Protein Family Models

This domain is found in Proline utilization A (PutA) proteins present in Geobacter sulfurreducens. PutA are bifunctional peripheral membrane flavoenzymes that catalyze the oxidation of l-proline to l-glutamate and couple the oxidation of imported proline imported to the reduction of membrane-associated quinones. This domain is located at the N-terminus and is referred to as the alpha domain. The hydrocarbon tail of Zwittergent 3-12 binds to an exposed hydrophobic patch of the alpha domain which contains aromatic and nonpolar residues. The domain may be involved in membrane association [1]. [1]. 24550478. Structures of the PutA peripheral membrane flavoenzyme reveal a. dynamic substrate-channeling tunnel and the quinone-binding. site.. Singh H, Arentson BW, Becker DF, Tanner JJ;. Proc Natl Acad Sci U S A. 2014;111:3389-3394. (from Pfam)

Date:

2024-08-14

This family represents mitochondrial respiratory chain complex III (or cytochrome b-c1 complex) assembly factors, including Cbp6 from yeast and its human orthologue UQCC2 (Ubiquinol-Cytochrome c Reductase Complex Assembly Factor 2) [1,2]. These proteins have diverged significantly among eukaryotes and UQCC2/Cbp6 have an overall low amino acid conservation [1]. UQCC2 interacts with UQCC1, the human orthologue of the Cbp6 binding partner Cbp3, to form a complex necessary for cytochrome b biogenesis [1]. Cbp3-Cbp6 complex interacts with mitochondrial ribosomes for efficient translation of cytochrome b transcript and it also interacts with newly synthesized cytochrome b to assist its correct assembly [2]. These proteins contain a LRY-like N-terminal sequence being related to the LYR superfamily of proteins, which function as subunits or assembly factors for respiratory complexes I, II, III, and V [3]. [1]. 24385928. Mutations in the UQCC1-interacting protein, UQCC2, cause human. complex III deficiency associated with perturbed cytochrome b. protein expression.. Tucker EJ, Wanschers BF, Szklarczyk R, Mountford HS, Wijeyeratne. XW, van den Brand MA, Leenders AM, Rodenburg RJ, Reljic B,. Compton AG, Frazier AE, Bruno DL, Christodoulou J, Endo H, Ryan. MT, Nijtmans LG, Huynen MA, Thorburn DR;. PLoS Genet. 2013;9:e1004034.. [2]. 21670217. Cbp3-Cbp6 interacts with the yeast mitochondrial ribosomal. tunnel exit and promotes cytochrome b synthesis and assembly.. Gruschke S, Kehrein K, Rompler K, Grone K, Israel L, Imhof A,. Herrmann JM, Ott M;. J Cell Biol. 2011;193:1101-1114.. [3]. 28634302. Structure of human Fe-S assembly subcomple. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-08-14

This entry represents the N-terminal HotDog domain of the dehydratase (DH) module of polyketide synthases [1]. Structural analysis shows these DH domains are double hotdogs in which the active site contains a histidine from the N-terminal hotdog and an aspartate from the C-terminal hotdog. Studies have uncovered that a substrate tunnel formed between the DH domains may be essential for loading substrates and unloading products [2]. [1]. 18952099. Crystal structure of the erythromycin polyketide synthase. dehydratase.. Keatinge-Clay A;. J Mol Biol. 2008;384:941-953.. [2]. 20152156. Crystal structures of dehydratase domains from the curacin. polyketide biosynthetic pathway.. Akey DL, Razelun JR, Tehranisa J, Sherman DH, Gerwick WH, Smith. JL;. Structure. 2010;18:94-105. (from Pfam)

Date:

2024-08-14

Sortilin, also known in mammals as neurotensin receptor-3, is the archetypical member of a Vps10-domain (Vps10-D) that binds neurotrophic factors and neuropeptides. This domain constitutes the entire luminal part of Sortilin and is activated in the trans-Golgi network by enzymatic propeptide cleavage [1,2]. The structure of the domain has been determined as a ten-bladed propeller, with up to 9 BNR or beta-hairpin turns in it. The mature receptor binds various ligands, including its own propeptide (Sort-pro), neurotensin, the pro-forms of nerve growth factor-beta (NGF)6 and brain-derived neurotrophic factor (BDNF)7, lipoprotein lipase (LpL), apo lipoprotein AV14 and the receptor-associated protein (RAP)1 [4,5]. [1]. 9013611. Molecular identification of a novel candidate sorting receptor. purified from human brain by receptor-associated protein. affinity chromatography.. Petersen CM, Nielsen MS, Nykjaer A, Jacobsen L, Tommerup N,. Rasmussen HH, Roigaard H, Gliemann J, Madsen P, Moestrup SK;. J Biol Chem. 1997;272:3599-3605.. [2]. 9756851. The 100-kDa neurotensin receptor is gp95/sortilin, a. non-G-protein-coupled receptor.. Mazella J, Zsurger N, Navarro V, Chabry J, Kaghad M, Caput D,. Ferrara P, Vita N, Gully D, Maffrand JP, Vincent JP;. J Biol Chem. 1998;273:26273-26276.. [3]. 10085125. Sortilin/neurotensin receptor-3 binds and mediates degradation. of lipoprotein lipase.. Nielsen MS, Jacobsen C, Olivecrona G, Gliemann J, Petersen CM;. J Biol Chem. 1999;274:8832-8836.. [4]. 19122660. Ligands bind to Sortilin in the tunnel of a ten-bladed. beta-propeller domain.. Quistgaard EM, Madsen P, Groftehauge MK, Nissen P, Petersen C. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-08-14

This is the N-terminal domain of DNA-directed RNA polymerase. This domain has a role in interaction with regions of upstream promoter DNA and the nascent RNA chain, leading to the processivity of the enzyme [1]. In order to make mRNA transcripts the RNA polymerase undergoes a transition from the initiation phase (which only makes short fragments of RNA) to an elongation phase. This domain undergoes a structural change in the transition from initiation to elongation phase. The structural change results in abolition of the promoter binding site, creation of a channel accommodating the heteroduplex in the active site and formation of an exit tunnel which the RNA transcript passes through after peeling off the heteroduplex [2]. [1]. 9670025. Structure of T7 RNA polymerase complexed to the transcriptional. inhibitor T7 lysozyme.. Jeruzalmi D, Steitz TA;. EMBO J. 1998;17:4101-4113.. [2]. 12242451. Structural basis for the transition from initiation to. elongation transcription in T7 RNA polymerase.. Yin YW, Steitz TA;. Science. 2002;298:1387-1395. (from Pfam)

Date:

2024-08-14

Members of this family of prokaryotic restriction endonucleases recognise the double-stranded sequence CYCGRG (where Y = T/C, and R = A/G) and cleave after C-1. They catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates [1]. [1]. 11250198. Restriction enzyme BsoBI-DNA complex: a tunnel for recognition. of degenerate DNA sequences and potential histidine catalysis.. van der Woerd MJ, Pelletier JJ, Xu S, Friedman AM;. Structure. 2001;9:133-144.. [2]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK. phosphodiesterase superfamily.. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski. K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam)

Date:

2024-08-14

This domain is the C-terminal bracelet domain of the rotavirus VP1 RNA-directed RNA polymerase. It surrounds the exit tunnel for dsRNA produced by replication and for the RNA template for transcription [1]. [1]. 19000820. Mechanism for coordinated RNA packaging and genome replication. by rotavirus polymerase VP1.. Lu X, McDonald SM, Tortorici MA, Tao YJ, Vasquez-Del Carpio R,. Nibert ML, Patton JT, Harrison SC;. Structure. 2008;16:1678-1688. (from Pfam)

Date:

2024-08-14

This protein family is related to archaeal non-canonical single- stranded DNA-binding proteins (ThermoDBPs) named ThermoDBP-related proteins. These proteins have been related to genome maintenance in particularly challenging environments, but their specific function is still unknown [1]. [1]. 24744237. Entrapment of DNA in an intersubunit tunnel system of a. single-stranded DNA-binding protein.. Ghalei H, von Moeller H, Eppers D, Sohmen D, Wilson DN, Loll B,. Wahl MC;. Nucleic Acids Res. 2014;42:6698-6708. (from Pfam)

Date:

2024-08-14

In the E. coli cytosol, a fraction of the newly synthesised proteins requires the activity of molecular chaperones for folding to the native state. The major chaperones implicated in this folding process are the ribosome-associated Trigger Factor (TF), and the DnaK and GroEL chaperones with their respective co-chaperones. Trigger Factor is an ATP-independent chaperone and displays chaperone and peptidyl-prolyl-cis-trans-isomerase (PPIase) activities in vitro. It is composed of three domains, an N-terminal domain which mediates association with the large ribosomal subunit (ribosome-binding domain, RBD), a central PPIase domain with homology to FKBP proteins, and a C-terminal substrate-binding domain (SBD) which forms the central body of the protein and has two helical arms that create a cavity [1,2]. The association between its N-terminal domain with the ribosomal protein L23 located next to the peptide tunnel exit is essential for the interaction with nascent polypeptides and its in vivo function [1]. This entry represents the C-terminal region of TF which has a multi-helical structure consisting of an irregular array of long and short helices structurally similar to the peptide-binding domain of the bacterial porin chaperone SurA [3]. [1]. 12603737. Trigger Factor and DnaK possess overlapping substrate pools and. binding specificities.. Deuerling E, Patzelt H, Vorderwulbecke S, Rauch T, Kramer G,. Schaffitzel E, Mogk A, Schulze-Specking A, Langen H, Bukau B;. Mol Microbiol 2003;47:1317-1328.. [2]. 29222465. The dynamic dimer structure of the chaperone Trigger Factor.. Morgado L, Burmann BM, Sharpe T, Mazur A, Hiller S;. N. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-08-14

nascent polypeptide-associated complex subunit alpha (NACA) is a component of the nascent polypeptide-associated complex (NAC), a dynamic component of the ribosomal exit tunnel, protecting the emerging polypeptides from interaction with other cytoplasmic proteins to ensure appropriate nascent protein targeting

Date:

2024-09-03

MlaD/PqiB family protein similar to PqiB (paraquat-inducible protein B), MlaD, which is a component of the Mla pathway, an ABC transport system that functions to maintain the asymmetry of the outer membrane, Escherichia coli intermembrane transport protein YebT and lipophilic envelope-spanning tunnel protein LetB

Date:

2023-09-01

uL22 family ribosomal protein has an essential role in ribosome architecture and function which modulates the shape of the protein Exit Tunnel.

Date:

2024-06-06

beta-ketoacyl synthase chain length factor similar to Xenorhabdus doucetiae ApeC that contains a defined hydrophobic binding tunnel that accommodates the growing polyene chain and acts as a molecular ruler in the biosynthesis of aryl polyene pigments

Date:

2019-05-10

nascent polypeptide-associated complex subunit alpha (NACA) is a component of the nascent polypeptide-associated complex (NAC), a dynamic component of the ribosomal exit tunnel, protecting the emerging polypeptides from interaction with other cytoplasmic proteins to ensure appropriate nascent protein targeting

Date:

2024-09-03

nascent polypeptide-associated complex subunit alpha (NACA) is a component of the nascent polypeptide-associated complex (NAC), a dynamic component of the ribosomal exit tunnel, protecting the emerging polypeptides from interaction with other cytoplasmic proteins to ensure appropriate nascent protein targeting

Date:

2024-09-03

50S ribosomal protein L29 binds 23S rRNA and is not essential for growth; it is one of the proteins that surrounds the polypeptide exit tunnel on the outside of the 50s ribosomal subunit

Date:

2017-05-17

50S ribosomal protein L31e is present in archaea and eukaryotes, binds the 23S rRNA and is one of six protein components encircling the polypeptide exit tunnel

Date:

2017-05-01

sodium ion-translocating decarboxylase subunit beta such as Acidaminococcus fermentans glutaconyl-CoA decarboxylase subunit beta, a tunnel subunit of the primary sodium pump glutaconyl-CoA decarboxylase

Date:

2018-04-11

Binds third domain of 23S rRNA and protein L29; part of exit tunnel

Date:

2020-10-26

Part of the polypeptide exit tunnel in the 50S ribosomal complex

Date:

2020-10-26