3L0C - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF SCP1 PHOSPHATASE D206A MUTANT WITH TRAPPED INORGANIC PHOSPHATE

Authors :   M. Zhang, Y. Zhang

Date :   09 Dec 09 (Deposition) - 23 Mar 10 (Release) - 19 May 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.45

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

Keywords :   Had Superfamily, Small C-Terminal Domain Phosphatase, Protein Phosphatase, Product-Trapping, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Zhang, J. Liu, Y. Kim, J. E. Dixon, S. L. Pfaff, G. N. Gill, J. P. Noel, Y. Zhang
Structural And Functional Analysis Of The Phosphoryl Transfer Reaction Mediated By The Human Small C-Terminal Domain Phosphatase, Scp1.
Protein Sci. V. 19 974 2010
PubMed-ID: 20222012 | Reference-DOI: 10.1002/PRO.375

Molecule 1 - CARBOXY-TERMINAL DOMAIN RNA POLYMERASE II POLYPEPTIDE A SMALL PHOSPHATASE 1
	Chains	:	A, B
	EC Number	:	3.1.3.16
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CTDSP1, NIF3, NLIIF, SCP1
	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

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION
2	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	PO4	1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:96 , ASP A:98 , ASN A:207 , PO4 A:596 , HOH A:618	BINDING SITE FOR RESIDUE MG A 257
2	AC2	SOFTWARE	ASP A:96 , LEU A:97 , ASP A:98 , THR A:152 , ALA A:153 , LYS A:190 , MG A:257	BINDING SITE FOR RESIDUE PO4 A 596
3	AC3	SOFTWARE	ASP B:96 , LEU B:97 , ASP B:98 , THR B:152 , ALA B:153 , SER B:154 , LYS B:190 , MG B:597	BINDING SITE FOR RESIDUE PO4 B 596
4	AC4	SOFTWARE	ASP B:96 , ASP B:98 , THR B:100 , ASN B:207 , PO4 B:596	BINDING SITE FOR RESIDUE MG B 597

(no "SS Bond" information available for 3L0C)

(no "Cis Peptide Bond" information available for 3L0C)

(no "SAP(SNP)/Variant" information available for 3L0C)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FCP1	PS50969	FCP1 homology domain profile.	CTDS1_HUMAN	86-244	2	A:86-244 B:86-244

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FCP1	PS50969	FCP1 homology domain profile.	CTDS1_HUMAN	86-244	1	A:86-244 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FCP1	PS50969	FCP1 homology domain profile.	CTDS1_HUMAN	86-244	1	- B:86-244

Asymmetric Unit (5, 10)

	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	2	A:77-107 B:77-107	31 31
1.11a	ENST00000273062	11a	ENSE00001038977	chr2:219267072-219267128	57	CTDS1_HUMAN	108-126	19	2	A:108-126 B:108-126	19 19
1.12b	ENST00000273062	12b	ENSE00001621424	chr2:219267758-219267850	93	CTDS1_HUMAN	127-157	31	2	A:127-157 B:127-157	31 31
1.13c	ENST00000273062	13c	ENSE00001038974	chr2:219267955-219268140	186	CTDS1_HUMAN	158-219	62	2	A:158-219 B:158-219	62 62
1.14f	ENST00000273062	14f	ENSE00000965954	chr2:219269020-219270664	1645	CTDS1_HUMAN	220-261	42	2	A:220-255 B:220-255	36 36

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:179
 aligned with CTDS1_HUMAN | Q9GZU7 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:179
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246         
          CTDS1_HUMAN    77 QYLLPEAKAQDSDKICVVIDLDETLVHSSFKPVNNADFIIPVEIDGVVHQVYVLKRPHVDEFLQRMGELFECVLFTASLAKYADPVADLLDKWGAFRARLFRESCVFHRGNYVKDLSRLGRDLRRVLILDNSPASYVFHPDNAVPVASWFDNMSDTELHDLLPFFEQLSRVDDVYSVLR 255
               SCOP domains d3l0ca_ A: automated matches                                                                                                                                                        SCOP domains
               CATH domains 3l0cA00 A:77-255  [code=3.40.50.1000, no name defined]                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhh..eeee......eeee........eeeeeee..eeeeeeeee..hhhhhhhhhhhhheeeee...hhhhhhhhhhhhh....eeeeehhhhheee..eee.hhhhh..hhh.eeeee.hhhhhh.hhh.eee..........hhhhhhhhhhhhhhhh.hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------FCP1  PDB: A:86-244 UniProt: 86-244                                                                                                                            ----------- PROSITE
               Transcript 1 Exon 1.10a  PDB: A:77-107      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:220-255           Transcript 1
                 3l0c A  77 QYLLPEAKAQDSDKICVVIDLDETLVHSSFKPVNNADFIIPVEIDGVVHQVYVLKRPHVDEFLQRMGELFECVLFTASLAKYADPVADLLDKWGAFRARLFRESCVFHRGNYVKDLSRLGRDLRRVLILANSPASYVFHPDNAVPVASWFDNMSDTELHDLLPFFEQLSRVDDVYSVLR 255
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246

Chain B from PDB  Type:PROTEIN  Length:179
 aligned with CTDS1_HUMAN | Q9GZU7 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:179
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246         
          CTDS1_HUMAN    77 QYLLPEAKAQDSDKICVVIDLDETLVHSSFKPVNNADFIIPVEIDGVVHQVYVLKRPHVDEFLQRMGELFECVLFTASLAKYADPVADLLDKWGAFRARLFRESCVFHRGNYVKDLSRLGRDLRRVLILDNSPASYVFHPDNAVPVASWFDNMSDTELHDLLPFFEQLSRVDDVYSVLR 255
               SCOP domains d3l0cb_ B: automated matches                                                                                                                                                        SCOP domains
               CATH domains 3l0cB00 B:77-255  [code=3.40.50.1000, no name defined]                                                                                                                              CATH domains
           Pfam domains (1) --------------NIF-3l0cB01 B:91-251                                                                                                                                             ---- Pfam domains (1)
           Pfam domains (2) --------------NIF-3l0cB02 B:91-251                                                                                                                                             ---- Pfam domains (2)
         Sec.struct. author .......hhhhh...eeee......eeee........eeeeeee..eeeeeeeee..hhhhhhhhhhhhheeeee...hhhhhhhhhhhhh....eeeeehhhhheee..eee.hhhhh..hhh.eeeee.hhhhhh.hhh.eee..........hhhhhhhhhhhhhh...hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------FCP1  PDB: B:86-244 UniProt: 86-244                                                                                                                            ----------- PROSITE
               Transcript 1 Exon 1.10a  PDB: B:77-107      Exon 1.11a         Exon 1.12b  PDB: B:127-157     Exon 1.13c  PDB: B:158-219 UniProt: 158-219                   Exon 1.14f  PDB: B:220-255           Transcript 1
                 3l0c B  77 QYLLPEAKAQDSDKICVVIDLDETLVHSSFKPVNNADFIIPVEIDGVVHQVYVLKRPHVDEFLQRMGELFECVLFTASLAKYADPVADLLDKWGAFRARLFRESCVFHRGNYVKDLSRLGRDLRRVLILANSPASYVFHPDNAVPVASWFDNMSDTELHDLLPFFEQLSRVDDVYSVLR 255
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: HAD-like (349)

Superfamily: HAD-like (349)

Family: NLI interacting factor-like phosphatase (10)

Protein domain: automated matches (8)

Human (Homo sapiens) [TaxId: 9606] (8)

1a	d3l0ca_	A:
1b	d3l0cb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1000, no name defined] (211)

Human (Homo sapiens) (42)

1a	3l0cA00	A:77-255
1b	3l0cB00	B:77-255

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HAD (186)

Family: NIF (7)

Homo sapiens (Human) (6)

1a	NIF-3l0cB01	B:91-251
1b	NIF-3l0cB02	B:91-251

Asymmetric Unit(hide GO term definitions)

Chain A,B (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.

Asymmetric Unit
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	3l0c
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	CTDS1_HUMAN \| Q9GZU7
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	3.1.3.16
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UniProtKB/Swiss-Prot
	CTDS1_HUMAN \| Q9GZU7	:	1t9z 1ta0 2ghq 2ght 3l0b 3l0y 3pgl 4ygy 4yh1

1ta0	SCP1 APO STRUCTURE
2ghq	SCP1-CTD COMPLEX WITH PHOSPHORYLATION AT BOTH SER2 AND SER5
2ght	SCP1-CTD COMPLEX WITH PHOSPHORYLATION AT SER5
3l0b

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

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