1M15 - JenaLib

Title :   TRANSITION STATE STRUCTURE OF ARGININE KINASE

Authors :   M. S. Yousef, F. Fabiola, J. L. Gattis, T. Somasundaram, M. S. Chapman

Date :   17 Jun 02 (Deposition) - 04 Dec 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.20

Chains :   Asym./Biol. Unit : A

Keywords :   Arginine Kinase, Creatine Kinase, Phosphagen Kinase, Transition State Analog, Adenosine Triphosphate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. S. Yousef, F. Fabiola, J. L. Gattis, T. Somasundaram, M. S. Chapman
Refinement Of The Arginine Kinase Transition-State Analogue Complex At 1. 2 A Resolution: Mechanistic Insights.
Acta Crystallogr. , Sect. D V. 58 2009 2002
PubMed-ID: 12454458 | Reference-DOI: 10.1107/S0907444902014683
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 5)

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:112 , LEU A:113 , ASP A:114 , PRO A:115 , GLY A:191 , GLN A:196 , GLY A:237 , ASP A:238 , HOH A:1098 , HOH A:1320	BINDING SITE FOR RESIDUE NO3 A 500
2	AC2	SOFTWARE	ARG A:126 , GLU A:225 , ARG A:229 , ASN A:274 , ARG A:309 , GLU A:314 , ADP A:400 , ARG A:403 , MG A:408 , HOH A:1220 , HOH A:1297 , HOH A:1298	BINDING SITE FOR RESIDUE NO3 A 405
3	AC3	SOFTWARE	ADP A:400 , NO3 A:405 , HOH A:1296 , HOH A:1297 , HOH A:1298	BINDING SITE FOR RESIDUE MG A 408
4	AC4	SOFTWARE	SER A:63 , GLY A:64 , VAL A:65 , GLY A:66 , TYR A:68 , GLU A:225 , CYS A:271 , THR A:273 , ASN A:274 , GLU A:314 , HIS A:315 , NO3 A:405 , HOH A:1224 , HOH A:1227 , HOH A:1240	BINDING SITE FOR RESIDUE ARG A 403
5	AC5	SOFTWARE	SER A:122 , ARG A:124 , ARG A:126 , HIS A:185 , TRP A:221 , ARG A:229 , MET A:233 , ARG A:280 , SER A:282 , VAL A:283 , HIS A:284 , ARG A:309 , THR A:311 , ARG A:312 , GLY A:313 , GLU A:314 , ASP A:324 , NO3 A:405 , MG A:408 , HOH A:1209 , HOH A:1210 , HOH A:1215 , HOH A:1230 , HOH A:1296 , HOH A:1297 , HOH A:1298	BINDING SITE FOR RESIDUE ADP A 400

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 3)

Exons (0, 0)

Sequences/Alignments

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

    Alignment length:357
                                                                                                                                                                                                                                                                                                                                                                                             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       311       321       331       341       351     | 
           KARG_LIMPO     2 VDQATLDKLEAGFKKLQEASDCKSLLKKHLTKDVFDSIKNKKTGMGATLLDVIQSGVENLDSGVGIYAPDAESYRTFGPLFDPIIDDYHGGFKLTDKHPPKEWGDINTLVDLDPGGQFIISTRVRCGRSLQGYPFNPCLTAEQYKEMEEKVSSTLSSMEDELKGTYYPLTGMSKATQQQLIDDHFLFKEGDRFLQTANACRYWPTGRGIFHNDAKTFLVWVNEEDHLRIISMQKGGDLKTVYKRLVTAVDNIESKLPFSHDDRFGFLTFCPTNLGTTMRASVHIQLPKLAKDRKVLEDIASKFNLQVRGTRGEHTESEGGVYDISNKRRLGLTEYQAVREMQDGILEMIKMEKAAA-   -
               SCOP domains d1m15a1 A:2-95 Arginine kinase, N-domain                                                      d1m15a2 A:96-357 Arginine kinase, C-terminal domain                                                                                                                                                                                                                   - SCOP domains
               CATH domains 1m15A01 A:2-95 Transferase Creatine Kinase, Chain A, domain 1                                 --1m15A02 A:98-357 Creatine Kinase; Chain                                                                                                                                                                                                                             - CATH domains
               Pfam domains ----------------ATP-gua_PtransN-1m15A02 A:18-93                                             --------------------ATP-gua_Ptrans-1m15A01 A:114-356                                                                                                                                                                                                                   -- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh........hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh...............hhhhh.........eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhh.......hhhhhhh..........eeee.....eeeee.....eeeeeeee..hhhhhhhhhhhhhhhhhh.....ee...ee...hhhhh....eeeeee.hhhhhhhhhhhhhhhhhh.eeee.............eeeee......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
                 1m15 A   2 VDQATLDKLEAGFKKLQEASDCKSLLKKHLTKDVFDSIKNKKTGMGATLLDVIQSGVENLDSGVGIYAPDAESYRTFGPLFDPIIDDYHGGFKLTDKHPPKQWGDINTLVGLDPAGQFIISTRVRCGRSLQGYPFNPCLTAEQYKEMEEKVSSTLSSMEDELKGTYYPLTGMSKATQQQLIDDHFLFKEGDRFLQTANACRYWPTGRGIFHNDAKTFLVWVNEEDHLRIISMQKGGDLKTVYKRLVTAVDNIESKLPFSHDDRFGFLTFCPTNLGTTMRASVHIQLPKLAKDRKVLEDIASKFNLQVRGTRGEHTESEGGVYDISNKRRLGLTEYQAVREMQDGILEMIKMEKAAAR 403
                                    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     ||
                                                                                                                                                                                                                                                                                                                                                                                             357|
                                                                                                                                                                                                                                                                                                                                                                                              403

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 (2, 2)

CATH Domains (2, 2)

Pfam Domains (2, 2)

Gene Ontology (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		ADP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ARG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NO3	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Trp A:204 - Pro A:205	[ RasMol ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1m15
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	KARG_LIMPO \| P51541
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.7.3.3
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description