3M10 - JenaLib

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Title :   SUBSTRATE-FREE FORM OF ARGININE KINASE

Authors :   M. S. Yousef, S. A. Clark, P. K. Pruett, T. Somasundaram, W. R. Ellington M. S. Chapman

Date :   03 Mar 10 (Deposition) - 16 Mar 10 (Release) - 23 Feb 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.73

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

Keywords :   Alpha-Beta, Atp-Binding, Kinase, Nucleotide-Binding, Guanidino Kinase, Phosphagen Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Niu, L. Bruschweiler-Li, O. Davulcu, J. J. Skalicky, R. Bruschweiler, M. S. Chapman
Arginine Kinase: Joint Crystallographic And Nmr Rdc Analyse Link Substrate-Associated Motions To Intrinsic Flexibility.
J. Mol. Biol. V. 405 479 2011
PubMed-ID: 21075117 | Reference-DOI: 10.1016/J.JMB.2010.11.007
(for further references see the PDB file header)

Molecule 1 - ARGININE KINASE
	Chains	:	A, B
	EC Number	:	2.7.3.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	ATLANTIC HORSESHOE CRAB
	Organism Scientific	:	LIMULUS POLYPHEMUS
	Organism Taxid	:	6850
	Synonym	:	AK

		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 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:124 , ARG A:126 , ARG A:229 , ARG A:280 , HOH A:512	BINDING SITE FOR RESIDUE SO4 A 400
2	AC2	SOFTWARE	ARG B:124 , ARG B:126 , ARG B:229 , ARG B:280 , HOH B:922	BINDING SITE FOR RESIDUE SO4 B 401

(no "SS Bond" information available for 3M10)

Asymmetric Unit

No.	Residues
1	Trp A:204	-	Pro A:205
2	Trp B:204	-	Pro B:205

(no "SAP(SNP)/Variant" information available for 3M10)

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PHOSPHAGEN_KINASE_N	PS51509	Phosphagen kinase N-terminal domain profile.	KARG_LIMPO	9-91	2	A:9-91 B:9-91
2	PHOSPHAGEN_KINASE_C	PS51510	Phosphagen kinase C-terminal domain profile.	KARG_LIMPO	119-356	2	A:119-356 B:119-356
3	PHOSPHAGEN_KINASE	PS00112	Phosphagen kinase active site signature.	KARG_LIMPO	271-277	2	A:271-277 B:271-277

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PHOSPHAGEN_KINASE_N	PS51509	Phosphagen kinase N-terminal domain profile.	KARG_LIMPO	9-91	1	A:9-91 -
2	PHOSPHAGEN_KINASE_C	PS51510	Phosphagen kinase C-terminal domain profile.	KARG_LIMPO	119-356	1	A:119-356 -
3	PHOSPHAGEN_KINASE	PS00112	Phosphagen kinase active site signature.	KARG_LIMPO	271-277	1	A:271-277 -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PHOSPHAGEN_KINASE_N	PS51509	Phosphagen kinase N-terminal domain profile.	KARG_LIMPO	9-91	1	- B:9-91
2	PHOSPHAGEN_KINASE_C	PS51510	Phosphagen kinase C-terminal domain profile.	KARG_LIMPO	119-356	1	- B:119-356
3	PHOSPHAGEN_KINASE	PS00112	Phosphagen kinase active site signature.	KARG_LIMPO	271-277	1	- B:271-277

(no "Exon" information available for 3M10)

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:347
 aligned with KARG_LIMPO | P51541 from UniProtKB/Swiss-Prot  Length:357

    Alignment length:356
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351      
           KARG_LIMPO     2 VDQATLDKLEAGFKKLQEASDCKSLLKKHLTKDVFDSIKNKKTGMGATLLDVIQSGVENLDSGVGIYAPDAESYRTFGPLFDPIIDDYHGGFKLTDKHPPKEWGDINTLVDLDPGGQFIISTRVRCGRSLQGYPFNPCLTAEQYKEMEEKVSSTLSSMEDELKGTYYPLTGMSKATQQQLIDDHFLFKEGDRFLQTANACRYWPTGRGIFHNDAKTFLVWVNEEDHLRIISMQKGGDLKTVYKRLVTAVDNIESKLPFSHDDRFGFLTFCPTNLGTTMRASVHIQLPKLAKDRKVLEDIASKFNLQVRGTRGEHTESEGGVYDISNKRRLGLTEYQAVREMQDGILEMIKMEKAAA 357
               SCOP domains d3m10a1 A:2-95 Arginine kinase, N-domain                                                      d3m10a2 A:96-357 Arginine kinase, C-terminal domain                                                                                                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.........hhhhhhhhhhh............hhhhhhhhhhhhhhhhhh...............hhhhh.........eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhh.hhhh.eeeee....hhhhhhhhhhhh......hhhhhh...........eeeee....eeeee.....eeeeeeee..hhhhhhhhhhhhhhhhhhhh...ee...ee............eeeeeee..hhhhhhhhhhhhhhhh.eeee.---------..eeeeee......hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------PHOSPHAGEN_KINASE_N  PDB: A:9-91 UniProt: 9-91                                     ---------------------------PHOSPHAGEN_KINASE_C  PDB: A:119-356 UniProt: 119-356                                                                                                                                                                                          - PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PHOSPHA-------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m10 A   2 VDQATLDKLEAGFKKLQEASDCKSLLKKHLTKDVFDSIKNKKTGMGATLLDVIQSGVENLDSGVGIYAPDAESYRTFGPLFDPIIDDYHGGFKLTDKHPPKQWGDINTLVGLDPAGQFIISTRVRCGRSLQGYPFNPCLTAEQYKEMEEKVSSTLSSMEDELKGTYYPLTGMSKATQQQLIDDHFLFKEGDRFLQTANACRYWPTGRGIFHNDAKTFLVWVNEEDHLRIISMQKGGDLKTVYKRLVTAVDNIESKLPFSHDDRFGFLTFCPTNLGTTMRASVHIQLPKLAKDRKVLEDIASKFNLQVRG---------GGVYDISNKRRLGLTEYQAVREMQDGILEMIKMEKAAA 357
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301        |-       321       331       341       351      
                                                                                                                                                                                                                                                                                                                                              310       320

Chain B from PDB  Type:PROTEIN  Length:346
 aligned with KARG_LIMPO | P51541 from UniProtKB/Swiss-Prot  Length:357

    Alignment length:356
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351      
           KARG_LIMPO     2 VDQATLDKLEAGFKKLQEASDCKSLLKKHLTKDVFDSIKNKKTGMGATLLDVIQSGVENLDSGVGIYAPDAESYRTFGPLFDPIIDDYHGGFKLTDKHPPKEWGDINTLVDLDPGGQFIISTRVRCGRSLQGYPFNPCLTAEQYKEMEEKVSSTLSSMEDELKGTYYPLTGMSKATQQQLIDDHFLFKEGDRFLQTANACRYWPTGRGIFHNDAKTFLVWVNEEDHLRIISMQKGGDLKTVYKRLVTAVDNIESKLPFSHDDRFGFLTFCPTNLGTTMRASVHIQLPKLAKDRKVLEDIASKFNLQVRGTRGEHTESEGGVYDISNKRRLGLTEYQAVREMQDGILEMIKMEKAAA 357
               SCOP domains d3m10b1 B:2-95 Arginine kinase, N-domain                                                      d3m10b2 B:96-357 Arginine kinase, C-terminal domain                                                                                                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------ATP-gua_PtransN-3m10B03 B:18-93                                             --------------------ATP-gua_Ptrans-3m10B01 B:114-356                                                                                                                                                                                                                   - Pfam domains (1)
           Pfam domains (2) ----------------ATP-gua_PtransN-3m10B04 B:18-93                                             --------------------ATP-gua_Ptrans-3m10B02 B:114-356                                                                                                                                                                                                                   - Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.........hhhhhhhhhhh............hhhhhhhhhhhhhhhhhh...............hhhhh.........eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhh.hhhh.eeeee....hhhhhhhhhhh.......hhhhhh...........eeeee....eeeee.....eeeeeeee..hhhhhhhhhhhhhhhhhhhh...ee...ee............eeeeeee..hhhhhhhhhhhhhhhh.eeee.----------.eeeeee......hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------PHOSPHAGEN_KINASE_N  PDB: B:9-91 UniProt: 9-91                                     ---------------------------PHOSPHAGEN_KINASE_C  PDB: B:119-356 UniProt: 119-356                                                                                                                                                                                          - PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PHOSPHA-------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m10 B   2 VDQATLDKLEAGFKKLQEASDCKSLLKKHLTKDVFDSIKNKKTGMGATLLDVIQSGVENLDSGVGIYAPDAESYRTFGPLFDPIIDDYHGGFKLTDKHPPKQWGDINTLVGLDPAGQFIISTRVRCGRSLQGYPFNPCLTAEQYKEMEEKVSSTLSSMEDELKGTYYPLTGMSKATQQQLIDDHFLFKEGDRFLQTANACRYWPTGRGIFHNDAKTFLVWVNEEDHLRIISMQKGGDLKTVYKRLVTAVDNIESKLPFSHDDRFGFLTFCPTNLGTTMRASVHIQLPKLAKDRKVLEDIASKFNLQVRG----------GVYDISNKRRLGLTEYQAVREMQDGILEMIKMEKAAA 357
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301        |-       321       331       341       351      
                                                                                                                                                                                                                                                                                                                                              310        321

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 "CATH Domain" information available for 3M10, only for superseded entry 1M80 replaced by 3M10)

Asymmetric Unit(hide GO term definitions)

Chain A,B (KARG_LIMPO | P51541)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004054	arginine kinase activity	Catalysis of the reaction: L-arginine + ATP = N(omega)-phospho-L-arginine + ADP + 2 H(+).
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	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: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.
	GO:0016772	transferase activity, transferring phosphorus-containing groups	Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
biological process
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	2.7.3.3
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	KARG_LIMPO \| P51541	:	1bg0 1m15 1p50 1p52 1rl9 1sd0 4gvy 4gvz 4gw0 4gw2 5j99 5j9a

1m15	TRANSITION STATE STRUCTURE
1m80	REPLACEMENT DEPOSITION (REFINEMENT AT HIGHER RESOLUTION)

Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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