1T9Z - JenaLib

Title :   THREE-DIMENSIONAL STRUCTURE OF A RNA-POLYMERASE II BINDING PROTEIN.

Authors :   T. Kamenski, S. Heilmeier, A. Meinhart, P. Cramer

Date :   19 May 04 (Deposition) - 31 Aug 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A

Keywords :   Alpha-Beta Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Kamenski, S. Heilmeier, A. Meinhart, P. Cramer
Structure And Mechanism Of Rna Polymerase Ii Ctd Phosphatases.
Mol. Cell V. 15 399 2004
PubMed-ID: 15304220 | Reference-DOI: 10.1016/J.MOLCEL.2004.06.035
(for further references see the PDB file header)

Compounds

Molecule 1 - CARBOXY-TERMINAL DOMAIN RNA POLYMERASE II POLYPEPTIDE A SMALL PHOSPHATASE 1
	Chains	:	A
	EC Number	:	3.1.3.16
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21B
	Expression System Strain	:	BL21(DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CTDSP1, NIF3, NLIIF
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	NUCLEAR LIM INTERACTOR-INTERACTING FACTOR 3, NLI- INTERACTING FACTOR 3, NLI-IF, SCP1

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (5, 5)

Asymmetric/Biological Unit (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.5a	ENST00000273062	5a	ENSE00001038975	chr2:219264478-219264880	403	CTDS1_HUMAN	1-23	23	0	-	-
1.9c	ENST00000273062	9c	ENSE00001038976	chr2:219266287-219266435	149	CTDS1_HUMAN	23-72	50	0	-	-
1.10a	ENST00000273062	10a	ENSE00001038973	chr2:219266834-219266938	105	CTDS1_HUMAN	73-107	35	1	A:76-107	32
1.11a	ENST00000273062	11a	ENSE00001038977	chr2:219267072-219267128	57	CTDS1_HUMAN	108-126	19	1	A:108-126	19
1.12b	ENST00000273062	12b	ENSE00001621424	chr2:219267758-219267850	93	CTDS1_HUMAN	127-157	31	1	A:127-157	31
1.13c	ENST00000273062	13c	ENSE00001038974	chr2:219267955-219268140	186	CTDS1_HUMAN	158-219	62	1	A:158-219	62
1.14f	ENST00000273062	14f	ENSE00000965954	chr2:219269020-219270664	1645	CTDS1_HUMAN	220-261	42	1	A:220-256	37

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:181
 aligned with CTDS1_HUMAN | Q9GZU7 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:181
                                    85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255 
          CTDS1_HUMAN    76 VQYLLPEAKAQDSDKICVVIDLDETLVHSSFKPVNNADFIIPVEIDGVVHQVYVLKRPHVDEFLQRMGELFECVLFTASLAKYADPVADLLDKWGAFRARLFRESCVFHRGNYVKDLSRLGRDLRRVLILDNSPASYVFHPDNAVPVASWFDNMSDTELHDLLPFFEQLSRVDDVYSVLRQ 256
               SCOP domains d1t9za_ A: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1, NRAMP1                                                                                        SCOP domains
               CATH domains -1t9zA00 A:77-256  [code=3.40.50.1000, no name defined]                                                                                                                               CATH domains
               Pfam domains ---------------NIF-1t9zA01 A:91-251                                                                                                                                             ----- Pfam domains
         Sec.struct. author ........hhhhh...eeee......eeee........eeeeeee..eeeeeeeee..hhhhhhhhhhhhheeeee...hhhhhhhhhhhhh....eeeeehhhhheee..eee.hhhhh..hhh.eeee..hhhhhh.hhhhh............hhhhhhhhhhhhhh...hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------FCP1  PDB: A:86-244 UniProt: 86-244                                                                                                                            ------------ PROSITE
               Transcript 1 Exon 1.10a  PDB: A:76-107       Exon 1.11a         Exon 1.12b  PDB: A:127-157     Exon 1.13c  PDB: A:158-219 UniProt: 158-219                   Exon 1.14f  PDB: A:220-256            Transcript 1
                 1t9z A  76 mQYLLPEAKAQDSDKICVVIDLDETLVHSSFKPVNNADFIIPVEIDGVVHQVYVLKRPHVDEFLQRmGELFECVLFTASLAKYADPVADmLDKWGAFRARLFRESCVFHRGNYVKDLSRLGRDLRRVLImDNSPASYVFHPDNAVPVASWFDNmSDTELHDLLPFFEQLSRVDDVYSVLRQ 256
                            |       85        95       105       115       125       135      |145       155       165       175       185       195       205       215       225   |   235       245       255 
                            |                                                               142-MSE                165-MSE                                 205-MSE                 229-MSE                       
                           76-MSE

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 (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CTDS1_HUMAN | Q9GZU7)

molecular function
	GO:0008420	CTD phosphatase activity	Catalysis of the reaction: phospho-(DNA-directed RNA polymerase) + H2O = (DNA-directed RNA polymerase) + phosphate.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016791	phosphatase activity	Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
	GO:0004721	phosphoprotein phosphatase activity	Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
	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).
biological process
	GO:2000134	negative regulation of G1/S transition of mitotic cell cycle	Any cell cycle regulatory process that prevents the commitment of a cell from G1 to S phase of the mitotic cell cycle.
	GO:0050768	negative regulation of neurogenesis	Any process that stops, prevents, or reduces the frequency, rate or extent of neurogenesis, the origin and formation of neurons.
	GO:0045665	negative regulation of neuron differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of neuron differentiation.
	GO:0001933	negative regulation of protein phosphorylation	Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein.
	GO:0006470	protein dephosphorylation	The process of removing one or more phosphoric residues from a protein.
	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.
cellular component
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	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.

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