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(-) Description

Title :  CRYSTAL STRUCTURE OF LSD1-COREST IN COMPLEX WITH (-)-TRANS-2-PHENYLCYCLOPROPYL-1-AMINE
 
Authors :  C. Binda, S. Valente, M. Romanenghi, S. Pilotto, R. Cirilli, A. Karytinos, G. Ciossani, O. A. Botrugno, F. Forneris, M. Tardugno, D. E. Edmondson, S. Minucci, A. Mattevi, A. Mai
Date :  31 Mar 10  (Deposition) - 05 May 10  (Release) - 12 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Amine Oxidase, Chromatin Regulator, Histone Inhibitor Binding, Methylation, Nucleosome Core, Oxidoreductase, Oxidoreductase/Repressor Complex, Chromatin Remodelling, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Binda, S. Valente, M. Romanenghi, S. Pilotto, R. Cirilli, A. Karytinos, G. Ciossani, O. A. Botrugno, F. Forneris, M. Tardugno, D. E. Edmondson, S. Minucci, A. Mattevi, A. Mai
Biochemical, Structural, And Biological Evaluation Of Tranylcypromine Derivatives As Inhibitors Of Histone Demethylases Lsd1 And Lsd2.
J. Am. Chem. Soc. V. 132 6827 2010
PubMed-ID: 20415477  |  Reference-DOI: 10.1021/JA101557K

(-) Compounds

Molecule 1 - LYSINE-SPECIFIC HISTONE DEMETHYLASE 1
    ChainsA
    EC Number1.-.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymLYSINE-SPECIFIC HISTONE DEMETHYLASE LSD1, FLAVIN-CONTAINING AMINE OXIDASE DOMAIN-CONTAINING PROTEIN 2, BRAF35-HDAC COMPLEX PROTEIN BHC110
 
Molecule 2 - REST COREPRESSOR 1
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCOREPRESSOR COREST, PROTEIN COREST

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2TCA1Ligand/IonPHENYLETHYLENECARBOXYLIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:285 , GLY A:287 , VAL A:288 , SER A:289 , LEU A:307 , GLU A:308 , ALA A:309 , ARG A:310 , GLY A:314 , GLY A:315 , ARG A:316 , VAL A:317 , LEU A:329 , GLY A:330 , ALA A:331 , MET A:332 , VAL A:333 , THR A:588 , ALA A:589 , VAL A:590 , THR A:624 , LEU A:625 , PRO A:626 , TRP A:751 , TRP A:756 , SER A:760 , TYR A:761 , GLY A:800 , GLU A:801 , ALA A:809 , THR A:810 , VAL A:811 , TCA A:901BINDING SITE FOR RESIDUE FAD A 900
2AC2SOFTWAREMET A:332 , THR A:335 , LYS A:661 , TYR A:761 , FAD A:900BINDING SITE FOR RESIDUE TCA A 901

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ala A:240 -Pro A:241
2Pro A:470 -Pro A:471
3Gln A:633 -Pro A:634
4Val A:640 -Pro A:641

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_076366E379KKDM1A_HUMANDisease (CPRF)864309715AE379K
2UniProtVAR_076367D556GKDM1A_HUMANDisease (CPRF)864309716AD556G
3UniProtVAR_076368Y761HKDM1A_HUMANDisease (CPRF)864309714AY761H

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SWIRMPS50934 SWIRM domain profile.KDM1A_HUMAN174-273  1A:174-273
2SANTPS51293 SANT domain profile.RCOR1_HUMAN190-241
381-432
  1-
B:378-429

(-) Exons   (22, 22)

Asymmetric/Biological Unit (22, 22)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002622411ENSE00001420913chr14:103059233-103059524292RCOR1_HUMAN1-98980--
1.2ENST000002622412ENSE00000660501chr14:103059603-10305966260RCOR1_HUMAN98-118210--
1.3ENST000002622413ENSE00000870514chr14:103148232-10314831584RCOR1_HUMAN118-146290--
1.4ENST000002622414ENSE00001678988chr14:103167615-10316766753RCOR1_HUMAN146-163180--
1.5ENST000002622415ENSE00001719953chr14:103173688-103173849162RCOR1_HUMAN164-217540--
1.6ENST000002622416ENSE00000660506chr14:103174802-103174920119RCOR1_HUMAN218-257400--
1.7ENST000002622417ENSE00000870515chr14:103177272-10317735079RCOR1_HUMAN257-283270--
1.8ENST000002622418ENSE00000660508chr14:103180760-103180954195RCOR1_HUMAN284-348651B:308-34538
1.9ENST000002622419ENSE00000660509chr14:103187344-10318742178RCOR1_HUMAN349-374261B:346-37126
1.10ENST0000026224110ENSE00000660510chr14:103187657-10318771458RCOR1_HUMAN375-394201B:372-39120
1.11ENST0000026224111ENSE00000870516chr14:103188524-103188753230RCOR1_HUMAN394-470771B:391-44050
1.12ENST0000026224112ENSE00001152549chr14:103192805-1031969124108RCOR1_HUMAN471-482120--

2.1aENST000003566341aENSE00001422377chr1:23345941-23346440500KDM1A_HUMAN1-1171170--
2.2ENST000003566342ENSE00000388542chr1:23356962-23357127166KDM1A_HUMAN118-173561A:171-1733
2.4aENST000003566344aENSE00000759117chr1:23376880-23377013134KDM1A_HUMAN173-217451A:173-21745
2.5ENST000003566345ENSE00000859702chr1:23380254-2338033279KDM1A_HUMAN218-244271A:218-24427
2.6aENST000003566346aENSE00000859703chr1:23381562-2338165493KDM1A_HUMAN244-275321A:244-27532
2.7ENST000003566347ENSE00000859704chr1:23382425-23382531107KDM1A_HUMAN275-310361A:275-31036
2.8ENST000003566348ENSE00000859705chr1:23383977-2338405882KDM1A_HUMAN311-338281A:311-33828
2.9ENST000003566349ENSE00000759111chr1:23385566-2338566095KDM1A_HUMAN338-369321A:338-36932
2.11ENST0000035663411ENSE00000759110chr1:23395032-23395174143KDM1A_HUMAN370-417481A:370-41748
2.12ENST0000035663412ENSE00000759108chr1:23395554-2339564491KDM1A_HUMAN417-447311A:417-44731
2.13ENST0000035663413ENSE00000859709chr1:23397718-23397852135KDM1A_HUMAN448-492451A:448-49245
2.14ENST0000035663414ENSE00000759106chr1:23398617-2339869074KDM1A_HUMAN493-517251A:493-51725
2.15bENST0000035663415bENSE00000388553chr1:23399785-23399896112KDM1A_HUMAN517-554381A:517-55438
2.16aENST0000035663416aENSE00000759050chr1:23403721-23403853133KDM1A_HUMAN555-599451A:555-59945
2.17bENST0000035663417bENSE00000859713chr1:23405483-23405670188KDM1A_HUMAN599-661631A:599-66163
2.18bENST0000035663418bENSE00000859714chr1:23406046-23406160115KDM1A_HUMAN662-700391A:662-70039
2.19ENST0000035663419ENSE00000859715chr1:23407939-23408066128KDM1A_HUMAN700-742431A:700-74243
2.20ENST0000035663420ENSE00000759046chr1:23408713-23408859147KDM1A_HUMAN743-791491A:743-79149
2.21cENST0000035663421cENSE00001564450chr1:23409672-23410182511KDM1A_HUMAN792-852611A:792-83645

(-) Sequences/Alignments

Asymmetric/Biological 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:666
 aligned with KDM1A_HUMAN | O60341 from UniProtKB/Swiss-Prot  Length:852

    Alignment length:666
                                   180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830      
          KDM1A_HUMAN   171 PSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAMYTL 836
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2xajA01 A:171-279 'winged helix' repressor DNA binding domain                                                ------------------------------------------------------------------------------------------------------------------------------2xajA03 A:406-521  [code=1.10.287.80, no name defined]                                                              --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---SWIRM-2xajA02 A:174-264                                                                    -----------------------Amino_oxidase-2xajA01 A:288-826                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            ---------- Pfam domains
         Sec.struct. author ..hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhh....................eeeee..hhhhhhhhhhhhhh..eeeee...........eeee..eeee....ee......hhhhhhhhh...eee...............hhhhhhhhhhhhhhhhhhhhhhhhh....ee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh...........hhhhhhh.....eee....hhhhhhhhh..eee..eeeeeeeee..eeeeeeee......eeeeee.eeee..hhhhhhh.....eee...hhhhhhhhhhhee...eeeeee...........eee.............eeee.....eeeeeehhhhhhhhh..hhhhhhhhhhhhhhhhhh........eeee.............ee......hhhhhhhhh.................eee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------K--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------H--------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---SWIRM  PDB: A:174-273 UniProt: 174-273                                                              ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) 2.2--------------------------------------------Exon 2.5  PDB: A:218-244   ------------------------------Exon 2.7  PDB: A:275-310            Exon 2.8  PDB: A:311-338    -------------------------------Exon 2.11  PDB: A:370-417 UniProt: 370-417      ------------------------------Exon 2.13  PDB: A:448-492 UniProt: 448-492   Exon 2.14  PDB: A:493-517-------------------------------------Exon 2.16a  PDB: A:555-599 UniProt: 555-599  --------------------------------------------------------------Exon 2.18b  PDB: A:662-700             ------------------------------------------Exon 2.20  PDB: A:743-791 UniProt: 743-791       Exon 2.21c  PDB: A:792-836 UniProt: 792-852   Transcript 2 (1)
           Transcript 2 (2) --Exon 2.4a  PDB: A:173-217 UniProt: 173-217   --------------------------Exon 2.6a  PDB: A:244-275       --------------------------------------------------------------Exon 2.9  PDB: A:338-369        -----------------------------------------------Exon 2.12  PDB: A:417-447      ---------------------------------------------------------------------Exon 2.15b  PDB: A:517-554            --------------------------------------------Exon 2.17b  PDB: A:599-661 UniProt: 599-661                    --------------------------------------Exon 2.19  PDB: A:700-742 UniProt: 700-742 ---------------------------------------------------------------------------------------------- Transcript 2 (2)
                 2xaj A 171 PSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAMYTL 836
                                   180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830      

Chain B from PDB  Type:PROTEIN  Length:133
 aligned with RCOR1_HUMAN | Q9UKL0 from UniProtKB/Swiss-Prot  Length:485

    Alignment length:133
                                   320       330       340       350       360       370       380       390       400       410       420       430       440   
          RCOR1_HUMAN   311 RKPPKGMFLSQEDVEAVSANATAATTVLRQLDMELVSVKRQIQNIKQTNSALKEKLDGGIEPYRLPEVIQKCNARWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDEVLQEWEAE 443
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------Myb_DNA-binding-2xajB01 B:378-422            ------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh............hhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhh....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) ----------------------------------------------------------------------SANT  PDB: B:378-429 UniProt: 381-432               ----------- PROSITE (1)
           Transcript 1 (1) Exon 1.8  PDB: B:308-345 [INCOMPLETE] Exon 1.9  PDB: B:346-371  Exon 1.10           ------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------Exon 1.11  PDB: B:391-440 UniProt: 394-470         Transcript 1 (2)
                 2xaj B 308 RKPPKGMFLSQEDVEAVSANATAATTVLRQLDMELVSVKRQIQNIKQTNSALKEKLDGGIEPYRLPEVIQKCNARWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDEVLQEWEAE 440
                                   317       327       337       347       357       367       377       387       397       407       417       427       437   

   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 2XAJ)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (71, 85)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KDM1A_HUMAN | O60341)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0043426    MRF binding    Interacting selectively and non-covalently with Myogenic Regulatory Factor (MRF), a member of the basic Helix-Loop-Helix (bHLH) superfamily of transcription factors.
    GO:0001085    RNA polymerase II transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription factor, any protein required to initiate or regulate transcription by RNA polymerase II.
    GO:0050681    androgen receptor binding    Interacting selectively and non-covalently with an androgen receptor.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0032451    demethylase activity    Catalysis of the removal of a methyl group from a substrate.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    GO:0004407    histone deacetylase activity    Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction represents the removal of an acetyl group from a histone, a class of proteins complexed to DNA in chromatin and chromosomes.
    GO:0032452    histone demethylase activity    Catalysis of the removal of a methyl group from a histone.
    GO:0032453    histone demethylase activity (H3-K4 specific)    Catalysis of the removal of a methyl group from lysine at position 4 of the histone H3 protein.
    GO:0032454    histone demethylase activity (H3-K9 specific)    Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 9) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 9 of the histone H3 protein.
    GO:0034648    histone demethylase activity (H3-dimethyl-K4 specific)    Catalysis of the removal of a methyl group from dimethylated lysine at position 4 of the histone H3 protein.
    GO:0030374    ligand-dependent nuclear receptor transcription coactivator activity    The function of a transcription cofactor that activates transcription in conjuction with a ligand-dependent nuclear receptor from a RNA polymerase II promoter; does not bind DNA itself.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0002039    p53 binding    Interacting selectively and non-covalently with one of the p53 family of proteins.
    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:0042162    telomeric DNA binding    Interacting selectively and non-covalently with a telomere, a specific structure at the end of a linear chromosome required for the integrity and maintenance of the end.
    GO:0061752    telomeric repeat-containing RNA binding    Interacting selectively and non-covalently with long non-coding RNA molecules transcribed from subtelomeric regions in most eukaryotes. Telomeric repeat-containing RNA (TERRA) molecules consist of subtelomeric-derived sequences and G-rich telomeric repeats.
    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:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0044212    transcription regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
biological process
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0034644    cellular response to UV    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 an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers.
    GO:0071480    cellular response to gamma radiation    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 gamma radiation stimulus. Gamma radiation is a form of electromagnetic radiation (EMR) or light emission of a specific frequency produced from sub-atomic particle interaction, such as electron-positron annihilation and radioactive decay. Gamma rays are generally characterized as EMR having the highest frequency and energy, and also the shortest wavelength, within the electromagnetic radiation spectrum.
    GO:0030851    granulocyte differentiation    The process in which a myeloid precursor cell acquires the specialized features of a granulocyte. Granulocytes are a class of leukocytes characterized by the presence of granules in their cytoplasm. These cells are active in allergic immune reactions such as arthritic inflammation and rashes. This class includes basophils, eosinophils and neutrophils.
    GO:0034720    histone H3-K4 demethylation    The modification of histone H3 by the removal of a methyl group from lysine at position 4 of the histone.
    GO:0033169    histone H3-K9 demethylation    The modification of histone H3 by the removal of a methyl group from lysine at position 9 of the histone.
    GO:0016575    histone deacetylation    The modification of histones by removal of acetyl groups.
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0055001    muscle cell development    The process whose specific outcome is the progression of a muscle cell over time, from its formation to the mature structure. Muscle cell development does not include the steps involved in committing an unspecified cell to the muscle cell fate.
    GO:0043392    negative regulation of DNA binding    Any process that stops or reduces the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
    GO:0043518    negative regulation of DNA damage response, signal transduction by p53 class mediator    Any process that stops, prevents, or reduces the frequency, rate or extent of the cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage.
    GO:0051572    negative regulation of histone H3-K4 methylation    Any process that stops, prevents, or reduces the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 4 of histone H3.
    GO:0051573    negative regulation of histone H3-K9 methylation    Any process that stops, prevents, or reduces the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 9 of histone H3.
    GO:1902166    negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator    Any process that stops, prevents or reduces the frequency, rate or extent of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator.
    GO:0032091    negative regulation of protein binding    Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding.
    GO:0043433    negative regulation of sequence-specific DNA binding transcription factor activity    Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    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:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0021983    pituitary gland development    The progression of the pituitary gland over time from its initial formation until its mature state. The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands.
    GO:0045648    positive regulation of erythrocyte differentiation    Any process that activates or increases the frequency, rate or extent of erythrocyte differentiation.
    GO:0033184    positive regulation of histone ubiquitination    Any process that activates or increases the frequency, rate or extent of the addition of a ubiquitin group to a histone protein.
    GO:0046886    positive regulation of hormone biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of hormones.
    GO:0045654    positive regulation of megakaryocyte differentiation    Any process that activates or increases the frequency, rate or extent of megakaryocyte differentiation.
    GO:2000179    positive regulation of neural precursor cell proliferation    Any process that activates or increases the frequency, rate or extent of neural precursor cell proliferation.
    GO:0051091    positive regulation of sequence-specific DNA binding transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    GO:2000648    positive regulation of stem cell proliferation    Any process that activates or increases the frequency, rate or extent of stem cell proliferation.
    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:0006482    protein demethylation    The removal of a methyl group, from a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.
    GO:1903827    regulation of cellular protein localization    Any process that modulates the frequency, rate or extent of cellular protein localization. Cellular protein localization is any process in which a protein is transported to, and/or maintained in, a specific location and encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell.
    GO:0010569    regulation of double-strand break repair via homologous recombination    Any process that modulates the frequency, rate or extent of the error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences.
    GO:0010725    regulation of primitive erythrocyte differentiation    Any process that modulates the rate, frequency, or extent of primitive erythrocyte differentiation. Primitive erythrocyte differentiation occurs as part of the process of primitive hemopoiesis.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    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:1990391    DNA repair complex    A protein complex involved in DNA repair processes including direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    GO:0005667    transcription factor complex    A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

Chain B   (RCOR1_HUMAN | Q9UKL0)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0004407    histone deacetylase activity    Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction represents the removal of an acetyl group from a histone, a class of proteins complexed to DNA in chromatin and chromosomes.
    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:0003714    transcription corepressor activity    Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0044212    transcription regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
    GO:0001078    transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.
biological process
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0070933    histone H4 deacetylation    The modification of histone H4 by the removal of one or more acetyl groups.
    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:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    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.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:1990391    DNA repair complex    A protein complex involved in DNA repair processes including direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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:0005667    transcription factor complex    A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.
    GO:0017053    transcriptional repressor complex    A protein complex that possesses activity that prevents or downregulates transcription.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KDM1A_HUMAN | O603412com 2dw4 2ejr 2h94 2hko 2iw5 2l3d 2uxn 2uxx 2v1d 2x0l 2xaf 2xag 2xah 2xaq 2xas 2y48 2z3y 2z5u 3abt 3abu 3zms 3zmt 3zmu 3zmv 3zmz 3zn0 3zn1 4bay 4czz 4kum 4uv8 4uv9 4uva 4uvb 4uvc 4uxn 4xbf 5afw 5h6q 5h6r 5it3 5l3b 5l3c 5l3d 5l3e 5l3f 5l3g 5lbq 5lgn 5lgt 5lgu 5lhg 5lhh 5lhi 5x60
        RCOR1_HUMAN | Q9UKL02iw5 2uxn 2uxx 2v1d 2x0l 2xaf 2xag 2xah 2xaq 2xas 2y48 3zms 3zmt 3zmu 3zmv 3zmz 3zn0 3zn1 4bay 4kum 4uv8 4uv9 4uva 4uvb 4uvc 4uxn 4xbf 5h6q 5h6r 5l3b 5l3c 5l3d 5l3e 5l3f 5l3g 5lbq 5lgn 5lgt 5lgu 5lhg 5lhh 5lhi 5x60

(-) Related Entries Specified in the PDB File

2com THE SOLUTION STRUCTURE OF THE 33RD FIBRONECTIN TYPE IIIDOMAIN OF HUMAN TENASCIN-X
2h94 CRYSTAL STRUCTURE AND MECHANISM OF HUMAN LYSINE-SPECIFICDEMETHYLASE-1
2iw5 STRUCTURAL BASIS FOR COREST-DEPENDENT DEMETHYLATION OF NUCLEOSOMES BY THE HUMAN LSD1 HISTONE DEMETHYLASE
2uxn STRUCTURAL BASIS OF HISTONE DEMETHYLATION BY LSD1 REVEALED BY SUICIDE INACTIVATION
2uxx HUMAN LSD1 HISTONE DEMETHYLASE-COREST IN COMPLEX WITH AN FAD-TRANYLCYPROMINE ADDUCT
2v1d STRUCTURAL BASIS OF LSD1-COREST SELECTIVITY IN HISTONE H3 RECOGNITION
2x0l CRYSTAL STRUCTURE OF A NEURO-SPECIFIC SPLICING VARIANT OF HUMAN HISTONE LYSINE DEMETHYLASE LSD1.
2xaf CRYSTAL STRUCTURE OF LSD1-COREST IN COMPLEX WITH PARA-BROMO-CIS-2-PHENYLCYCLOPROPYL-1 -AMINE
2xag CRYSTAL STRUCTURE OF LSD1-COREST IN COMPLEX WITH PARA-BROMO-(-)-TRANS-2- PHENYLCYCLOPROPYL-1-AMINE
2xah CRYSTAL STRUCTURE OF LSD1-COREST IN COMPLEX WITH (PLUS)-TRANS-2-PHENYLCYCLOPROPYL-1- AMINE
2xaq CRYSTAL STRUCTURE OF LSD1-COREST IN COMPLEX WITH A TRANYCYPROMINE DERIVATIVE (MC2584, 13B)
2xas CRYSTAL STRUCTURE OF LSD1-COREST IN COMPLEX WITH A TRANYCYPROMINE DERIVATIVE (MC2580, 14E)