O81488 (ALFL4_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
PHD finger protein ALFIN-LIKE 4
Short name=Protein AL4

Gene names

Name:	AL4
Ordered Locus Names:	At5g26210
ORF Names:	F9D12.13, T19G15_60

Organism

Arabidopsis thaliana (Mouse-ear cress) [Reference proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	255 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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.
Subunit structure	Interacts with H3K4me3 and to a lesser extent with H3K4me2. Ref.8
Subcellular location	Nucleus Ref.8.
Tissue specificity	Ubiquitously expressed. Ref.8
Domain	The PHD-type zinc finger mediates the binding to H3K4me3. Ref.8
Sequence similarities	Belongs to the Alfin family. Contains 1 PHD-type zinc finger.
Sequence caution	The sequence AAC26230.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Domain	Zinc-finger
Ligand	Metal-binding Zinc
Molecular function	Chromatin regulator
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	chromatin modification Inferred from electronic annotation. Source: UniProtKB-KW regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	cytosol Inferred from direct assay PubMed 21166475. Source: TAIR nucleus Inferred from direct assay Ref.8. Source: TAIR
Molecular_function	methylated histone residue binding Inferred from direct assay Ref.8. Source: TAIR zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 255

255

PHD finger protein ALFIN-LIKE 4

PRO_0000059336

Regions

Zinc finger

199 – 251

53

PHD-type

Compositional bias

177 – 199

23

Glu-rich

Sites

Binding site

209

1

Histone H3K4me3 By similarity

Binding site

215

1

Histone H3K4me3 By similarity

Binding site

219

1

Histone H3K4me3 By similarity

Binding site

224

1

Histone H3K4me3 By similarity

Experimental info

Sequence conflict

186

1

E → G in BAE98515. Ref.4

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

255

Helix Strand Turn

Details...

Beta strand

203 – 205

3

Beta strand

211 – 213

3

Beta strand

215 – 217

3

Beta strand

219 – 221

3

Beta strand

224 – 226

3

Turn

227 – 231

5

Helix

236 – 239

4

Helix

246 – 249

4

Sequences

	Sequence		Length	Mass (Da)
	O81488 [UniParc]. Last modified August 30, 2005. Version 2. Checksum: 077571EBCB255BB0	FASTA	255	28,779
	10 20 30 40 50 60 MEAGGAYNPR TVEEVFRDFK GRRAGMIKAL TTDVQEFFRL CDPEKENLCL YGHPNEHWEV 70 80 90 100 110 120 NLPAEEVPPE LPEPVLGINF ARDGMAEKDW LSLVAVHSDA WLLAVAFFFG ARFGFDKADR 130 140 150 160 170 180 KRLFNMVNDL PTIFEVVAGT AKKQGKDKSS VSNNSSNRSK SSSKRGSESR AKFSKPEPKD 190 200 210 220 230 240 DEEEEEEGVE EEDEDEQGET QCGACGESYA ADEFWICCDL CEMWFHGKCV KITPARAEHI 250 KQYKCPSCSN KRARS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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]	"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.
[8]	"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.
+	Additional computationally mapped references.

Web resources

PlantsUBQ

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

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

IPI

IPI00537748.

PIR

T01840.

RefSeq

NP_197993.1. NM_122522.4.

UniGene

At.49064.
At.68496.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1WE9	NMR	-	A	201-251	[»]

ProteinModelPortal

O81488.

SMR

O81488. Positions 201-255.

ModBase

Search...

Protein-protein interaction databases

STRING

3702.AT5G26210.1-P.

Proteomic databases

PaxDb

O81488.

PRIDE

O81488.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblPlants

AT5G26210.1; AT5G26210.1; AT5G26210.

GeneID

832690.

KEGG

ath:AT5G26210.

Organism-specific databases

TAIR

At5g26210.

Phylogenomic databases

eggNOG

NOG251997.

HOGENOM

HOG000238550.

InParanoid

O81488.

OMA

NEHWEVN.

PhylomeDB

O81488.

ProtClustDB

CLSN2686751.

Gene expression databases

ArrayExpress

O81488.

Genevestigator

O81488.

GermOnline

AT5G26210. Arabidopsis thaliana.

Family and domain databases

Gene3D

3.30.40.10. 1 hit.

InterPro

IPR021998. DUF3594.
IPR019786. Zinc_finger_PHD-type_CS.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]

Pfam

PF12165. DUF3594. 1 hit.
PF00628. PHD. 1 hit.
[Graphical view]

SMART

SM00249. PHD. 1 hit.
[Graphical view]

SUPFAM

SSF57903. FYVE_PHD_ZnF. 1 hit.

PROSITE

PS01359. ZF_PHD_1. 1 hit.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

O81488.

Entry information

Entry name

ALFL4_ARATH

Accession

Primary (citable) accession number: O81488
Secondary accession number(s): Q0WWI3, Q2HIV6, Q8LBJ5

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 30, 2005
Last sequence update:	August 30, 2005
Last modified:	May 1, 2013
This is version 91 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program