3LLA - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE ALPHA-KINASE DOMAIN OF MYOSIN HEAVY CHAIN KINASE A COMPLEX WITH AMPPCP

Authors :   Q. Ye, Z. Jia

Date :   28 Jan 10 (Deposition) - 16 Mar 10 (Release) - 16 Mar 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.11

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

Keywords :   Protein Kinase Like Fold, Atp-Binding, Kinase, Nucleotide- Binding, Serine/Threonine-Protein Kinase, Alpha-Kinase, Coiled Coil, Wd Repeat, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Q. Ye, S. W. Crawley, Y. Yang, G. P. Cote, Z. Jia
Crystal Structure Of The {Alpha}-Kinase Domain Of Dictyostelium Myosin Heavy Chain Kinase A.
Sci. Signal. V. 3 Ra17 2010
PubMed-ID: 20197546 | Reference-DOI: 10.1126/SCISIGNAL.2000525

Molecule 1 - MYOSIN HEAVY CHAIN KINASE A
	Chains	:	A, B
	EC Number	:	2.7.11.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 552-841
	Gene	:	DDB_G0291231, MHCKA, MHKA
	Organism Common	:	SLIME MOLD
	Organism Scientific	:	DICTYOSTELIUM DISCOIDEUM
	Organism Taxid	:	44689
	Strain	:	AX3
	Synonym	:	MHCK-A

		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 (3, 6)

No.	Name	Count	Type	Full Name
1	ACP	2	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2	PO4	2	Ligand/Ion	PHOSPHATE ION
3	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	ACP	1	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2	PO4	1	Ligand/Ion	PHOSPHATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	ACP	1	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2	PO4	1	Ligand/Ion	PHOSPHATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:742 , HIS A:794 , CYS A:796 , CYS A:800	BINDING SITE FOR RESIDUE ZN A 2002
2	AC2	SOFTWARE	HOH A:112 , HOH A:148 , HOH A:181 , HOH A:202 , HOH A:236 , HOH A:241 , ALA A:587 , GLU A:588 , GLY A:589 , ALA A:590 , LEU A:591 , ARG A:592 , VAL A:643 , LYS A:645 , GLU A:713 , PRO A:714 , LEU A:716 , PHE A:720 , LYS A:722 , ASP A:766	BINDING SITE FOR RESIDUE ACP A 1304
3	AC3	SOFTWARE	HOH A:6 , HOH A:128 , HOH A:355 , LYS A:684 , ARG A:734 , SER A:735 , THR A:736	BINDING SITE FOR RESIDUE PO4 A 5954
4	AC4	SOFTWARE	HIS B:742 , HIS B:794 , CYS B:796 , CYS B:800	BINDING SITE FOR RESIDUE ZN B 2001
5	AC5	SOFTWARE	HOH B:65 , HOH B:138 , HOH B:190 , HOH B:215 , HOH B:256 , HOH B:300 , ALA B:587 , GLU B:588 , GLY B:589 , ALA B:590 , LEU B:591 , ARG B:592 , VAL B:643 , LYS B:645 , GLU B:713 , PRO B:714 , LEU B:716 , ASP B:766	BINDING SITE FOR RESIDUE ACP B 1303
6	AC6	SOFTWARE	HOH B:129 , HOH B:284 , LYS B:684 , ARG B:734 , SER B:735 , THR B:736	BINDING SITE FOR RESIDUE PO4 B 5953

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

Asymmetric Unit

No.	Residues
1	Ser A:554	-	Glu A:555
2	Gly A:611	-	Thr A:612
3	Phe A:617	-	Pro A:618
4	Phe B:617	-	Pro B:618
5	Lys B:808	-	Leu B:809

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALPHA_KINASE	PS51158	Alpha-type protein kinase domain profile.	MHCKA_DICDI	564-808	2	A:564-808 B:564-808

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALPHA_KINASE	PS51158	Alpha-type protein kinase domain profile.	MHCKA_DICDI	564-808	1	A:564-808 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALPHA_KINASE	PS51158	Alpha-type protein kinase domain profile.	MHCKA_DICDI	564-808	1	- B:564-808

(no "Exon" information available for 3LLA)

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:255
 aligned with MHCKA_DICDI | P42527 from UniProtKB/Swiss-Prot  Length:1146

    Alignment length:258
                                   561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801        
          MHCKA_DICDI   552 ISSETGEMGILWEFDPIINKWIRLSMKLKVERKPFAEGALREAYHTVSLGVGTDENYPLGTTTKLFPPIEMISPISKNNEAMTQLKNGTKFVLKLYKKEAEQQASRELYFEDVKMQMVCRDWGNKFNQKKPPKKIEFLMSWVVELIDRSPSSNGQPILCSIEPLLVGEFKKNNSNYGAVLTNRSTPQAFSHFTYELSNKQMIVVDIQGVDDLYTDPQIHTPDGKGFGLGNLGKAGINKFITTHKCNAVCALLDLDVKL 809
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeeee....eeeeeeeeeee.....ee...eeeeeeeeeeeee.........-....hhhhh.......hhhhhh....eeeeeee..--....hhhhhhhhhhhhhhhhhhhhhhhh.......ee...eeeee...........eeeeeee......ee............hhhhhhhhhhhhhh....eee..eee..eee..eee...........hhhhhhhhhhhhh..hhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------ALPHA_KINASE  PDB: A:564-808 UniProt: 564-808                                                                                                                                                                                                        - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3lla A 552 ISSETGEMGILWEFDPIINKWIRLSMKLKVERKPFAEGALREAYHTVSLGVGTDENYPLGTT-KLFPPIEMISPISKNNEAMTQLKNGTKFVLKLYKK--EQQASRELYFEDVKMQMVCRDWGNKFNQKKPPKKIEFLMSWVVELIDRSPSSNGQPILCSIEPLLVGEFKKNNSNYGAVLTNRSTPQAFSHFTYELSNKQMIVVDIQGVDDLYTDPQIHTPDGKGFGLGNLGKAGINKFITTHKCNAVCALLDLDVKL 809
                                   561       571       581       591       601       611 | |   621       631       641       | -|      661       671       681       691       701       711       721       731       741       751       761       771       781       791       801        
                                                                                       613 |                               649  |                                                                                                                                                             
                                                                                         615                                  652

Chain B from PDB  Type:PROTEIN  Length:254
 aligned with MHCKA_DICDI | P42527 from UniProtKB/Swiss-Prot  Length:1146

    Alignment length:260
                                   561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811
          MHCKA_DICDI   552 ISSETGEMGILWEFDPIINKWIRLSMKLKVERKPFAEGALREAYHTVSLGVGTDENYPLGTTTKLFPPIEMISPISKNNEAMTQLKNGTKFVLKLYKKEAEQQASRELYFEDVKMQMVCRDWGNKFNQKKPPKKIEFLMSWVVELIDRSPSSNGQPILCSIEPLLVGEFKKNNSNYGAVLTNRSTPQAFSHFTYELSNKQMIVVDIQGVDDLYTDPQIHTPDGKGFGLGNLGKAGINKFITTHKCNAVCALLDLDVKLGG 811
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------Alpha_kinase-3llaB01 B:586-   800                                                                                                                                                                                      ----------- Pfam domains (1)
           Pfam domains (2) ----------------------------------Alpha_kinase-3llaB02 B:586-   800                                                                                                                                                                                      ----------- Pfam domains (2)
         Sec.struct. author ......eeeeeeeee....eeeeeeeeeee.....ee...eeeeeeeeeeeee........---...hhhhh.......hhhhhh....eeeeeee..--....hhhhhhhhhhhhhhhhhhhhhhhh.......ee...eeeee......-....eeeeeee....................hhhhhhhhhhhhhh....eee.......ee...eee...........hhhhhhhhhhhhh..hhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------ALPHA_KINASE  PDB: B:564-808 UniProt: 564-808                                                                                                                                                                                                        --- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lla B 552 ISSETGEMGILWEFDPIINKWIRLSMKLKVERKPFAEGALREAYHTVSLGVGTDENYPLGT---LFPPIEMISPISKNNEAMTQLKNGTKFVLKLYKK--EQQASRELYFEDVKMQMVCRDWGNKFNQKKPPKKIEFLMSWVVELIDRSPS-NGQPILCSIEPLLVGEFKKNNSNYGAVLTNRSTPQAFSHFTYELSNKQMIVVDIQGVDDLYTDPQIHTPDGKGFGLGNLGKAGINKFITTHKCNAVCALLDLDVKLGG 811
                                   561       571       581       591       601       611|   |  621       631       641       | -|      661       671       681       691       701| |    711       721       731       741       751       761       771       781       791       801       811
                                                                                      612 616                              649  |                                               702 |                                                                                                           
                                                                                                                              652                                                 704

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 '\|'

(no "SCOP Domain" information available for 3LLA)

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Alpha_kinase] (5)

Family: Alpha_kinase (5)

Dictyostelium discoideum (Slime mold) (5)

1a	Alpha_kinase-3llaB01	B:586-800
1b	Alpha_kinase-3llaB02	B:586-800

Asymmetric Unit(hide GO term definitions)

Chain A,B (MHCKA_DICDI | P42527)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016887	ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
	GO:0051015	actin filament binding	Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0045159	myosin II binding	Interacting selectively and non-covalently with a class II myosin, any member of the class of 'conventional' double-headed myosins that includes muscle myosin.
	GO:0016905	myosin heavy chain kinase activity	Catalysis of the reaction: ATP + myosin-heavy-chain = ADP + myosin-heavy-chain phosphate.
	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: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: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:0051764	actin crosslink formation	The process in which two or more actin filaments are connected together by proteins that act as crosslinks between the filaments. The crosslinked filaments may be on the same or differing axes.
	GO:0051017	actin filament bundle assembly	The assembly of actin filament bundles; actin filaments are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness.
	GO:0006935	chemotaxis	The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
	GO:0000281	mitotic cytokinesis	A cell cycle process that results in the division of the cytoplasm of a cell after mitosis, resulting in the separation of the original cell into two daughter cells.
	GO:0031037	myosin II filament disassembly	The disassembly of a bipolar filament composed of myosin II molecules.
	GO:0018107	peptidyl-threonine phosphorylation	The phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.
	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:0046777	protein autophosphorylation	The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
	GO:0051260	protein homooligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
cellular component
	GO:0005938	cell cortex	The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		ACP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:611 - Thr A:612	[ RasMol ]
		Lys B:808 - Leu B:809	[ RasMol ]
		Phe A:617 - Pro A:618	[ RasMol ]
		Phe B:617 - Pro B:618	[ RasMol ]
		Ser A:554 - Glu A:555	[ RasMol ]

Biological Units
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Access by PDB/NDB ID
	3lla
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Access by UniProt ID/Accession number
	MHCKA_DICDI \| P42527
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	2.7.11.7
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		Pathway	:	KEGG \| MetaCyc

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		Disease Information	:	OMIM

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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	MHCKA_DICDI \| P42527
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UniProtKB/Swiss-Prot
	MHCKA_DICDI \| P42527	:	3lkm 3lmh 3lmi 3pdt 4zme 4zmf 4zs4 5dyj 5e4h 5e9e

3lkm	THE SAME PROTEIN COMPLEXED WITH AMP
3lmh	THE SAME PROTEIN COMPLEXED WITH ADP
3lmi	THE SAME PROTEIN COMPLEX WITH ATP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (23, 23)

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