Protein Domains

1
Protein Domains
2
Zinc Finger
Zinc finger motif A fragment derived from a
mouse gene regulatory protein is shown, with
three zinc fingers bound spirally in the major
groove of a DNA molecule. The inset shows the
coordination of a zinc atom by characteristically
spaced cysteine and histidine residues in a
single zinc finger motif.
(PDB 1aay)
3
HTH Helix Turn Helix
(PDB 1lmb)
Helix-turn-helix The DNA-binding domain of the
bacterial gene regulatory protein lambda
repressor, with the two helix-turn-helix motifs
shown in color. The two helices closest to the
DNA are the reading or recognition helices, which
bind in the major groove and recognize specific
gene regulatory sequences in the DNA.
(PDB 1lmb)
4
4 Helix Bundle
a
Four-helix bundle motif The four-helix bundle
motif can comprise an entire protein domain, and
occurs in proteins with many different
biochemical functions. Shown in figure a is human
growth hormone, a signaling molecule shown in
Figure b is cytochrome b562, an
electron-transport protein. In Figure c the
protein myohemerythrin is shown its function is
oxygen transport.
b
c
5
Catalytic Triad
Catalytic triad The catalytic triad of aspartic
acid, histidine and serine in (a) subtilisin, a
bacterial serine protease, and (b) chymotrypsin,
a mammalian serine protease. The two protein
structures are quite different, and the elements
of the catalytic triad are in different positions
in the primary sequence, but the active-site
arrangement of the aspartic acid, histidine and
serine is similar.
6
TIM Barrel

• TIM Barrel
• Triose phosphate isomerase (a) is shown together
  with alanine racemase (b). In alanine racemase,
  the TIM-barrel domain is interrupted by an
  inserted domain.
• TIM Barrels have been referred to as the
  perfect domain.
• Many different proteins have this domain
  structure.

7
Beta Helix

• Beta helix
• The parallel beta helix is a relatively new
  domain and consists of three beta-sheets arranged
  in three faces of the protein
• Many side chain interactions serve to zip up
  the protein and help stabilize it
• A common fold for carbohydrate interacting
  proteins

8
Beta Helix
Amino Acid Stacks
Top View of Parallel Beta-helix
9
14-3-3

• 14-3-3 proteins are 30 kDa polypeptides with nine
  closely related members in mammals.
• They are involved in regulating various pathways
  including signaling apoptosis and passage through
  the cell cycle.
• 14-3-3 proteins form homo and heterodimeric
  cup-like structures that bind to discrete
  phosphoserine-containing motifs.

10
Ankyrin

• Breedan and Nasmyth first reported a 33 amino
  acid repeat common among a small number of
  proteins.
• Subsequently, a cytoskeletal protein named
  Ankyrin was identified that was composed almost
  entirely of these short repeats.
• ANK repeats have been identified in over 1700
  different proteins from viruses, prokaryotes and
  eukaryotes.

11
ARM

• The approximately 40 amino acid Armadillo (ARM)
  repeat was first identified in the Drosophila
  segment polarity gene product Armadillo (the
  homologue of mammalian ß-catenin).
• Found in over 240 different proteins of diverse
  cellular function from yeast to man.
• The ARM domain is implicated in mediating
  protein-protein interactions, but no common
  features among the target proteins recognized by
  the ARM repeats have been identified.

12
BH1-4

• Bcl-2 Homology (BH14) domains are found in
  proteins that inhibit apoptosis including Bcl-2,
  Bcl-xL and Bcl-xW.
• Bcl-2 family members form homodimers and
  heterodimers between pro- and antiapoptotic
  family members.
• Homodimerization of Bcl-2 involves a head to
  tail interaction. The N-terminal region, where
  the BH4 domain resides, interacts with the more
  distal region of Bcl-2 where BH1, BH2 and BH3 are
  located. The BH3 domain is required for
  dimerization and apoptosis induction. Conversely,
  Bcl-2/Bax heterodimerization involves a
  tail-to-tail interaction that requires the BH1,
  BH2 and BH3 region of Bcl-2 and a central region
  in Bax where the BH3 domain is located.

13
BRCT

• The BRCT domain (BRCA1 C-terminus) is a conserved
  proteinprotein interaction region of
  approximately 95 amino acids found predominantly
  in proteins involved in cell cycle checkpoint
  functions responsive to DNA damage.
• It was first identified in the breast cancer
  suppressor protein BRCA1 but is also found in DNA
  repair proteins such as DNA ligase III and XRCC1,
  which form strong heterodimers through their BRCT
  domains.
• The C-terminal BRCT domain of BRCA1 has been
  reported to bind to the central domain of p53,
  allowing BRCA1 to act as a coactivator of p53.

14
Bromo

• Approximately 110 amino acids in length, the
  Bromo domain is found in many chromatin-associated
  proteins such as histone acetylases and the
  ATPase component of certain nucleosome-remodeling
  complexes.
• Bromo domains have been identified in over 100
  proteins from yeast to man. The Bromo domains of
  PCAF and Gcn5p have been shown to interact
  specifically with peptides containing acetylated
  lysine residues.
• Recognition of acetyl-lysine is similar to that
  of acetyl-CoA by histone acetyltransferases, the
  bromodomain is the only domain known to interact
  with acetylated lysine containing peptides.

15
C1

• C1 domains are approximately 50 amino acids long,
  enriched in cysteines, and are involved in the
  recruitment of proteins to the membrane.
• Typically, C1 domains bind phorbol esters or
  diacylglycerol, which are necessary for membrane
  localization. With phorbol ester bound, the upper
  surface of the C1 domain forms a contiguous
  hydrophobic surface in the domain. This enables
  the region to be buried into the lipid bilayer
  stabilizing membrane insertion.
• The middle portion of the domain contains a
  number of basic residues that can interact with
  lipid headgroups in the membrane, while the lower
  half of the C1 domain contains two zinc-binding
  sites that are important to maintain the fold of
  the domain.

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C2

• The C2 domain, a region containing approximately
  130 residues, is involved in binding
  phospholipids in a calcium-dependent manner or
  calcium-independent manner.
• C2 domains are found in over 100 different
  proteins with functions ranging from signal
  transduction to vesicular trafficking.
• Calcium binding to the C2 domain of synaptotagmin
  induces little conformational change in the C2
  domain but rather induces a change in
  electrostatic potential, thereby enhancing
  phospholipid binding.
• This suggests that the C2 domain functions as an
  electrostatic switch. In addition to
  electrostatic interactions, side chains in the
  calcium binding loops influence the binding of
  different C2 domains to either neutral or
  negatively charged phospholipids.

17
CARD Caspase Recruitment

• Caspase Recruitment Domains (CARDs) are modules
  of 90100 amino acids involved in apoptosis
  signaling pathways.
• CARDs mediate the association of adaptor
  proteins and procaspases through
  heterodimerization of their respective CARDs,
  recruiting procaspases to upstream signaling
  complexes and allowing autoactivation.
• Dimerization of CARDs is believed to be mediated
  primarily by electrostatic interactions between
  complementary charged surfaces with a binding
  specificity achieved by particular charge
  patterns between CARD binding partners.

18
CC Coiled Coils

• Coiled-coils (CC) function as oligomerization
  domains for a wide variety of proteins including
  structural proteins, motor proteins and
  transcription factors.
• The coiled-coil structure is conserved from
  viruses to plants and mammals and it has been
  predicted that approximately 5 of proteins
  encoded in sequenced genomes contain
  coiled-coils.
• Coiled-coils typically consists of two or more
  a-helices that wrap around each other with a
  superhelical twist. Sequences with a propensity
  to assume coiled-coil structures are
  characterized by the heptad repeat pattern
  (abcdefg)n, where a and d are hydrophobic, and e
  and g are charged or polar.

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CH Calponin Homology

• The calponin homology (CH) domain is a protein
  module of approximately 110 amino acids present
  in cytoskeletal and signal transduction proteins.
  
• Two CH domains in tandem form an F-actin binding
  region at the N-termini of spectrin-like proteins
  such as dystrophin and a-actinin.
• Type 1 and 2 are found together in tandem in
  cytoskeletal proteins such as dystrophin,
  spectrin and filamin. Type 3 CH domains are found
  in proteins that regulate muscle contraction,
  such as calponin, as well as in signaling
  proteins such as Vav, ARHGEF6 and IQGAP.

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Death Domains

• Death domains (DD) are 80100 residues long
  motifs involved in apoptotic signal transduction.
  
• They are found both in cytoplasmic proteins and
  in transmembrane proteins including members of
  the tumor necrosis factor receptor superfamily.
• Death domains serve as recruiting modules through
  their ability to heterodimerize with the death
  domains of distinct proteins, including adaptor
  proteins such as FADD. Due to the significant
  polarization of charged residues on the surface
  of the death domain, dimerization is believed to
  arise primarily through electrostatic
  interactions.

21
EF Hand

• The EF-hand motif contains approximately 40
  residues and is involved in binding intracellular
  calcium.
• EF-hand domains are often found in single or
  multiple pairs, giving rise to various
  structural/functional variations in proteins
  containing EF-hand motifs.
• Proteins containing EF-hands can be grouped into
  two functional categoriesregulatory or
  structural.
• Binding of calcium to regulatory EF-hand
  domaincontaining proteins induces a
  conformational change, which is transmitted to
  their target proteins, often catalyzing enzymatic
  reactions.
• In contrast, binding of calcium to structural
  EF-hand domaincontaining proteins does not
  induce a significant conformational change.
  Structural EF-hand domains seem to play a role in
  buffering intracellular calcium levels.

22
F Box

• The F-box domain is a 4248 amino acid conserved
  domain found at the N-terminus of F-box proteins.
  
• F-box proteins act as adaptor components of the
  modular E3 ubiquitin ligase SCF complex that
  functions in phosphorylation-mediated
  ubiquitination.
• The F-box domain mediates interaction with SKP1,
  which links F-box proteins to a core
  ubiquitin-ligase complex composed of Rbx1,
  cdc53/Cul1 and the E2 conjugating enzyme cdc34.
  The C-terminal region of F-box proteins are also
  composed of various modular domains that interact
  with target substrates, often in a
  phosphorylation-dependent manner.

23
FERM

• Previously known as the B4.1 (band 4.1) homology
  and ERM domain, the FERM domain is named for the
  four proteins in which this domain was originally
  described F for Band 4.1, E for Ezrin, R for
  Radixin, M for Moesin.
• The FERM domain is approximately 150 amino acids
  in length and is found in a number of
  cytoskeletal-associated proteins that are found
  at the interface between the plasma membrane and
  the cytoskeleton.
• The FERM domain is responsible for PIP2 regulated
  membrane binding of ERM (Ezrin/Radixin/Moesin)
  proteins that play a role in formation of
  membrane associated cytoskeleton by linking actin
  filaments to adhesion proteins.

24
FHA Forkhead Associated

• The FHA domain, or Forkhead-Associated domain,
  was originally identified as a conserved region
  of forkhead transcription factors.
• It is 65100 amino acids long, contains several
  highly conserved key residues, and is found
  primarily in eukaryotic nuclear proteins. FHA
  domaincontaining proteins are also found in
  certain prokaryotes, such as mycoplasma bacteria.
  
• The FHA domain mediates phosphopeptide
  interactions with proteins phosphorylated by
  serine/threonine kinases. The first FHA domain of
  Rad53 binds to a pTXXD motif with a Kd 1.6 µM,
  while other FHA domains also bind to pTXXX
  peptides.

25
GYF Gly - Tyr - Phe

• The glycine-tyrosine-phenylalanine, or GYF domain
  was first reported in the CD2 binding protein
  CDBP2 as a domain capable of binding to a
  proline-rich peptide sequence in the CD2 tail
  region.
• Despite functioning as a proline-rich peptide
  binding domain, the GYF fold is structurally
  unrelated to the SH3 or WW domains.
• The GYF domain of CDBP2 binds to a PPPPGHR repeat
  in the CD2 tail via a relatively smooth, concave
  surface that forms a continuous hydrophobic patch
  containing many of the GYF domainconserved
  residues.

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LRR Leucine Rich Repeat

• Domain binding and function Leucine-Rich Repeats
  (LRR) are 2228 amino acid motifs that are found
  in a number of proteins with diverse functions
  and cellular locations.
• These repeats are usually involved in
  proteinprotein interactions, and in series they
  form nonglobular, crescent-shaped structures.
• The crescent shape adopted by series of
  leucine-rich repeats creates a solventexposed
  elongated concave surface of parallel ß-strands
  that acts as a scaffold for proteinprotein
  interactions.
• The function of each LRR crescent is specified by
  different residues arranged in an appropriate
  orientation on the surface of the
  three-dimensional fold. For example, RNAse
  inhibitor and U2A' LRR scaffolds appear to
  interact with their targets via the concave inner
  surface of the crescent, while in the case of S.
  pombe Rna1p, the Ran binding site appears to be
  located on the side face of the crescent within
  the loop regions connecting the ß-strands and
  a-helices.

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PDZ

• PDZ domains bind to the C-terminal 45 residues
  of their target proteins, frequently
  transmembrane receptors or ion channels.
• The consensus binding sequence contains a
  hydrophobic residue, commonly Val or Ile, at the
  very C-terminus. Residues at the -2 and -3
  positions are important in determining
  specificity.
• PDZ domains can also heterodimerize with PDZ
  domains of different proteins, potentially
  regulating intracellular signaling.

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PH Pleckstrin Homology

• Pleckstrin-homology (PH) domains are found in a
  wide variety of signaling proteins that associate
  with membranes.
• Some PH domains bind with high affinity (low µM
  or nM Kd) to specific phosphoinositides such as
  phosphatidylinositol-4,5-bisphosphate, PI-3, 4-P2
  or PI-3,4,5-P3.
• Binding to phosphoinositides may allow PH
  proteins to respond to lipid messengers for
  example by relocation to membranes. The C-termini
  of some PH domains have also been reported to
  bind the ß/? subunits of heterotrimeric
  G-proteins.

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Phox

• The Phox homology (PX) domain is the most
  recently identified member of the family of
  phospholipid-binding domains.
• Consisting of 120 amino acids, the PX domain is
  found in more than 100 proteins, including the
  p40phox and p47phox components of the NADPH
  oxidase complex, sorting nexins, phospholipases
  D1 and 2 and the kinases PI3K and CISK.
• Biochemical and cell biology studies have
  established that PX domains function
  predominantly as D3-phosphorylated
  phosphoinositide PI(3)P binding modules,
  targeting the PX domain-containing proteins to
  the membranes.

30
RING

• The RING finger is a specialized type of Zn
  finger consisting of 4060 residues that binds
  two atoms of zinc, and is involved in mediating
  proteinprotein interactions.
• The presence of a RING finger domain is a
  characteristic of RING-class E3 ubiquitin protein
  ligases capable of transfering ubiquitin from an
  E2 enzyme to a substrate protein.
• The RING domain mediates the interaction with the
  appropriate E2 enzyme. Unlike HECT E3s that form
  a thioester with ubiquitin, RING fingers likely
  mediate ubiquitination by facilitating the direct
  transfer of ubiquitin from E2s to lysine residues
  on the target substrate.

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SH2

• Src-homology 2 (SH2) domains are modules of 100
  amino acids that bind to specific phospho
  (pY)-containing peptide motifs.
• Conventional SH2 domains have a conserved pocket
  that recognizes pY, and a more variable pocket
  that binds 3-6 residues C-terminal to the pY and
  confers specificity.
• The SAP SH2 domain recognizes Y as well as pY in
  the context of residues N and C terminal,
  suggesting an alternate 3-pronged model may apply
  in some cases. Phosphopeptides of optimal
  sequence bind to SH2 domains with dissociation
  constants of 50-500 nM.

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SH3

• Src-homology 3 (SH3) domains bind to Pro-rich
  peptides that form a left-handed poly-Pro type II
  helix, with the minimal consensus Pro-X-X-Pro.
  Each Pro is usually preceded by an aliphatic
  residue. Each in the aliphatic-Pro pair binds to
  a hydrophobic pocket on the SH3 domain.
• The ligand can, in principle, bind in either
  orientation. An additional non-Pro residue,
  frequently Arg, can form part of the binding core
  and contacts the SH3 domain. Such peptides
  usually bind to the SH3 domain with a Kd in the
  µM range. The binding affinity and specificity
  can be markedly increased by tertiary
  interactions involving loops on the SH3 domain.

33
SNARE

• While the mechanism by which a vesicle fuses with
  its proper membrane target is poorly understood,
  it appears to involve a highly conserved set of
  proteins called SNAREs (Soluble NSF Attachment
  protein SNAP Receptors).
• SNARE proteins are believed to mediate most, if
  not all, cellular membrane fusion events. Most
  SNAREs are C-terminally anchored integral
  membrane proteins capable of entering into a
  coiled-coil interaction with other SNARE
  proteins.
• All SNARE proteins share a homologous domain of
  approximately 60 amino acids referred to as the
  SNARE domain. The SNARE domain acts as a
  proteinprotein interaction module in the
  assembly of a SNARE protein complex. While
  monomeric SNARE motifs are largely unstructured,
  they assemble into a protease resistant core
  complex.

34
TRAF

• The approximately 150 amino acid TRAF domain is
  found in Tumor Necrosis Factor (TNF)
  receptor-associated factors.
• TRAF proteins appear to be a relatively recent
  evolutionary development as there is just one C.
  elegans TRAF protein and only two Drosophila, and
  six mammalian TRAF proteins. All mammalian TRAFs
  localize to the cytoplasm except TRAF4 which is
  found in the nucleus.
• TRAF proteins are recruited to the membrane
  through interactions of their TRAF domains with
  activated TNF receptors, IL-1/Toll receptors or
  through intermediate proteins such as the TRADDs.
  TRAFs primarily act in cell survival upon
  interacting with TNF receptors by activating the
  NFkB and AP-1 transcription factors.

35
WD40

• WD40 repeats are found in a number of eukaryotic
  proteins that cover a wide variety of functions
  including adaptor/regulatory modules in signal
  transduction, pre-mRNA processing, cytoskeleton
  assembly and cell cycle control.
• The only common functional theme of WD40 domains
  is to serve as a stable propeller-like platform
  to which proteins can bind either stably or
  reversibly. Unlike the non-WD40 propeller family
  of proteins, there are no cases of WD40 proteins
  with catalytic activity.
• The WD40 domains of ß-TRCP and Cdc4 have been
  implicated in recognizing phosphorylated serine
  and threonine containing peptides, demonstrating
  that in some cases WD40 repeat forming
  ß-propeller structures can serve in
  phospho-peptide recognition.

36
WW

• WW domains are small 38 to 40 amino acid residue
  modules that have been implicated in binding to
  Pro-rich sequences.
• WW domains and SH3 domains can potentially bind
  overlapping sites. In addition, the Pin1 WW
  domain functions as a phospho-serine or
  phosphothreonine binding module, suggesting that
  certain WW domains have evolved an alternate mode
  of action.
• WW domains bind peptide ligands with dissociation
  constants in the µM range.