3QY2 - JenaLib

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Description

Title :   CRYSTAL STRUCTURE OF THE P93A MONOMER MUTANT OF S. CEREVISIAE CKS1

Authors :   E. R. M. Balog, O. C. Saetern, W. Finch, C. O. Hoeft, V. Thai, S. L. Harvey, D. K. Kellogg, S. M. Rubin

Date :   02 Mar 11 (Deposition) - 29 Jun 11 (Release) - 10 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.59

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

Keywords :   Protein Kinase Activator, Ubiquitin Binding, Transcription, Cdc28 Kinase, Cell Cycle, Cyclin-Dependent Kinase, Transferase Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. R. Balog, O. C. Saetern, W. Finch, C. O. Hoeft, V. Thai, S. L. Harvey, D. R. Kellogg, S. M. Rubin
The Structure Of A Monomeric Mutant Cks Protein Reveals Multiple Functions For A Conserved Hinge-Region Proline.
J. Mol. Biol. V. 411 520 2011
PubMed-ID: 21704044 | Reference-DOI: 10.1016/J.JMB.2011.05.045

Compounds

Molecule 1 - CYCLIN-DEPENDENT KINASES REGULATORY SUBUNIT
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 1-117
	Gene	:	CKS1, YBR135W, YBR1011
	Mutation	:	YES
	Organism Common	:	BREWER'S YEAST,LAGER BEER YEAST,YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	CELL DIVISION CONTROL PROTEIN CKS1

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (1, 1)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	FLC	1	Ligand/Ion	CITRATE ANION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	FLC	-1	Ligand/Ion	CITRATE ANION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	FLC	1	Ligand/Ion	CITRATE ANION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	FLC	2	Ligand/Ion	CITRATE ANION

Biological Unit 4 (1, 2)

No.	Name	Count	Type	Full Name
1	FLC	2	Ligand/Ion	CITRATE ANION

Sites (1, 1)

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:2 , ARG B:33 , ARG B:42 , GLN B:81 , SER B:82 , TRP B:85 , HOH B:131	BINDING SITE FOR RESIDUE FLC B 3585

SS Bonds (0, 0)

(no "SS Bond" information available for 3QY2)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 3QY2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 3QY2)

PROSITE Motifs (2, 4)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CKS_1	PS00944	Cyclin-dependent kinases regulatory subunits signature 1.	CKS1_YEAST	30-48	2	A:30-48 B:30-48
2	CKS_2	PS00945	Cyclin-dependent kinases regulatory subunits signature 2.	CKS1_YEAST	91-101	2	A:91-101 B:91-101

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CKS_1	PS00944	Cyclin-dependent kinases regulatory subunits signature 1.	CKS1_YEAST	30-48	1	A:30-48 -
2	CKS_2	PS00945	Cyclin-dependent kinases regulatory subunits signature 2.	CKS1_YEAST	91-101	1	A:91-101 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CKS_1	PS00944	Cyclin-dependent kinases regulatory subunits signature 1.	CKS1_YEAST	30-48	1	- B:30-48
2	CKS_2	PS00945	Cyclin-dependent kinases regulatory subunits signature 2.	CKS1_YEAST	91-101	1	- B:91-101

Biological Unit 3 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CKS_1	PS00944	Cyclin-dependent kinases regulatory subunits signature 1.	CKS1_YEAST	30-48	4	A:30-48 B:30-48
2	CKS_2	PS00945	Cyclin-dependent kinases regulatory subunits signature 2.	CKS1_YEAST	91-101	4	A:91-101 B:91-101

Biological Unit 4 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CKS_1	PS00944	Cyclin-dependent kinases regulatory subunits signature 1.	CKS1_YEAST	30-48	4	A:30-48 B:30-48
2	CKS_2	PS00945	Cyclin-dependent kinases regulatory subunits signature 2.	CKS1_YEAST	91-101	4	A:91-101 B:91-101

Exons (1, 2)

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YBR135W	1	YBR135W.1	II:504848-505300	453	CKS1_YEAST	1-150	150	2	A:1-105 B:7-111	105 105

Sequences/Alignments

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:105
 aligned with CKS1_YEAST | P20486 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:105
                                    10        20        30        40        50        60        70        80        90       100     
           CKS1_YEAST     1 MYHHYHAFQGRKLTDQERARVLEFQDSIHYSPRYSDDNYEYRHVMLPKAMLKVIPSDYFNSEVGTLRILTEDEWRGLGITQSLGWEHYECHAPEPHILLFKRPLN 105
               SCOP domains d3qy2a_ A: automated matches                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhee...ee...eeeeeee.hhhhhhhhhhhhh..........hhhhhhhh........eee........eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------CKS_1  PDB: A:30-48------------------------------------------CKS_2      ---- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-105 UniProt: 1-150 [INCOMPLETE]                                                        Transcript 1
                 3qy2 A   1 MYHHYHAFQGRKLTDQERARVLEFQDSIHYSPRYSDDNYEYRHVMLPKAMLKVIPSDYFNSEVGTLRILTEDEWRGLGITQSLGWEHYECHAAEPHILLFKRPLN 105
                                    10        20        30        40        50        60        70        80        90       100

Chain B from PDB  Type:PROTEIN  Length:105
 aligned with CKS1_YEAST | P20486 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:105
                                    16        26        36        46        56        66        76        86        96       106     
           CKS1_YEAST     7 AFQGRKLTDQERARVLEFQDSIHYSPRYSDDNYEYRHVMLPKAMLKVIPSDYFNSEVGTLRILTEDEWRGLGITQSLGWEHYECHAPEPHILLFKRPLNYEAELR 111
               SCOP domains d3qy2b_ B: automated matches                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------CKS-3qy2B01 B:27-105                                                           ------ Pfam domains (1)
           Pfam domains (2) --------------------CKS-3qy2B02 B:27-105                                                           ------ Pfam domains (2)
         Sec.struct. author .......hhhhhhhhhhhhhhhee...ee...eeeeeee.hhhhhhhhhhhhh..........hhhhhhhh........eee........eeeeeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------CKS_1  PDB: B:30-48------------------------------------------CKS_2      ---------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:7-111 UniProt: 1-150 [INCOMPLETE]                                                        Transcript 1
                 3qy2 B   7 AFQGRKLTDQERARVLEFQDSIHYSPRYSDDNYEYRHVMLPKAMLKVIPSDYFNSEVGTLRILTEDEWRGLGITQSLGWEHYECHAAEPHILLFKRPLNYEAELR 111
                                    16        26        36        46        56        66        76        86        96       106

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, 2)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Cell cycle regulatory proteins (11)

Superfamily: Cell cycle regulatory proteins (11)

Family: Cell cycle regulatory proteins (11)

Protein domain: automated matches (2)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (1)

1a	d3qy2a_	A:
1b	d3qy2b_	B:

CATH Domains (0, 0)

(no "CATH Domain" information available for 3QY2)

Pfam Domains (1, 2)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: CKS] (3)

Family: CKS (3)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (2)

1a	CKS-3qy2B01	B:27-105
1b	CKS-3qy2B02	B:27-105

Gene Ontology (14, 14)

Asymmetric Unit(hide GO term definitions)

Chain A,B (CKS1_YEAST | P20486)

molecular function
	GO:0016538	cyclin-dependent protein serine/threonine kinase regulator activity	Modulates the activity of a cyclin-dependent protein serine/threonine kinase, enzymes of the protein kinase family that are regulated through association with cyclins and other proteins.
	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: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:0030295	protein kinase activator activity	Binds to and increases the activity of a protein kinase, an enzyme which phosphorylates a protein.
	GO:0043130	ubiquitin binding	Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
biological process
	GO:0032147	activation of protein kinase activity	Any process that initiates the activity of an inactive protein kinase.
	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:0051301	cell division	The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
	GO:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0007346	regulation of mitotic cell cycle	Any process that modulates the rate or extent of progress through the mitotic cell cycle.
	GO:0060303	regulation of nucleosome density	Any process that modulates the number of nucleosomes in a given region of a chromosome.
	GO:0045859	regulation of protein kinase activity	Any process that modulates the frequency, rate or extent of protein kinase activity.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0000307	cyclin-dependent protein kinase holoenzyme complex	Cyclin-dependent protein kinases (CDKs) are enzyme complexes that contain a kinase catalytic subunit associated with a regulatory cyclin partner.

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Related Entries

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	CKS1_YEAST \| P20486	:	1qb3 4lpa

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