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0PRD16_HUMAN*   SwissProt (?) | Description Local Annotation Link Reference
General Information
NamePRDM16
DescriptionPr-domain zinc finger protein 16 (transcription factor mel1).
SpeciesHomo sapiens (NCBI taxonomy ID: 9606)
GO0005634 nucleus (IC)
0003700 transcription factor activity (NAS)
0006355 regulation of transcription, DNA-dependent (IC)

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schematic display of those terms with internal associations, click the node and browse the corresponding GO term
Domain Architecture (Details)
InterPro domains unassigned to SynO:
The SET domain appears generally as one part of a larger multidomain protein.nd recently there were described three structures of very different proteins with distinct domain compositions: Neurospora crassa DIM-5. member of the Su(var) family of HKMTs which methylate histone H3 on lysine 9.uman SET7 (also called SET9).hich methylates H3 on lysine 4 and garden pea Rubisco LSMT.n enzyme that does not modify histones.ut instead methylates lysine 14 in the flexible tail of the large subunit of the enzyme Rubisco. The SET domain itself turned out to be an uncommon structure. Although in all three studies.lectron density maps revealed the location of the AdoMet or AdoHcy cofactor.he SET domain bears no similarity at all to the canonical/AdoMet-dependent methyltransferase fold. Strictly conserved in the C-terminal motif of the SET domain tyrosine could be involved in abstracting a proton from the protonated amino group of the substrate lysine.romoting its nucleophilic attack on the sulphonium methyl group of the AdoMet cofactor. In contrast to the AdoMet-dependent protein methyltranferases of the classical type.hich tend to bind their polypeptide substrates on top of the cofactor.t is noted from the Rubisco LSMT structure that the AdoMet seems to bind in a separate cleft.uggesting how a polypeptide substrate could be subjected to multiple rounds of methylation without having to be released from the enzyme. In contrast.ET7/9 is able to add only a single methyl group to its substrate. It has been demonstrated that association of SET domain and myotubularin-related proteins modulates growth control . The SET domain-containing Drosophila melanogaster (Fruit fly) protein.nhancer of zeste.as a function in segment determination and the mammalian homologue may be involved in the regulation of gene transcription and chromatin structure.Histone lysine methylation is part of the histone code that regulated chromatin function and epigenetic control of gene function. Histone lysine methyltransferases (HMTase) differ both in their substrate specificity for the various acceptor lysines as well as in their product specificity for the number of methyl groups (one.wo.r three) they transfer. With just one exception .he HMTases belong to SET family that can be classified according to the sequences surrounding the SET domain . Structural studies on the human SET7/9. mono-methylase.ave revealed the molecular basis for the specificity of the enzyme for the histone-target and the roles of the invariant residues in the SET domain in determining the methylation specificities . The pre-SET domain.s found in the SUV39 SET family.ontains nine invariant cysteine residues that are grouped into two segments separated by a region of variable length. These 9 cysteines coordinate 3 zinc ions to form to form a triangular cluster.here each of the zinc ions is coordinated by 4 four cysteines to give a tetrahedral configuration. The function of this domain is structural.olding together 2 long segments of random coils.The C-terminal region including the post-SET domain is disordered when not interacting with a histone tail and in the absence of zinc. The three conserved cysteines in the post-SET domain form a zinc-binding site when coupled to a fourth conserved cysteine in the knot-like structure close to the SET domain active site . The structured post-SET region brings in the C-terminal residues that participate in S-adenosylmethine-binding and histone tail interactions. The three conserved cysteine residues are essential for HMTase activity.s replacement with serine abolishes HMTase activity .
  IPR001214:SET
Zinc finger domains .re nucleic acid-binding protein structures first identified in the Xenopus laevis transcription factor TFIIIA. These domains have since been found in numerous nucleic acid-binding proteins. A zinc finger domain is composed of 25 to 30 amino-acid residues including 2 conserved Cys and 2 conserved His residues in a C-2-C-12-H-3-H type motif. The 12 residues separating the second Cys and the first His are mainly polar and basic.mplicating this region in particular in nucleic acid binding. The zinc finger motif is an unusually small.elf-folding domain in which Zn is a crucial component of its tertiary structure. All bind 1 atom of Zn in a tetrahedral array to yield a finger-like projection.hich interacts with nucleotides in the major groove of the nucleic acid. The Zn binds to the conserved Cys and His residues. Fingers have been found to bind to about 5 base pairs of nucleic acid containing short runs of guanine residues. They have the ability to bind to both RNA and DNA.nd it has been suggested that the zinc finger may thus represent the original nucleic acid binding protein. It has also been suggested that a Zn-centred domain could be used in a protein interaction..g. in protein kinase C. Many classes of zinc fingers are characterized according to the number and positions of the histidine and cysteine residues involved in the zinc atom coordination. In the first class to be characterized.alled C2H2.he first pair of zinc coordinating residues are cysteines.hile the second pair are histidines.
  IPR007087:Zinc finger, C2H2-type
IPR007087:zf-C2H2 
Evalue:-7.37675094604492 
Location:951-973IPR007087:zf-C2H2 
Evalue:-6.82390880584717 
Location:337-360IPR007087:zf-C2H2 
Evalue:-6.67778062820435 
Location:309-331IPR007087:zf-C2H2 
Evalue:-6.22184896469116 
Location:979-1002IPR007087:zf-C2H2 
Evalue:-5.95860719680786 
Location:366-388IPR007087:zf-C2H2 
Evalue:-4.95860719680786 
Location:423-445IPR007087:zf-C2H2 
Evalue:-4.88605642318726 
Location:281-303IPR007087:zf-C2H2 
Evalue:-4.14266729354858 
Location:394-416IPR007087:zf-C2H2 
Evalue:-4.00877380371094 
Location:1008-1030IPR001214:SET 
Evalue:-3 
Location:84-217IPR007087:zf-C2H2 
Evalue:-1.82390868663788 
Location:230-253IPR003006:IG_MHC 
Evalue:0 
Location:0-0
SequencesProtein: PRD16_HUMAN (1276 aa)
mRNA: AB051462 AF294278 NM_022114
Local Annotation
Synapse Ontology
A process that increases long-term neuronal synaptic plasticity, the ability of neuronal synapses to change long-term as circumstances require. Long-term neuronal synaptic plasticity generally involves increase or decrease in actual synapse numbers.
sdb:0039 positive regulation of long-term neuronal synaptic plasticity  (Evidence:keywords)
KO assignmentNot mapped to KEGG
Loci Structure (Details)Loci index, Chromosomal location, Length, Possible relational loci clusterExon1: 40 residues, 2975603-2975720Exon2: 118 residues, 3092548-3092898Exon3: 19 residues, 3150510-3150561Exon4: 47 residues, 3291575-3291710Exon5: 36 residues, 3302914-3303017Exon6: 71 residues, 3309214-3309422Exon7: 51 residues, 3311162-3311310Exon8: 53 residues, 3311918-3312072Exon9: 474 residues, 3317807-3319224Exon10: 30 residues, 3320986-3321071Exon11: 58 residues, 3324251-3324421Exon12: 28 residues, 3325090-3325168Exon13: 58 residues, 3332004-3332174Exon14: 60 residues, 3332474-3332649Exon15: 81 residues, 3337295-3337532Exon16: 60 residues, 3338389-3338564Exon17: 1649 residues, 3340100-3345043Exon18: 2 residues, -Jump to PRD16_HUMANExon1: 34 residues, 2975620-2975720Exon2: 118 residues, 3092548-3092898Exon3: 19 residues, 3150510-3150561Exon4: 48 residues, 3291575-3291713Exon5: 36 residues, 3302914-3303017Exon6: 71 residues, 3309214-3309422Exon7: 51 residues, 3311162-3311310Exon8: 53 residues, 3311918-3312072Exon9: 474 residues, 3317807-3319224Exon10: 30 residues, 3320986-3321071Exon11: 58 residues, 3324251-3324421Exon12: 28 residues, 3325090-3325168Exon13: 58 residues, 3332004-3332174Exon14: 60 residues, 3332474-3332649Exon15: 81 residues, 3337295-3337532Exon16: 60 residues, 3338389-3338564Exon17: 207 residues, 3340100-3340717Exon18: 2 residues, -Jump to PRD16_HUMANExon1: 24 residues, 2975651-2975720Exon2: 118 residues, 3092548-3092898Exon3: 19 residues, 3150510-3150561Exon4: 47 residues, 3291575-3291710Exon5: 36 residues, 3302914-3303017Exon6: 71 residues, 3309214-3309422Exon7: 51 residues, 3311162-3311310Exon8: 53 residues, 3311918-3312072Exon9: 474 residues, 3317807-3319224Exon10: 31 residues, 3320983-3321071Exon11: 58 residues, 3324251-3324421Exon12: 28 residues, 3325090-3325168Exon13: 58 residues, 3332004-3332174Exon14: 60 residues, 3332474-3332649Exon15: 81 residues, 3337295-3337532Exon16: 60 residues, 3338389-3338564Exon17: 1649 residues, 3340100-3345043Exon18: 2 residues, -Jump to PRD16_HUMAN  
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