1F62,4NN2,3RSN,2K16,1X4I,3V43,4COS,4L7X,1MM2,2PUY,2YSM,2YT5,1WEW,2KFT,1WEV,2E6R,4Q6F,3KV5,2L5U,2KGG,3O37,4BBQ,2KU3,2KWJ,2KYU,3O7A,4GND,4L58,4BHW,2LGG,2RI7,2YSM,2KWJ,3V43,2M85,2XB1,2JWO,1WEE,2LRI,1WEQ,2G6Q,3N9L


Conserved Protein Domain Family
PHD_SF
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cd15489: PHD_SF 
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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.
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Statistics
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PSSM-Id: 276966
Aligned: 196 rows
Threshold Bit Score: 24.9702
Created: 28-Mar-2013
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
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Zn binding sitehistone H3
Conserved site includes 8 residues -Click on image for an interactive view with Cn3D
Feature 1: Zn binding site [ion binding site], 8 residue positions
Conserved feature residue pattern:C C C [CH] H [CH] C [CH]Click to see conserved feature residue pattern help
Evidence:
  • Structure:1F62; Human BAZ1B binds two Zn2+ ions through its PHD finger.
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  • Structure:2JWO; Mouse RAG2 binds two Zn2+ ions through its PHD finger.
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  • Structure:2M85; Human E3 ubiquitin-protein ligase SHPRH binds two Zn2+ ions through its PHD finger.
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  • Structure:4NN2; Human Borjeson-Forssman-Lehmann syndrome-associated protein PHF6 binds three Zn2+ ions through its ePHD finger.
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  • Comment:The extended PHD finger, characterized by Cys2HisCys5HisCys2His, binds three Zn ions - two of the sites are conserved in other PHD fingers.
  • Structure:2PUY; Human PF21A binds two Zn2+ through its PHD finger.
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Sequence Alignment
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Format: Row Display: Color Bits: Type Selection: 
Feature 1          #  #              #          #     #  #                       #  #
1F62_A          2 RCkvCRKkge---ddkLILCd--------eCNk-aFHlfCLrpalye---------vpdgeWQCpaC 47   human
3RSN_A          7 SVd-EENgrql--gevELQCg--------iCTk-wFTadTFgidtsscl-----pfxtnysFHCnvC 56   human
1WEE_A         18 DCk-CGTkddd--gerMLACd--------gCGv-wHHtrCIginnad---------alpskFLCfrC 63   thale cress
XP_004937509  135 TCviCRQtvgnvasyhTLVCp--------aCKhawFHraCVqqka------------lnegIACfrC 181  chicken
CAD25118       10 RCy-CRLgse---dpdMLHCd--------tCGn-wLHtvCCgffsnkd------rriprreFSCfyC 57   Encephalitozoon cuniculi G...
P29375       1163 FCi-CRKtas----gfMLQCe--------lCKd-wFHnsCVplpksssqkkgsswqakevkFLCplC 1215 human
Q5T6S3        197 YCy-CGGpgew--ylrMLQCy--------rCRq-wFHeaCTqclnepmm-----fgdrfylFFCsvC 246  human
Q9SUM4        166 SCciCRKyddnkdpslWLTCssdppfegesCGf-sCHleCAfnteksglg--kdkqsegccFYCvsC 229  thale cress
O43189        188 YCy-CGGpgew--nlkMLQCr--------sCLq-wFHeaCTqclskpll-----ygdrfyeFECcvC 237  human
XP_002602499   31 TCy-CGKgrd----glMYFCd--------gCKl-wFHpgCLktnrpscl-----egdnffrFTCarC 78   Florida lancelet

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