2I6L - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN MITOGEN ACTIVATED PROTEIN KINASE 6 (MAPK6)

Authors :   P. Filippakopoulos, A. P. Turnbull, P. Savitsky, O. Fedorov, G. Berridge, S. Das, J. Elkins, M. Soundararajan, X. W. Yang, D. Doyle, E. Papagrigoriou, A. C. W. Pike, G. Bunkonczi, E. Ugochukwu, J. Debreczeni, F. Von Delft, A. Edwards, C. Arrowsmith, M. Sundstrom S. Knapp, Structural Genomics Consortium (Sgc)

Date :   29 Aug 06 (Deposition) - 12 Sep 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

Chains :   Asym./Biol. Unit : A,B

Keywords :   Mapk6, Erk3, Mitogen Activated Protein Kinase 6, Extracellular Signal Regulated Kinase 3, Serine Phosphorylation, Threonine Phosphorylation, Structural Genomics, Structural Genomics Consortium, Sgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Filippakopoulos, A. P. Turnbull, P. Savitsky, O. Fedorov, G. Berridge, S. Das, J. Elkins, M. Soundararajan, X. W. Yang, D. Doyle, E. Papagrigoriou, A. C. W. Pike, G. Bunkonczi, E. Ugochukwu, J. Debreczeni, F. Von Delft, A. Edwards, C. Arrowsmith, M. Sundstrom, S. Knapp
Crystal Structure Of The Human Mitogen Activated Protein Kinase 6
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - MITOGEN-ACTIVATED PROTEIN KINASE 6
	Chains	:	A, B
	EC Number	:	2.7.11.24
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	BL21 (DE3)-R3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MAPK6, ERK3, PRKM6
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	EXTRACELLULAR SIGNAL-REGULATED KINASE 3, ERK-3, MAP KINASE ISOFORM P97, P97- MAPK

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2I6L)

(no "Site" information available for 2I6L)

(no "SS Bond" information available for 2I6L)

(no "Cis Peptide Bond" information available for 2I6L)

Asymmetric/Biological Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_042256	L	290	V	MK06_HUMAN	Polymorphism	35697691	A/B	V	290	V

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

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	MK06_HUMAN	26-50	2	A:26-50 B:26-50
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	MK06_HUMAN	148-160	2	A:148-160 B:148-160

Asymmetric/Biological Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000261845	1	ENSE00001559491	chr15:52311417-52311573	157	MK06_HUMAN	-	0	0	-	-
1.2	ENST00000261845	2	ENSE00000942191	chr15:52338027-52339212	1186	MK06_HUMAN	1-185	185	2	A:13-178 (gaps) B:21-172 (gaps)	166 152
1.3	ENST00000261845	3	ENSE00000931423	chr15:52342190-52342334	145	MK06_HUMAN	186-234	49	2	A:187-234 B:187-234	48 48
1.4	ENST00000261845	4	ENSE00000688875	chr15:52350830-52350994	165	MK06_HUMAN	234-289	56	2	A:234-289 B:234-289 (gaps)	56 56
1.5	ENST00000261845	5	ENSE00000688876	chr15:52353496-52353697	202	MK06_HUMAN	289-356	68	2	A:289-321 B:289-320	33 32
1.6	ENST00000261845	6	ENSE00000884734	chr15:52356099-52358462	2364	MK06_HUMAN	356-721	366	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:292
 aligned with MK06_HUMAN | Q16659 from UniProtKB/Swiss-Prot  Length:721

    Alignment length:309
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312         
           MK06_HUMAN    13 GFDLGSRYMDLKPLGCGGNGLVFSAVDNDCDKRVAIKKIVLTDPQSVKHALREIKIIRRLDHDNIVKVFEILGPSGSQLTDDVGSLTELNSVYIVQEYMETDLANVLEQGPLLEEHARLFMYQLLRGLKYIHSANVLHRDLKPANLFINTEDLVLKIGDFGLARIMDPHYSHKGHLSEGLVTKWYRSPRLLLSPNNYTKAIDMWAAGCIFAEMLTGKTLFAGAHELEQMQLILESIPVVHEEDRQELLSVIPVYIRNDMTEPHKPLTQLLPGISREALDFLEQILTFSPMDRLTAEEALSHPYMSIYSF 321
               SCOP domains d2i6la_ A: aut     omated matches                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2i6lA01 A:13-1     12 Phosphorylase Kinase; domain 1                                                2i6lA02 A:113-321 Transferase(Phosphotransferase) domain 1                                                                                                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeeeee.-----..eeeeee.....eeeeeeee..hhhhhhhhhhhhhhhhh........eeeee.........----.....eeeeeee...eehhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eeee....eeee.........--------..hhhhh.....hhhhhhh....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhh.....hhhhhh...hhhhhhhhhh....hhhhh.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V------------------------------- SAPs(SNPs)
                    PROSITE -------------PROTEIN_KINASE_ATP       -------------------------------------------------------------------------------------------------PROTEIN_KINAS----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:13-178 (gaps) UniProt: 1-185 [INCOMPLETE]                                                                                                                   Exon 1.3  PDB: A:187-234 UniProt: 186-234        ------------------------------------------------------Exon 1.5  PDB: A:289-321          Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.4  PDB: A:234-289 UniProt: 234-289               -------------------------------- Transcript 1 (2)
                 2i6l A  13 GFDLGSRYMDLKPL-----GLVFSAVDNDCDKRVAIKKIVLTDPQSVKHALREIKIIRRLDHDNIVKVFEILGPSGSQLTD----LTELNSVYIVQEYMETDLANVLEQGPLLEEHARLFMYQLLRGLKYIHSANVLHRDLKPANLFINTEDLVLKIGDFGLARIM--------HLSEGLVTKWYRSPRLLLSPNNYTKAIDMWAAGCIFAEMLTGKTLFAGAHELEQMQLILESIPVVHEEDRQELLSVIPVYIRNDMTEPHKPLTQLLPGISREAVDFLEQILTFSPMDRLTAEEALSHPYMSIYSF 321
                                    22   |    32        42        52        62        72        82        92|    | 102       112       122       132       142       152       162       172     |   -    |  192       202       212       222       232       242       252       262       272       282       292       302       312         
                                        26    32                                                           93   98                                                                             178      187

Chain B from PDB  Type:PROTEIN  Length:269
 aligned with MK06_HUMAN | Q16659 from UniProtKB/Swiss-Prot  Length:721

    Alignment length:300
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320
           MK06_HUMAN    21 MDLKPLGCGGNGLVFSAVDNDCDKRVAIKKIVLTDPQSVKHALREIKIIRRLDHDNIVKVFEILGPSGSQLTDDVGSLTELNSVYIVQEYMETDLANVLEQGPLLEEHARLFMYQLLRGLKYIHSANVLHRDLKPANLFINTEDLVLKIGDFGLARIMDPHYSHKGHLSEGLVTKWYRSPRLLLSPNNYTKAIDMWAAGCIFAEMLTGKTLFAGAHELEQMQLILESIPVVHEEDRQELLSVIPVYIRNDMTEPHKPLTQLLPGISREALDFLEQILTFSPMDRLTAEEALSHPYMSIYS 320
               SCOP domains d2i6lb   _ B: automated matches                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2i6lB0   1 B:21-112 Phosphorylase Kinase; domain 1                                          2i6lB02 B:113-320 Transferase(Phosphotransferase) domain 1                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee.---....eeeeee....eeeeeeee...hhhhhhhhhhhhhhhhhh.......eeeee.........---------.eeeeee...eehhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eeee....eeee...--------------..hhhhh.....hhhhhhh....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.....hhhhhhhhhhhh..-----......hhhhhh...hhhhhhhhhh....hhhhh.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V------------------------------ SAPs(SNPs)
                    PROSITE -----PROTEIN_KINASE_ATP       -------------------------------------------------------------------------------------------------PROTEIN_KINAS---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:21-172 (gaps) UniProt: 1-185 [INCOMPLETE]                                                                                                           Exon 1.3  PDB: B:187-234 UniProt: 186-234        ------------------------------------------------------Exon 1.5  PDB: B:289-320         Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.4  PDB: B:234-289 (gaps) UniProt: 234-289        ------------------------------- Transcript 1 (2)
                 2i6l B  21 MDLKPL---GNGLVFSAVDNDCDKRVAIKKIVLTDPQSVKHALREIKIIRRLDHDNIVKVFEILGPSGSQLTD---------SVYIVQEYMETDLANVLEQGPLLEEHARLFMYQLLRGLKYIHSANVLHRDLKPANLFINTEDLVLKIGDF--------------HLSEGLVTKWYRSPRLLLSPNNYTKAIDMWAAGCIFAEMLTGKTLFAGAHELEQMQLILESIPVVHEEDRQELLSVIPV-----MTEPHKPLTQLLPGISREAVDFLEQILTFSPMDRLTAEEALSHPYMSIYS 320
                                 |  30        40        50        60        70        80        90  |      -  |    110       120       130       140       150       160       170 |       -      |190       200       210       220       230       240       250       260    |    -|      280       290       300       310       320
                                26  30                                                             93       103                                                                  172            187                                                                           265   271

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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

Fold: Protein kinase-like (PK-like) (2589)

Superfamily: Protein kinase-like (PK-like) (2589)

Family: automated matches (529)

Protein domain: automated matches (529)

Human (Homo sapiens) [TaxId: 9606] (438)

1a	d2i6la_	A:
1b	d2i6lb_	B:

Asymmetric/Biological Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Phosphorylase Kinase; domain 1 (1392)

Homologous Superfamily: Phosphorylase Kinase; domain 1 (1392)

Human (Homo sapiens) (1036)

1a	2i6lA01	A:13-112
1b	2i6lB01	B:21-112

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Transferase(Phosphotransferase); domain 1 (1379)

Homologous Superfamily: Transferase(Phosphotransferase) domain 1 (1379)

Human (Homo sapiens) (1049)

2a	2i6lB02	B:113-320
2b	2i6lA02	A:113-321

(no "Pfam Domain" information available for 2I6L)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (MK06_HUMAN | Q16659)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004707	MAP kinase activity	Catalysis of the reaction: protein + ATP = protein phosphate + ADP. This reaction is the phosphorylation of proteins. Mitogen-activated protein kinase; a family of protein kinases that perform a crucial step in relaying signals from the plasma membrane to the nucleus. They are activated by a wide range of proliferation- or differentiation-inducing signals; activation is strong with agonists such as polypeptide growth factors and tumor-promoting phorbol esters, but weak (in most cell backgrounds) by stress stimuli.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
	GO:0004672	protein kinase activity	Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
	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.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0000165	MAPK cascade	An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
	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:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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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