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Protein

PHD finger protein ALFIN-LIKE 4

Gene

AL4

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Histone-binding component that specifically recognizes H3 tails trimethylated on 'Lys-4' (H3K4me3), which mark transcription start sites of virtually all active genes.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei209 – 2091Histone H3K4me3By similarity
Binding sitei215 – 2151Histone H3K4me3By similarity
Binding sitei219 – 2191Histone H3K4me3By similarity
Binding sitei224 – 2241Histone H3K4me3By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri199 – 25153PHD-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  • methylated histone binding Source: TAIR
  • zinc ion binding Source: InterPro

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
PHD finger protein ALFIN-LIKE 4
Short name:
Protein AL4
Cleaved into the following chain:
Gene namesi
Name:AL4
Ordered Locus Names:At5g26210
ORF Names:F9D12.13, T19G15_60
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 5

Organism-specific databases

TAIRiAT5G26210.

Subcellular locationi

  • Nucleus 1 Publication

GO - Cellular componenti

  • cytosol Source: TAIR
  • nucleus Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 255255PHD finger protein ALFIN-LIKE 4PRO_0000059336Add
BLAST
Initiator methionineiRemoved; alternateBy similarity
Chaini2 – 255254PHD finger protein ALFIN-LIKE 4, N-terminally processedPRO_0000434374Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1 – 11N-acetylmethionineCombined sources

Keywords - PTMi

Acetylation

Proteomic databases

PaxDbiO81488.
PRIDEiO81488.

PTM databases

iPTMnetiO81488.

Expressioni

Tissue specificityi

Ubiquitously expressed.1 Publication

Gene expression databases

GenevisibleiO81488. AT.

Interactioni

Subunit structurei

Interacts with H3K4me3 and to a lesser extent with H3K4me2.1 Publication

GO - Molecular functioni

  • methylated histone binding Source: TAIR

Protein-protein interaction databases

BioGridi17965. 1 interaction.
STRINGi3702.AT5G26210.1.

Structurei

Secondary structure

1
255
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi203 – 2053Combined sources
Beta strandi211 – 2133Combined sources
Beta strandi215 – 2173Combined sources
Beta strandi219 – 2213Combined sources
Beta strandi224 – 2263Combined sources
Turni227 – 2315Combined sources
Helixi236 – 2394Combined sources
Helixi246 – 2494Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1WE9NMR-A201-251[»]
ProteinModelPortaliO81488.
SMRiO81488. Positions 201-255.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO81488.

Family & Domainsi

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi177 – 19923Glu-richAdd
BLAST

Domaini

The PHD-type zinc finger mediates the binding to H3K4me3.1 Publication

Sequence similaritiesi

Belongs to the Alfin family.Curated
Contains 1 PHD-type zinc finger.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri199 – 25153PHD-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG1632. Eukaryota.
ENOG410YG6P. LUCA.
HOGENOMiHOG000238550.
InParanoidiO81488.
OMAiHPNEHWE.
PhylomeDBiO81488.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR021998. Alfin.
IPR019786. Zinc_finger_PHD-type_CS.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF12165. DUF3594. 1 hit.
PF00628. PHD. 1 hit.
[Graphical view]
SMARTiSM00249. PHD. 1 hit.
[Graphical view]
SUPFAMiSSF57903. SSF57903. 1 hit.
PROSITEiPS01359. ZF_PHD_1. 1 hit.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

O81488-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEAGGAYNPR TVEEVFRDFK GRRAGMIKAL TTDVQEFFRL CDPEKENLCL
60 70 80 90 100
YGHPNEHWEV NLPAEEVPPE LPEPVLGINF ARDGMAEKDW LSLVAVHSDA
110 120 130 140 150
WLLAVAFFFG ARFGFDKADR KRLFNMVNDL PTIFEVVAGT AKKQGKDKSS
160 170 180 190 200
VSNNSSNRSK SSSKRGSESR AKFSKPEPKD DEEEEEEGVE EEDEDEQGET
210 220 230 240 250
QCGACGESYA ADEFWICCDL CEMWFHGKCV KITPARAEHI KQYKCPSCSN

KRARS
Length:255
Mass (Da):28,779
Last modified:August 30, 2005 - v2
Checksum:i077571EBCB255BB0
GO

Sequence cautioni

The sequence AAC26230.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti186 – 1861E → G in BAE98515 (Ref. 4) Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF077407 Genomic DNA. Translation: AAC26230.1. Sequence problems.
CP002688 Genomic DNA. Translation: AED93537.1.
BT024475 mRNA. Translation: ABD19656.1.
AK226367 mRNA. Translation: BAE98515.1.
AB493760 mRNA. Translation: BAH30598.1.
AY087173 mRNA. Translation: AAM64729.1.
PIRiT01840.
RefSeqiNP_197993.1. NM_122522.4.
UniGeneiAt.49064.
At.68496.

Genome annotation databases

EnsemblPlantsiAT5G26210.1; AT5G26210.1; AT5G26210.
GeneIDi832690.
GrameneiAT5G26210.1; AT5G26210.1; AT5G26210.
KEGGiath:AT5G26210.

Cross-referencesi

Web resourcesi

PlantsUBQ

A functional genomics database for the ubiquitin/26S proteasome proteolytic pathway in plants

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF077407 Genomic DNA. Translation: AAC26230.1. Sequence problems.
CP002688 Genomic DNA. Translation: AED93537.1.
BT024475 mRNA. Translation: ABD19656.1.
AK226367 mRNA. Translation: BAE98515.1.
AB493760 mRNA. Translation: BAH30598.1.
AY087173 mRNA. Translation: AAM64729.1.
PIRiT01840.
RefSeqiNP_197993.1. NM_122522.4.
UniGeneiAt.49064.
At.68496.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1WE9NMR-A201-251[»]
ProteinModelPortaliO81488.
SMRiO81488. Positions 201-255.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi17965. 1 interaction.
STRINGi3702.AT5G26210.1.

PTM databases

iPTMnetiO81488.

Proteomic databases

PaxDbiO81488.
PRIDEiO81488.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT5G26210.1; AT5G26210.1; AT5G26210.
GeneIDi832690.
GrameneiAT5G26210.1; AT5G26210.1; AT5G26210.
KEGGiath:AT5G26210.

Organism-specific databases

TAIRiAT5G26210.

Phylogenomic databases

eggNOGiKOG1632. Eukaryota.
ENOG410YG6P. LUCA.
HOGENOMiHOG000238550.
InParanoidiO81488.
OMAiHPNEHWE.
PhylomeDBiO81488.

Miscellaneous databases

EvolutionaryTraceiO81488.
PROiO81488.

Gene expression databases

GenevisibleiO81488. AT.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR021998. Alfin.
IPR019786. Zinc_finger_PHD-type_CS.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF12165. DUF3594. 1 hit.
PF00628. PHD. 1 hit.
[Graphical view]
SMARTiSM00249. PHD. 1 hit.
[Graphical view]
SUPFAMiSSF57903. SSF57903. 1 hit.
PROSITEiPS01359. ZF_PHD_1. 1 hit.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana."
    Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E., Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.
    , Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L., O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D., Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M., Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L., Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B., Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P., Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M., Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D., Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A., Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I., Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T., Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A., McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U., Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M., Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G., Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W., Bevan M., Fransz P.F.
    Nature 408:823-826(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  2. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  3. "Arabidopsis ORF clones."
    Shinn P., Chen H., Kim C.J., Ecker J.R.
    Submitted (FEB-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  4. "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs."
    Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.
    , Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y., Shinozaki K.
    Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  5. "ORF cloning and analysis of Arabidopsis transcription factor genes."
    Fujita M., Mizukado S., Seki M., Shinozaki K., Mitsuda N., Takiguchi Y., Takagi M.
    Submitted (MAR-2009) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  6. "Full-length cDNA from Arabidopsis thaliana."
    Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A.
    Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  7. "Comparative large-scale characterisation of plant vs. mammal proteins reveals similar and idiosyncratic N-alpha acetylation features."
    Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T., Giglione C.
    Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  8. "Solution structure of PHD domain in nucleic acid binding protein-like NP_197993."
    RIKEN structural genomics initiative (RSGI)
    Submitted (NOV-2004) to the PDB data bank
    Cited for: STRUCTURE BY NMR OF 201-251.
  9. "Arabidopsis ING and Alfin1-like protein families localize to the nucleus and bind to H3K4me3/2 via plant homeodomain fingers."
    Lee W.Y., Lee D., Chung W.I., Kwon C.S.
    Plant J. 58:511-524(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE FAMILY, DOMAIN PHD-TYPE ZINC-FINGER, SUBCELLULAR LOCATION, INTERACTION WITH HISTONES H3K4ME3 AND H3K4ME2, TISSUE SPECIFICITY.

Entry informationi

Entry nameiALFL4_ARATH
AccessioniPrimary (citable) accession number: O81488
Secondary accession number(s): Q0WWI3, Q2HIV6, Q8LBJ5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 30, 2005
Last sequence update: August 30, 2005
Last modified: February 17, 2016
This is version 114 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.