2I53 - JenaLib

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Title :   CRYSTAL STRUCTURE OF CYCLIN K

Authors :   K. Baek, R. S. Brown, G. Birrane, J. A. A. Ladias

Date :   23 Aug 06 (Deposition) - 02 Jan 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym./Biol. Unit : A

Keywords :   Cell Cycle, Transcription, Cyclin K, Cyclin Box, Cdk9, Positive Transcription Elongation Factor, P-Tefb (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Baek, R. S. Brown, G. Birrane, J. A. Ladias
Crystal Structure Of Human Cyclin K, A Positive Regulator Of Cyclin-Dependent Kinase 9.
J. Mol. Biol. V. 366 563 2007
PubMed-ID: 17169370 | Reference-DOI: 10.1016/J.JMB.2006.11.057
(for further references see the PDB file header)

Molecule 1 - CYCLIN K
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PGEX-2T
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL DOMAIN, RESIDUES 11-267
	Gene	:	CCNK
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 3)

No.	Name	Count	Type	Full Name
1	ACT	3	Ligand/Ion	ACETATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:48 , TYR A:49 , ARG A:92 , ARG A:232 , HOH A:514	BINDING SITE FOR RESIDUE ACT A 301
2	AC2	SOFTWARE	HIS A:85 , SER A:86 , GLN A:89 , HOH A:502	BINDING SITE FOR RESIDUE ACT A 302
3	AC3	SOFTWARE	MET A:230 , TYR A:231 , ARG A:232 , HOH A:328	BINDING SITE FOR RESIDUE ACT A 303

(no "SS Bond" information available for 2I53)

(no "Cis Peptide Bond" information available for 2I53)

(no "SAP(SNP)/Variant" information available for 2I53)

(no "PROSITE Motif" information available for 2I53)

Asymmetric/Biological Unit (7, 7)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000389879	1	ENSE00001389751	chr14:99947739-99947816	78	CCNK_HUMAN	-	0	0	-	-
1.2a	ENST00000389879	2a	ENSE00001189086	chr14:99958963-99959211	249	CCNK_HUMAN	1-66	66	1	A:14-66	53
1.3	ENST00000389879	3	ENSE00000660281	chr14:99959851-99959932	82	CCNK_HUMAN	66-93	28	1	A:66-93	28
1.4	ENST00000389879	4	ENSE00000660282	chr14:99961835-99961966	132	CCNK_HUMAN	94-137	44	1	A:94-137	44
1.5	ENST00000389879	5	ENSE00000660283	chr14:99967103-99967208	106	CCNK_HUMAN	138-173	36	1	A:138-173	36
1.6	ENST00000389879	6	ENSE00000660284	chr14:99967693-99967750	58	CCNK_HUMAN	173-192	20	1	A:173-192	20
1.7b	ENST00000389879	7b	ENSE00000660285	chr14:99968544-99968713	170	CCNK_HUMAN	192-249	58	1	A:192-249	58
1.8c	ENST00000389879	8c	ENSE00001383836	chr14:99969056-99969321	266	CCNK_HUMAN	249-337	89	1	A:249-267	19
1.10	ENST00000389879	10	ENSE00001484271	chr14:99969948-99969981	34	CCNK_HUMAN	338-349	12	0	-	-
1.12	ENST00000389879	12	ENSE00001335508	chr14:99973413-99973484	72	CCNK_HUMAN	349-373	25	0	-	-
1.13b	ENST00000389879	13b	ENSE00001335506	chr14:99976494-99977851	1358	CCNK_HUMAN	373-580	208	0	-	-

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:254
 aligned with CCNK_HUMAN | O75909 from UniProtKB/Swiss-Prot  Length:580

    Alignment length:254
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263    
           CCNK_HUMAN    14 SANLDHTKPCWYWDKKDLAHTPSQLEGLDPATEARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDIIKTARSLLNDVQFGQFGDDPKEEVMVLERILLQTIKFDLQVEHPYQFLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKPMYRRWWEQFVQDVPVDVLEDICHQILDLYSQGKQQMPH 267
               SCOP domains d2i53a1 A:14-157 Cyclin K                                                                                                                       d2i53a2 A:158-267 Cyclin K                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhh......hhhhhh....hhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: A:14-66 UniProt: 1-66 [INCOMPLETE]   ---------------------------Exon 1.4  PDB: A:94-137 UniProt: 94-137     Exon 1.5  PDB: A:138-173            ------------------Exon 1.7b  PDB: A:192-249 UniProt: 192-249                ------------------ Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------Exon 1.3  PDB: A:66-93      -------------------------------------------------------------------------------Exon 1.6            --------------------------------------------------------Exon 1.8c           Transcript 1 (2)
                 2i53 A  14 SANLDHTKPCWYWDKKDLAHTPSQLEGLDPATEARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDIIKTARSLLNDVQFGQFGDDPKEEVMVLERILLQTIKFDLQVEHPYQFLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKPMYRRWWEQFVQDVPVDVLEDICHQILDLYSQGKQQMPH 267
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Cyclin-like (137)

Superfamily: Cyclin-like (137)

Family: Cyclin (117)

Protein domain: Cyclin K (1)

Human (Homo sapiens) [TaxId: 9606] (1)

1a	d2i53a1	A:14-157
1b	d2i53a2	A:158-267

(no "CATH Domain" information available for 2I53)

(no "Pfam Domain" information available for 2I53)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CCNK_HUMAN | O75909)

molecular function
	GO:0008353	RNA polymerase II carboxy-terminal domain kinase activity	Catalysis of the reaction: ATP + (DNA-directed RNA polymerase II) = ADP + phospho-(DNA-directed RNA polymerase II); phosphorylation occurs on residues in the carboxy-terminal domain (CTD) repeats.
	GO:0004693	cyclin-dependent protein serine/threonine kinase activity	Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate. This reaction requires the binding of a regulatory cyclin subunit and full activity requires stimulatory phosphorylation by a CDK-activating kinase (CAK).
	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: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:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
	GO:0004674	protein serine/threonine kinase activity	Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
biological process
	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: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:0044828	negative regulation by host of viral genome replication	A process in which a host organism stops, prevents or reduces the frequency, rate or extent of viral genome replication.
	GO:0071157	negative regulation of cell cycle arrest	Any process that decreases the rate, frequency, or extent of cell cycle arrest, the process in which the cell cycle is halted during one of the normal phases.
	GO:0045737	positive regulation of cyclin-dependent protein serine/threonine kinase activity	Any process that activates or increases the frequency, rate or extent of CDK activity.
	GO:2001165	positive regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues	Any process that activates or increases the frequency, rate or extent of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues.
	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:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0000079	regulation of cyclin-dependent protein serine/threonine kinase activity	Any process that modulates the frequency, rate or extent of cyclin-dependent protein serine/threonine kinase activity.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0042795	snRNA transcription from RNA polymerase II promoter	The synthesis of small nuclear RNA (snRNA) from a DNA template by RNA Polymerase II (Pol II), originating at a Pol II promoter.
	GO:0006368	transcription elongation from RNA polymerase II promoter	The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II.
	GO:0006366	transcription from RNA polymerase II promoter	The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0002944	cyclin K-CDK12 complex	A protein complex consisting of cyclin Kand cyclin-dependent kinase 12 (CDK12). Cyclins are characterized by periodicity in protein abundance throughout the cell cycle. Cyclin-dependent kinases represent a family of serine/threonine protein kinases that become active upon binding to a cyclin regulatory partner.
	GO:0002945	cyclin K-CDK13 complex	A protein complex consisting of cyclin Kand cyclin-dependent kinase 13 (CDK13). Cyclins are characterized by periodicity in protein abundance throughout the cell cycle. Cyclin-dependent kinases represent a family of serine/threonine protein kinases that become active upon binding to a cyclin regulatory partner.
	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/Biological Unit
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	CCNK_HUMAN \| O75909	:	4cxa 4nst 4un0 5acb 5efq

1bu2	1BU2 IS THE CRYSTAL STRUCTURE OF VIRAL CYCLIN FROM HERPESVIRUS SAIMIRI DETERMINED AT 3.00 ANGSTROM RESOLUTION
1jkw	1JKW IS THE CRYSTAL STRUCTURE OF CYCLIN MCS2 DETERMINED AT 2.60 ANGSTROM RESOLUTION
1kxu	1KXU IS THE CRYSTAL STRUCTURE OF CYCLIN H DETERMINED AT 2.60 ANGSTROM RESOLUTION
1vin	1VIN IS THE CRYSTAL STRUCTURE OF BOVINE CYCLIN A3 DETERMINED AT 2.00 ANGSTROM RESOLUTION

Description

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Ligands, Modified Residues, Ions (1, 3)

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Exons (7, 7)

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