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(-) Description

Title :  NMR STRUCTURE OF UHRF1 PHD DOMAINS IN A COMPLEX WITH HISTONE H3 PEPTIDE
 
Authors :  C. Wang, J. Shen, Z. Yang, P. Chen, B. Zhao, W. Hu, W. Lan, X. Tong, H. Wu, G.
Date :  28 Jul 11  (Deposition) - 28 Sep 11  (Release) - 28 Sep 11  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
NMR Structure *:  A,B  (1x)
Keywords :  Uhrf1, Phd, Histone H3, Ligase-Dna Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Wang, J. Shen, Z. Yang, P. Chen, B. Zhao, W. Hu, W. Lan, X. Tong, H. Wu, G. Li, C. Cao
Structural Basis For Site-Specific Reading Of Unmodified R2 Of Histone H3 Tail By Uhrf1 Phd Finger.
Cell Res. V. 21 1379 2011
PubMed-ID: 21808299  |  Reference-DOI: 10.1038/CR.2011.123

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE UHRF1
    ChainsA
    EC Number6.3.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPETDUET
    Expression System Vector TypeVECTOR
    FragmentUNP RESIDUES 298-366
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymINVERTED 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
 
Molecule 2 - HISTONE H3 PEPTIDE
    ChainsB
    EngineeredYES
    Other DetailsTHE PEPTIDE WAS CHEMICALLY SYNTHESIZED.
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
NMR Structure (20x)AB
NMR Structure * (1x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

NMR Structure (2, 4)
No.NameCountTypeFull Name
1M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
2ZN3Ligand/IonZINC ION
NMR Structure * (1, 1)
No.NameCountTypeFull Name
1M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
2ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

NMR Structure (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:315 , CYS A:318 , CYS A:326 , CYS A:329BINDING SITE FOR RESIDUE ZN A 380
2AC2SOFTWARECYS A:331 , CYS A:334 , HIS A:354 , CYS A:357BINDING SITE FOR RESIDUE ZN A 381
3AC3SOFTWARECYS A:346 , CYS A:349 , CYS A:373 , CYS A:376BINDING SITE FOR RESIDUE ZN A 382

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2LGK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2LGK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2LGK)

(-) PROSITE Motifs  (3, 3)

NMR Structure (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_PHD_1PS01359 Zinc finger PHD-type signature.UHRF1_HUMAN302-363  1A:315-376
2ZF_PHD_2PS50016 Zinc finger PHD-type profile.UHRF1_HUMAN310-366  1A:323-379
3ZF_RING_2PS50089 Zinc finger RING-type profile.UHRF1_HUMAN318-364
724-763
  1A:331-377
-
NMR Structure * (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_PHD_1PS01359 Zinc finger PHD-type signature.UHRF1_HUMAN302-363  1A:315-376
2ZF_PHD_2PS50016 Zinc finger PHD-type profile.UHRF1_HUMAN310-366  1A:323-379
3ZF_RING_2PS50089 Zinc finger RING-type profile.UHRF1_HUMAN318-364
724-763
  1A:331-377
-

(-) Exons   (0, 0)

(no "Exon" information available for 2LGK)

(-) Sequences/Alignments

NMR Structure
   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:69
 aligned with UHRF1_HUMAN | Q96T88 from UniProtKB/Swiss-Prot  Length:793

    Alignment length:69
                                   307       317       327       337       347       357         
          UHRF1_HUMAN   298 SGPSCKHCKDDVNRLCRVCACHLCGGRQDPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRND 366
               SCOP domains --------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............................hhhhh.ee....ee....................hhhhhh. 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:323-379 UniProt: 310-366                 PROSITE (2)
                PROSITE (3) --------------------ZF_RING_2  PDB: A:331-377 UniProt: 318-364     -- PROSITE (3)
                 Transcript --------------------------------------------------------------------- Transcript
                 2lgk A 311 SGPSCKHCKDDVNRLCRVCACHLCGGRQDPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRND 379
                                   320       330       340       350       360       370         

Chain B from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ............ Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 2lgk B   1 ARTKQTARkSTG  12
                                    10  
                                    9-M3L

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2LGK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2LGK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2LGK)

(-) Gene Ontology  (39, 39)

NMR Structure(hide GO term definitions)
Chain A   (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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        UHRF1_HUMAN | Q96T882faz 2l3r 2lgg 2lgl 2pb7 3ask 3asl 3bi7 3clz 3db3 3db4 3dwh 3fl2 3shb 3sou 3sow 3sox 3t6r 3zvy 3zvz 4gy5 4qqd 5c6d 5iay

(-) Related Entries Specified in the PDB File

2lgg 2lgl