3SOX - JenaLib

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Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   STRUCTURE OF UHRF1 PHD FINGER IN THE FREE FORM

Authors :   E. Rajakumara, D. J. Patel

Date :   30 Jun 11 (Deposition) - 03 Aug 11 (Release) - 03 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.65

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A  (2x)
Biol. Unit 4: B  (2x)

Keywords :   Phd Finger, Histone Binding, Histone H3, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Rajakumara, Z. Wang, H. Ma, L. Hu, H. Chen, Y. Lin, R. Guo, F. Wu, H. Li, F. Lan, Y. G. Shi, Y. Xu, D. J. Patel, Y. Shi
Phd Finger Recognition Of Unmodified Histone H3R2 Links Uhrf1 To Regulation Of Euchromatic Gene Expression.
Mol. Cell V. 43 275 2011
PubMed-ID: 21777816 | Reference-DOI: 10.1016/J.MOLCEL.2011.07.006

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE UHRF1
	Chains	:	A, B
	EC Number	:	6.3.2.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P-1
	Expression System Strain	:	ROSETTA2 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UHRF1 (UNP RESIDUES 298-367)
	Gene	:	ICBP90, NP95, RNF106, UHRF1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	INVERTED CCAAT BOX-BINDING PROTEIN OF 90 KDA, NUCLEAR PROTEIN 95, NUCLEAR ZINC FINGER PROTEIN NP95, HUNP95, RING FINGER PROTEIN 106, TRANSCRIPTION FACTOR ICBP90, UBIQUITIN-LIKE PHD AND RING FINGER DOMAIN-CONTAINING PROTEIN 1, UBIQUITIN-LIKE-CONTAINING PHD AND RING FINGER DOMAINS PROTEIN 1

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (2x)	:	A
Biological Unit 4 (2x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 8)

No.	Name	Count	Type	Full Name
1	ZN	8	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:315 , CYS A:318 , CYS A:326 , CYS A:329	BINDING SITE FOR RESIDUE ZN A 1
2	AC2	SOFTWARE	CYS A:331 , CYS A:334 , HIS A:354 , CYS A:357	BINDING SITE FOR RESIDUE ZN A 2
3	AC3	SOFTWARE	CYS A:346 , CYS A:349 , CYS A:373 , CYS A:376	BINDING SITE FOR RESIDUE ZN A 3
4	AC4	SOFTWARE	HIS A:332 , GLU A:375	BINDING SITE FOR RESIDUE ZN A 7
5	AC5	SOFTWARE	CYS B:331 , CYS B:334 , HIS B:354 , CYS B:357	BINDING SITE FOR RESIDUE ZN B 4
6	AC6	SOFTWARE	CYS B:315 , CYS B:318 , CYS B:326 , CYS B:329	BINDING SITE FOR RESIDUE ZN B 5
7	AC7	SOFTWARE	CYS B:346 , CYS B:349 , CYS B:373 , CYS B:376	BINDING SITE FOR RESIDUE ZN B 6
8	AC8	SOFTWARE	HIS B:332 , GLU B:375	BINDING SITE FOR RESIDUE ZN B 8

(no "SS Bond" information available for 3SOX)

Asymmetric Unit

No.	Residues
1	Asp A:359	-	Pro A:360
2	Asp B:359	-	Pro B:360

(no "SAP(SNP)/Variant" information available for 3SOX)

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_PHD_1	PS01359	Zinc finger PHD-type signature.	UHRF1_HUMAN	302-363	2	A:315-376 B:315-376
2	ZF_PHD_2	PS50016	Zinc finger PHD-type profile.	UHRF1_HUMAN	310-366	2	A:323-376 B:323-376
3	ZF_RING_2	PS50089	Zinc finger RING-type profile.	UHRF1_HUMAN	318-364 724-763	2	A:331-376 B:331-376 -

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_PHD_1	PS01359	Zinc finger PHD-type signature.	UHRF1_HUMAN	302-363	1	A:315-376 -
2	ZF_PHD_2	PS50016	Zinc finger PHD-type profile.	UHRF1_HUMAN	310-366	1	A:323-376 -
3	ZF_RING_2	PS50089	Zinc finger RING-type profile.	UHRF1_HUMAN	318-364 724-763	1	A:331-376 - -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_PHD_1	PS01359	Zinc finger PHD-type signature.	UHRF1_HUMAN	302-363	1	- B:315-376
2	ZF_PHD_2	PS50016	Zinc finger PHD-type profile.	UHRF1_HUMAN	310-366	1	- B:323-376
3	ZF_RING_2	PS50089	Zinc finger RING-type profile.	UHRF1_HUMAN	318-364 724-763	1	- B:331-376 -

Biological Unit 3 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_PHD_1	PS01359	Zinc finger PHD-type signature.	UHRF1_HUMAN	302-363	2	A:315-376 -
2	ZF_PHD_2	PS50016	Zinc finger PHD-type profile.	UHRF1_HUMAN	310-366	2	A:323-376 -
3	ZF_RING_2	PS50089	Zinc finger RING-type profile.	UHRF1_HUMAN	318-364 724-763	2	A:331-376 - -

Biological Unit 4 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_PHD_1	PS01359	Zinc finger PHD-type signature.	UHRF1_HUMAN	302-363	2	- B:315-376
2	ZF_PHD_2	PS50016	Zinc finger PHD-type profile.	UHRF1_HUMAN	310-366	2	- B:323-376
3	ZF_RING_2	PS50089	Zinc finger RING-type profile.	UHRF1_HUMAN	318-364 724-763	2	- B:331-376 -

(no "Exon" information available for 3SOX)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:65
 aligned with UHRF1_HUMAN | Q96T88 from UniProtKB/Swiss-Prot  Length:793

    Alignment length:65
                                   308       318       328       338       348       358     
          UHRF1_HUMAN   299 GPSCKHCKDDVNRLCRVCACHLCGGRQDPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPEC 363
               SCOP domains d3soxa_ A: automated matches                                      SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........................hhh.eee......eee...................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---ZF_PHD_1  PDB: A:315-376 UniProt: 302-363                      PROSITE (1)
                PROSITE (2) -----------ZF_PHD_2  PDB: A:323-376 UniProt: 310-366              PROSITE (2)
                PROSITE (3) -------------------ZF_RING_2  PDB: A:331-376 UniProt: 318-364     PROSITE (3)
                 Transcript ----------------------------------------------------------------- Transcript
                 3sox A 312 GPSCKHCKDDVNRLCRVCACHLCGGRQDPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPEC 376
                                   321       331       341       351       361       371

Chain B from PDB  Type:PROTEIN  Length:65
 aligned with UHRF1_HUMAN | Q96T88 from UniProtKB/Swiss-Prot  Length:793

    Alignment length:65
                                   308       318       328       338       348       358     
          UHRF1_HUMAN   299 GPSCKHCKDDVNRLCRVCACHLCGGRQDPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPEC 363
               SCOP domains d3soxb_ B: automated matches                                      SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........................hhh.eee......eee...................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---ZF_PHD_1  PDB: B:315-376 UniProt: 302-363                      PROSITE (1)
                PROSITE (2) -----------ZF_PHD_2  PDB: B:323-376 UniProt: 310-366              PROSITE (2)
                PROSITE (3) -------------------ZF_RING_2  PDB: B:331-376 UniProt: 318-364     PROSITE (3)
                 Transcript ----------------------------------------------------------------- Transcript
                 3sox B 312 GPSCKHCKDDVNRLCRVCACHLCGGRQDPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPEC 376
                                   321       331       341       351       361       371

Legend:		→ Mismatch	(orange background)
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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Small proteins (3458)

Fold: FYVE/PHD zinc finger (57)

Superfamily: FYVE/PHD zinc finger (57)

Family: automated matches (18)

Protein domain: automated matches (18)

Human (Homo sapiens) [TaxId: 9606] (16)

1a	d3soxa_	A:
1b	d3soxb_	B:

(no "CATH Domain" information available for 3SOX)

(no "Pfam Domain" information available for 3SOX)

Asymmetric Unit(hide GO term definitions)

Chain A,B (UHRF1_HUMAN | Q96T88)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000987	core promoter proximal region sequence-specific DNA binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to the core promoter. The transcribed region might be described as a gene, cistron, or operon.
	GO:0044729	hemi-methylated DNA-binding	Interacting selectively and non-covalently with double-stranded hemi-methylated DNA at replication foci (one strand methylated, while the other strand is unmethylated). Methylation of cytosine or adenine in DNA is an important mechanism for establishing stable heritable epigenetic marks.
	GO:0042393	histone binding	Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008327	methyl-CpG binding	Interacting selectively and non-covalently with a methylated cytosine/guanine dinucleotide.
	GO:0035064	methylated histone binding	Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
	GO:0031493	nucleosomal histone binding	Interacting selectively and non-covalently with a histone that is assembled into a nucleosome.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0061630	ubiquitin protein ligase activity	Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues.
	GO:0004842	ubiquitin-protein transferase activity	Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006281	DNA repair	The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0008283	cell proliferation	The multiplication or reproduction of cells, resulting in the expansion of a cell population.
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0010390	histone monoubiquitination	The modification of histones by addition of a single ubiquitin group.
	GO:0016574	histone ubiquitination	The modification of histones by addition of ubiquitin groups.
	GO:0010216	maintenance of DNA methylation	Any process involved in maintaining the methylation state of a nucleotide sequence.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:2000373	positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity	Any process that activates or increases the frequency, rate or extent of DNA topoisomerase (ATP-hydrolyzing) activity.
	GO:0032270	positive regulation of cellular protein metabolic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0051865	protein autoubiquitination	The ubiquitination by a protein of one or more of its own amino acid residues, or residues on an identical protein. Ubiquitination occurs on the lysine residue by formation of an isopeptide crosslink.
	GO:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a protein.
	GO:0042787	protein ubiquitination involved in ubiquitin-dependent protein catabolic process	The process in which a ubiquitin group, or multiple groups, are covalently attached to the target protein, thereby initiating the degradation of that protein.
	GO:0090308	regulation of methylation-dependent chromatin silencing	Any process that modulates the rate, frequency, or extent of the repression of transcription by methylation of DNA, leading to the formation of heterochromatin.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0000791	euchromatin	A dispersed and relatively uncompacted form of chromatin.
	GO:0000792	heterochromatin	A compact and highly condensed form of chromatin.
	GO:0000790	nuclear chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
	GO:0005720	nuclear heterochromatin	A condensed form of chromatin, occurring in the nucleus during interphase, that stains strongly with basophilic dyes. The DNA of heterochromatin is typically replicated at a later stage in the cell-division cycle than euchromatin.
	GO:0016363	nuclear matrix	The dense fibrillar network lying on the inner side of the nuclear membrane.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0005657	replication fork	The Y-shaped region of a replicating DNA molecule, resulting from the separation of the DNA strands and in which the synthesis of new strands takes place. Also includes associated protein complexes.

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3sou	STRUCTURE OF UHRF1 PROTEIN IN COMPLEX WITH HISTONE PEPTIDE
3sow	STRUCTURE OF UHRF1 PROTEIN IN COMPLEX WITH METHYLATED HISTONE PEPTIDE

Description

Compounds

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Ligands, Modified Residues, Ions (1, 8)

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