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Conserved domains on  [gi|2201633689|ref|XP_046758648|]
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rab effector Noc2 isoform X2 [Gallus gallus]

Protein Classification

PHD finger domain-containing protein( domain architecture ID 366290)

PHD (plant homeodomain) finger domain-containing protein

Gene Ontology:  GO:0008270|GO:0005515
PubMed:  16297627|21514168

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PHD_SF super family cl22851
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 47-159 5.39e-34

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


The actual alignment was detected with superfamily member pfam02318:

Pssm-ID: 473978  Cd Length: 118  Bit Score: 120.17  E-value: 5.39e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2201633689  47 LSPQELEVILEVIRKAEKLDVVEQQRIGRLVERL--ENMRKNAMGN----GLSQCLLCSELLGLLGSTSVFCQDCKKKVC 120
Cdd:pfam02318   3 LTDEEAEHVWEVVQRDFDLRKKEEERLGELKGKLdkESSKRELLGNqahlGETHCIRCLQPFGFLVNSKRQCLDCRKNVC 82

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2201633689 121 TKCGIETfgaQKRPLWLCKICSEQREVWKRSGAWFYKGL 159
Cdd:pfam02318  83 KKCGVYN---KPEQGWLCDPCSEARELKKGSLEWFYKNV 118
 
Name Accession Description Interval E-value
FYVE_2 pfam02318
FYVE-type zinc finger; This FYVE-type zinc finger is found at the N-terminus of effector ...
 47-159 5.39e-34

FYVE-type zinc finger; This FYVE-type zinc finger is found at the N-terminus of effector proteins including rabphilin-3A and regulating synaptic membrane exocytosis protein 2.


Pssm-ID: 426716  Cd Length: 118  Bit Score: 120.17  E-value: 5.39e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2201633689  47 LSPQELEVILEVIRKAEKLDVVEQQRIGRLVERL--ENMRKNAMGN----GLSQCLLCSELLGLLGSTSVFCQDCKKKVC 120
Cdd:pfam02318   3 LTDEEAEHVWEVVQRDFDLRKKEEERLGELKGKLdkESSKRELLGNqahlGETHCIRCLQPFGFLVNSKRQCLDCRKNVC 82

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2201633689 121 TKCGIETfgaQKRPLWLCKICSEQREVWKRSGAWFYKGL 159
Cdd:pfam02318  83 KKCGVYN---KPEQGWLCDPCSEARELKKGSLEWFYKNV 118
FYVE_RPH3L cd15763
FYVE-related domain found in Rab effector Noc2 and similar proteins; Rab effector Noc2, also ...
 86-149 7.57e-28

FYVE-related domain found in Rab effector Noc2 and similar proteins; Rab effector Noc2, also termed No C2 domains protein, or rabphilin-3A-like protein (RPH3AL), is a Rab3 effector that mediates the regulation of secretory vesicle exocytosis in neurons and certain endocrine cells. It also functions as a Rab27 effector and is involved in isoproterenol (IPR)-stimulated amylase release from acinar cells. Noc2 contains an N-terminal Rab3A effector domain which harbors a conserved zinc finger, but lacks tandem C2 domains. The FYVE domain of Noc2 resembles a FYVE-related domain that is structurally similar to the canonical FYVE domains but lacks the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif.


Pssm-ID: 277302  Cd Length: 64  Bit Score: 102.35  E-value: 7.57e-28
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2201633689  86 NAMGNGLSQCLLCSELLGLLGSTSVFCQDCKKKVCTKCGIETFGAQKRPLWLCKICSEQREVWK 149
Cdd:cd15763     1 NVMGNGLSQCLLCGELLGFLGSSSVFCQDCRKKVCTKCGIETSGSQKRPLWLCKICSEQREVWK 64
 
Name Accession Description Interval E-value
FYVE_2 pfam02318
FYVE-type zinc finger; This FYVE-type zinc finger is found at the N-terminus of effector ...
 47-159 5.39e-34

FYVE-type zinc finger; This FYVE-type zinc finger is found at the N-terminus of effector proteins including rabphilin-3A and regulating synaptic membrane exocytosis protein 2.


Pssm-ID: 426716  Cd Length: 118  Bit Score: 120.17  E-value: 5.39e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2201633689  47 LSPQELEVILEVIRKAEKLDVVEQQRIGRLVERL--ENMRKNAMGN----GLSQCLLCSELLGLLGSTSVFCQDCKKKVC 120
Cdd:pfam02318   3 LTDEEAEHVWEVVQRDFDLRKKEEERLGELKGKLdkESSKRELLGNqahlGETHCIRCLQPFGFLVNSKRQCLDCRKNVC 82

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2201633689 121 TKCGIETfgaQKRPLWLCKICSEQREVWKRSGAWFYKGL 159
Cdd:pfam02318  83 KKCGVYN---KPEQGWLCDPCSEARELKKGSLEWFYKNV 118
FYVE_RPH3L cd15763
FYVE-related domain found in Rab effector Noc2 and similar proteins; Rab effector Noc2, also ...
 86-149 7.57e-28

FYVE-related domain found in Rab effector Noc2 and similar proteins; Rab effector Noc2, also termed No C2 domains protein, or rabphilin-3A-like protein (RPH3AL), is a Rab3 effector that mediates the regulation of secretory vesicle exocytosis in neurons and certain endocrine cells. It also functions as a Rab27 effector and is involved in isoproterenol (IPR)-stimulated amylase release from acinar cells. Noc2 contains an N-terminal Rab3A effector domain which harbors a conserved zinc finger, but lacks tandem C2 domains. The FYVE domain of Noc2 resembles a FYVE-related domain that is structurally similar to the canonical FYVE domains but lacks the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif.


Pssm-ID: 277302  Cd Length: 64  Bit Score: 102.35  E-value: 7.57e-28
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2201633689  86 NAMGNGLSQCLLCSELLGLLGSTSVFCQDCKKKVCTKCGIETFGAQKRPLWLCKICSEQREVWK 149
Cdd:cd15763     1 NVMGNGLSQCLLCGELLGFLGSSSVFCQDCRKKVCTKCGIETSGSQKRPLWLCKICSEQREVWK 64
FYVE_RP3A cd15762
FYVE-related domain found in rabphilin-3A and similar proteins; Rabphilin-3A, also termed ...
 89-165 2.82e-26

FYVE-related domain found in rabphilin-3A and similar proteins; Rabphilin-3A, also termed exophilin-1, is an effector protein that binds to the GTP-bound form of Rab3A, which is one of the most abundant Rab proteins in neurons and predominantly localized to synaptic vesicles. Rabphilin-3A is homologous to alpha-Rab3-interacting molecules (RIMs). It is a multi-domain protein containing an N-terminal Rab3A effector domain, a proline-rich linker region, and two tandem C2 domains. The effector domain binds specifically to the activated GTP-bound state of Rab3A and harbors a conserved FYVE zinc finger. The C2 domains are responsible for the binding of phosphatidylinositol-4,5-bisphosphate (PIP2) , a key player in the neurotransmitter release process. Thus, Rabphilin-3A has also been implicated in vesicle trafficking. The FYVE domain of Rabphilin-3A resembles a FYVE-related domain that is structurally similar to the canonical FYVE domains but lacks the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif.


Pssm-ID: 277301  Cd Length: 80  Bit Score: 98.87  E-value: 2.82e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2201633689  89 GNGLSQCLLCSELLGLLGSTSVFCQDCKKKVCTKCGIETfGAQKRPLWLCKICSEQREVWKRSGAWFYKGLPKYITP 165
Cdd:cd15762     1 GDGVNRCILCGEQLGGAGSACVVCEDCKKNVCTKCGVQT-NNRPHSVWLCKICSEQREVWKRSGAWFFKGLPKQVLP 76
FYVE_RP3A_like cd15746
FYVE-related domain found in rabphilin-3A, Rab effector Noc2, and similar proteins; This ...
 107-143 1.59e-16

FYVE-related domain found in rabphilin-3A, Rab effector Noc2, and similar proteins; This family includes rabphilin-3A and Rab effector Noc2. Rabphilin-3A, also termed exophilin-1, is an effector protein that binds to the GTP-bound form of Rab3A, which is one of the most abundant Rab proteins in neurons and predominantly localized to synaptic vesicles. Rabphilin-3A is homologous to alpha-Rab3-interacting molecules (RIMs). It is a multi-domain protein containing an N-terminal Rab3A effector domain, a proline-rich linker region, and two tandem C2 domains. The effector domain binds specifically to the activated GTP-bound state of Rab3A and harbors a conserved FYVE zinc finger. The C2 domains are responsible for the binding of phosphatidylinositol-4,5-bisphosphate (PIP2) , a key player in the neurotransmitter release process. Thus, Rabphilin-3A has also been implicated in vesicle trafficking. Rab effector Noc2, also termed No C2 domains protein, or rabphilin-3A-like protein (RPH3AL), is a Rab3 effector that mediates the regulation of secretory vesicle exocytosis in neurons and certain endocrine cells. It also functions as a Rab27 effector and is involved in isoproterenol (IPR)-stimulated amylase release from acinar cells. Noc2 contains an N-terminal Rab3A effector domain which only harbors a conserved FYVE zinc finger. The FYVE domains of Rabphilin-3A and Noc2 resemble a FYVE-related domain that is structurally similar to the canonical FYVE domains but lacks the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif.


Pssm-ID: 277285  Cd Length: 55  Bit Score: 71.91  E-value: 1.59e-16
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 2201633689 107 STSVFCQDCKKKVCTKCGIETFGAQKRPLWLCKICSE 143
Cdd:cd15746    19 ASPVLCKDCRKAVCTKCGVETTNSNKQPIWLCKICSE 55
FYVE_BSN_PCLO cd15751
FYVE-related domain found in protein bassoon and piccolo; This family includes protein bassoon ...
 112-146 1.23e-03

FYVE-related domain found in protein bassoon and piccolo; This family includes protein bassoon and piccolo. Protein bassoon, also termed zinc finger protein 231, is a core component of the presynaptic cytomatrix. It is a vertebrate-specific active zone scaffolding protein that plays a key role in structural organization and functional regulation of presynaptic release sites. Bassoon may modulate synaptic transmission efficiency by binding to presynaptic P/Q-type voltage-dependent calcium channel (VDCC) complexes and modify the channel function. As one of the most highly phosphorylated synaptic proteins, bassoon can interact with the small ubiquitous adaptor protein 14-3-3 in a phosphorylation-dependent manner, which modulates its anchoring to the presynaptic cytomatrix. Protein piccolo, also termed aczonin, is a neuron-specific presynaptic active zone scaffolding protein that mainly interacts with a detergent-resistant cytoskeletal-like subcellular fraction and is involved in the organization of the interplay between neurotransmitter vesicles, the cytoskeleton, and the plasma membrane at synaptic active zones. It binds profilin, an actin-binding protein implicated in actin cytoskeletal dynamics. It also functions as a presynaptic low-affinity Ca2+ sensor and has been implicated in Ca2+ regulation of neurotransmitter release. Both bassoon and piccolo contain two N-terminal FYVE zinc fingers, a PDZ domain and two C-terminal C2 domains. Their FYVE domain resembles a FYVE-related domain that is structurally similar to the canonical FYVE domains but lacks the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif.


Pssm-ID: 277290 [Multi-domain]  Cd Length: 62  Bit Score: 36.66  E-value: 1.23e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 2201633689 112 CQDCKKKVCTKCGI-ETFGAQKRPLWLCKICSEQRE 146
Cdd:cd15751    24 CTDCKNRVCNQCGFnSTPPVTKVKEWLCLNCQKKRA 59
FYVE_Slp3_4_5 cd15747
FYVE-related domain found in the synaptotagmin-like proteins 3, 4, 5; The synaptotagmin-like ...
 112-143 5.89e-03

FYVE-related domain found in the synaptotagmin-like proteins 3, 4, 5; The synaptotagmin-like proteins 1-5 (Slp1-5) family belongs to the carboxyl-terminal-type (C-type) tandem C2 proteins superfamily, which also contains the synaptotagmin and the Doc2 families. Slp proteins are putative membrane trafficking proteins that are characterized by the presence of a unique N-terminal Slp homology domain (SHD), and C-terminal tandem C2 domains (known as the C2A domain and C2B domain). The SHD consists of two conserved regions, designated SHD1 (Slp homology domain 1) and SHD2. The SHD1 and SHD2 of Slp3, Slp4 and Slp5 are separated by a putative FYVE zinc finger. By contrast, Slp1 and Slp2 lack such zinc finger and their SHD1 and SHD2 are linked together. This model corresponds to the FYVE zinc finger. At this point, Slp1 and Slp2 are not included in this model. Moreover, the FYVE domains of Slp3, Slp4 and Slp5 resemble a FYVE-related domain that is structurally similar to the canonical FYVE domains but lacks the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif.


Pssm-ID: 277286  Cd Length: 48  Bit Score: 34.20  E-value: 5.89e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2201633689 112 CQDCKKKVCTKCGIETFGAqkrPLWLCKICSE 143
Cdd:cd15747    20 CPKCSHKVCKKCRVLTSNT---GKWLCTVCHK 48
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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