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30  structures 642  species 7  interactions 697  sequences 5  architectures

Family: Apocytochr_F_C (PF01333)

Summary: Apocytochrome F, C-terminal

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This is the Wikipedia entry entitled "Cytochrome f". More...

Cytochrome f Edit Wikipedia article

Apocytochr_F_C
PDB 1ci3 EBI.jpg
cytochrome f from the b6f complex of Phormidium laminosum
Identifiers
Symbol Apocytochr_F_C
Pfam PF01333
Pfam clan CL0105
InterPro IPR002325
PROSITE PDOC00169
SCOP 1ctm
SUPERFAMILY 1ctm
TCDB 3.D.3
OPM superfamily 345
OPM protein 3h1j

Cytochrome f is the largest subunit of cytochrome b6f complex (plastoquinol—plastocyanin reductase; EC 1.10.99.1). In its structure and functions, the cytochrome b6f complex bears extensive analogy to the cytochrome bc1 complex of mitochondria and photosynthetic purple bacteria. Cytochrome f (cyt f) plays a role analogous to that of cytochrome c1, in spite of their different structures.[1]

The 3D structure of Brassica rapa (Turnip) cyt f has been determined.[2] The lumen-side segment of cyt f includes two structural domains: a small one above a larger one that, in turn, is on top of the attachment to the membrane domain. The large domain consists of an anti-parallel beta-sandwich and a short haem-binding peptide, which form a three-layer structure. The small domain is inserted between beta-strands F and G of the large domain and is an all-beta domain. The haem nestles between two short helices at the N terminus of cyt f. Within the second helix is the sequence motif for the c-type cytochromes, CxxCH (residues 21-25), which is covalently attached to the haem through thioether bonds to Cys-21 and Cys-24. His-25 is the fifth haem iron ligand. The sixth haem iron ligand is the alpha-amino group of Tyr-1 in the first helix.[2] Cyt f has an internal network of water molecules that may function as a proton wire.[2] The water chain appears to be a conserved feature of cyt f.


References[edit]

  1. ^ Prince RC, George GN (June 1995). "Cytochrome f revealed". Trends Biochem. Sci. 20 (6): 217–8. PMID 7631417. 
  2. ^ a b c Martinez SE, Huang D, Ponomarev M, Cramer WA, Smith JL (June 1996). "The heme redox center of chloroplast cytochrome f is linked to a buried five-water chain". Protein Sci. 5 (6): 1081–92. doi:10.1002/pro.5560050610. PMC 2143431. PMID 8762139. 

Further reading[edit]

  • Bendall, D.S. (2004). "The unfinished story of cytochrome f". Photosynth. Res. 80 (1–3): 265–276. doi:10.1023/B:PRES.0000030454.23940.f9. PMID 16328825. 
  • Cramer, W.A., Martinez, S.E., Huang, D., Tae, G.S., Everly, R.M., Heymann, J.B., Cheng, R.H., Baker, T.S. and Smith, J.L. (1994). "Structural aspects of the cytochrome b6f complex; structure of the lumen-side domain of cytochrome f". J. Bioenerg. Biomembr. 26 (1): 31–47. doi:10.1007/BF00763218. PMID 8027021. 

External links[edit]

This article incorporates text from the public domain Pfam and InterPro IPR002325

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Apocytochrome F, C-terminal Provide feedback

This is a sub-family of cytochrome C. See PF00034.

Literature references

  1. Martinez SE, Huang D, Szczepaniak A, Cramer WA, Smith JL; , Structure 1994;2:95-105.: Crystal structure of chloroplast cytochrome f reveals a novel cytochrome fold and unexpected heme ligation. PUBMED:8081747 EPMC:8081747


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002325

The cytochrome b6f integral membrane protein complex transfers electrons between the two reaction centre complexes of oxygenic photosynthetic membranes, and participates in formation of the transmembrane electrochemical proton gradient by also transferring protons from the stromal to the internal lumen compartment [PUBMED:]. The cytochrome b6f complex contains four polypeptides: cytochrome f (285 aa); cytochrome b6 (215 aa); Rieske iron-sulphur protein (179 aa); and subunit IV (160 aa) [PUBMED:8027021]. In its structure and functions, the cytochrome b6f complex bears extensive analogy to the cytochrome bc1 complex of mitochondria and photosynthetic purple bacteria; cytochrome f (cyt f) plays a role analogous to that of cytochrome c1, in spite of their different structures [PUBMED:7631417].

Gene Ontology

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Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Hybrid (CL0105), which has the following description:

This superfamily contains proteins with a hybrid motif [1]. This motif is embedded in structurally diverse proteins.

The clan contains the following 17 members:

Apocytochr_F_C Biotin_lipoyl Biotin_lipoyl_2 Complex1_51K DUF2118 DUF2254 GCV_H HlyD HlyD_2 HlyD_3 NQRA OEP Peptidase_M23 PTS_EIIA_1 PYNP_C QRPTase_N RnfC_N

Alignments

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

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(49)
Full
(697)
Representative proteomes NCBI
(553)
Meta
(134)
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(16)
RP35
(40)
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(56)
RP75
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  Seed
(49)
Full
(697)
Representative proteomes NCBI
(553)
Meta
(134)
RP15
(16)
RP35
(40)
RP55
(56)
RP75
(66)
Alignment:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(49)
Full
(697)
Representative proteomes NCBI
(553)
Meta
(134)
RP15
(16)
RP35
(40)
RP55
(56)
RP75
(66)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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Trees

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_1294 (release 3.0)
Previous IDs: Apocytochrome_F;
Type: Domain
Author: Finn RD, Bateman A
Number in seed: 49
Number in full: 697
Average length of the domain: 114.80 aa
Average identity of full alignment: 74 %
Average coverage of the sequence by the domain: 37.15 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 28.5 28.5
Trusted cut-off 28.5 28.7
Noise cut-off 28.4 28.4
Model length: 118
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 7 interactions for this family. More...

PetL Cytochrom_B_N PetN PetM CytB6-F_Fe-S PetG Cytochrom_B_C

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 Apocytochr_F_C domain has been found. There are 30 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 seqence.

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