006/jmbi.2001.4834. PMID 11469861.
  11. ^ Maggio-Hall LA, Escalante-Semerena JC (October 1999). "In vitro synthesis of the nucleotide loop of cobalamin by Salmonella typhimurium enzymes". Proc. Natl. Acad. Sci. U.S.A. 96 (21): 11798–803. doi:10.1073/pnas.96.21.11798. PMC 18366. PMID 10518530.
  12. ^ Maggio-Hall LA, Claas KR, Escalante-Semerena JC (May 2004). "The last step in coenzyme B(12) synthesis is localized to the cell membrane in bacteria and archaea". Microbiology. 150 (Pt 5): 1385–95. doi:10.1099/mic.0.26952-0. PMID 15133100.
  13. ^ Thompson TB, Thomas MG, Escalante-Semerena JC, Rayment I (May 1998). "Three-dimensional structure of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase from Salmonella typhimurium determined to 2.3 A resolution". Biochemistry. 37 (21): 7686–95. CiteSeerX 10.1.1.565.1238. doi:10.1021/bi973178f. PMID 9601028.
  14. ^ Hashimoto Y, Nishiyama M, Horinouchi S, Beppu T (October 1994). "Nitrile hydratase gene from Rhodococcus sp. N-774 requirement for its downstream region for efficient expression". Biosci. Biotechnol. Biochem. 58 (10): 1859–65. doi:10.1271/bbb.58.1859. PMID 7765511.
  15. ^ Zambelli B, Musiani F, Savini M, Tucker P, Ciurli S (March 2007). "Biochemical studies on Mycobacterium tuberculosis UreG and comparative modeling reveal structural and functional conservation among the bacterial UreG family". Biochemistry. 46 (11): 3171–82. doi:10.1021/bi6024676. PMID 17309280.
  16. ^ a b Pollich M, Klug G (August 1995). "Identification and sequence analysis of genes involved in late steps in cobalamin (vitamin B12) synthesis in Rhodobacter capsulatus". J. Bacteriol. 177 (15): 4481–7. doi:10.1128/jb.177.15.4481-4487.1995. PMC 177200. PMID 7635831.
  17. ^ a b Roth JR, Lawrence JG, Rubenfield M, Kieffer-Higgins S, Church GM (June 1993). "Characterization of the cobalamin (vitamin B12) biosynthetic genes of Salmonella typhimurium". J. Bacteriol. 175 (11): 3303–16. doi:10.1128/jb.175.11.3303-3316.1993. PMC 204727. PMID 8501034.
  18. ^ Roessner CA, Williams HJ, Scott AI (April 2005). "Genetically engineered production of 1-desmethylcobyrinic acid, 1-desmethylcobyrinic acid a,c-diamide, and cobyrinic acid a,c-diamide in Escherichia coli implies a role for CbiD in C-1 methylation in the anaerobic pathway to cobalamin". J. Biol. Chem. 280 (17): 16748–53. doi:10.1074/jbc.M501805200. PMID 15741157.
  19. ^ Raux E, Lanois A, Warren MJ, Rambach A, Thermes C (October 1998). "Cobalamin (vitamin B12) biosynthesis: identification and characterization of a Bacillus megaterium cobI operon". Biochem. J. 335 (1): 159–66. doi:10.1042/bj3350159. PMC 1219764. PMID 9742225.
  20. ^ Scott AI, Roessner CA (August 2002). "Biosynthesis of cobalamin (vitamin B(12))". Biochem. Soc. Trans. 30 (4): 613–20. doi:10.1042/bst0300613. PMID 12196148.
  21. ^ a b Kajiwara Y, Santander PJ, Roessner CA, Pérez LM, Scott AI (August 2006). "Genetically engineered synthesis and structural characterization of cobalt-precorrin 5A and -5B, two new intermediates on the anaerobic pathway to vitamin B12: definition of the roles of the CbiF and CbiG enzymes". J. Am. Chem. Soc. 128 (30): 9971–8. doi:10.1021/ja062940a. PMID 16866557.
  22. ^ Kim W, Major TA, Whitman WB (December 2005). "Role of the precorrin 6-X reductase gene in cobamide biosynthesis in Methanococcus maripaludis". Archaea. 1 (6): 375–84. doi:10.1155/2005/903614. PMC 2685584. PMID 16243778.
  23. ^ Shearer N, Hinsley AP, Van Spanning RJ, Spiro S (November 1999). "Anaerobic growth of Paracoccus denitrificans requires cobalamin: characterization of cobK and cobJ genes". J. Bacteriol. 181 (22): 6907–13. PMC 94164. PMID 10559155.
  24. ^ Roth, J. R.; Lawrence, J. G.; Rubenfield, M.; Kieffer-Higgins, S.; Church, G. M. (1993). "Characterization of the cobalamin (vitamin B12) biosynthetic genes of Salmonella typhimurium". Journal of Bacteriology. 175 (11): 3303–3316. doi:10.1128/jb.175.11.3303-3316.1993. PMC 204727. PMID 8501034.
  25. ^ Yin J, Xu LX, Cherney MM, Raux-Deery E, Bindley AA, Savchenko A, Walker JR, Cuff ME, Warren MJ, James MN (March 2006). "Crystal structure of the vitamin B12 biosynthetic cobaltochelatase, CbiXS, from Archaeoglobus fulgidus". J. Struct. Funct. Genomics. 7 (1): 37–50. doi:10.1007/s10969-006-9008-x. PMID 16835730.
  26. ^ Brindley AA, Raux E, Leech HK, Schubert HL, Warren MJ (June 2003). "A story of chelatase evolution: identification and characterization of a small 13-15-kDa "ancestral" cobaltochelatase (CbiXS) in the archaea". J. Biol. Chem. 278 (25): 22388–95. doi:10.1074/jbc.M302468200. PMID 12686546.
  27. ^ Woodson JD, Escalante-Semerena JC (March 2004). "CbiZ, an amidohydrolase enzyme required for salvaging the coenzyme B12 precursor cobinamide in archaea". Proc. Natl. Acad. Sci. U.S.A. 101 (10): 3591–6. doi:10.1073/pnas.0305939101. PMC 373507. PMID 14990804.
This article incorporates text from the public domain Pfam and InterPro: IPR004485
This article incorporates text from the public domain Pfam and InterPro: IPR003805
This article incorporates text from the public domain Pfam and InterPro: IPR006538
This article incorporates text from the public domain Pfam and InterPro: IPR003203
This article incorporates text from the public domain Pfam and InterPro: IPR003495
This article incorporates text from the public domain Pfam and InterPro: IPR011629
This article incorporates text from the public domain Pfam and InterPro: IPR002586
This article incorporates text from the public domain Pfam and InterPro: IPR002748
This article incorporates text from the public domain Pfam and InterPro: IPR002750
This article incorporates text from the public domain Pfam and InterPro: IPR003723
This article incorporates text from the public domain Pfam and InterPro: IPR002751
This article incorporates text from the public domain Pfam and InterPro: IPR003705
This article incorporates text from the public domain Pfam and InterPro: IPR003339
This article incorporates text from the public domain Pfam and InterPro: IPR002762
This article incorporates text from the public domain Pfam and InterPro: IPR002808

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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Cobalt transport protein Provide feedback

This family consists of various cobalt transport proteins Most of which are found in Cobalamin (Vitamin B12) biosynthesis operons. In Salmonella the cbiN cbiQ (product CbiQ in this family) and cbiO are likely to form an active cobalt transport system [1].

Literature references

  1. Roth JR, Lawrence JG, Rubenfield M, Kieffer-Higgins S, Church GM; , J Bacteriol 1993;175:3303-3316.: Characterization of the cobalamin (vitamin B12) biosynthetic genes of Salmonella typhimurium. PUBMED:8501034 EPMC:8501034


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003339

ECF (energy-coupling factor) transporters are a subgroup of ABC (ATP-binding cassette) transporters involved in the uptake of vitamins and micronutrients in prokaryotes [PUBMED:22574898]. ECF transporters are protein complexes consisting of a conserved module (two peripheral ATPases and the integral membrane protein EcfT) and a non-conserved integral membrane protein responsible for substrate specificity (S-component) [PUBMED:21135102].

This entry represents the transmembrane component from a number of ECF transporters, including cobalt-specific transporter CbiQ, and nickel-specific transporter NikQ [PUBMED:16352848]. It also includes uncharacterised eukaryotic proteins.

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Curation and family details

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Curation View help on the curation process

Seed source: Pfam-B_673 (release 5.2)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bashton M , Bateman A
Number in seed: 17
Number in full: 9607
Average length of the domain: 210.30 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 76.84 %

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HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.4 21.4
Trusted cut-off 21.4 21.4
Noise cut-off 21.3 21.3
Model length: 218
Family (HMM) version: 16
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Species distribution

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the CbiQ domain has been found. There are 11 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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