2BTY - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   ACETYLGLUTAMATE KINASE FROM THERMOTOGA MARITIMA COMPLEXED WITH ITS INHIBITOR ARGININE

Authors :   F. Gil-Ortiz, M. L. Fernandez-Murga, I. Fita, V. Rubio

Date :   08 Jun 05 (Deposition) - 13 Dec 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.75

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

Keywords :   N-Acetyl-L-Glutamate Kinase, Amino Acid Kinase, Phosphoryl Group Transfer, Arginine Metabolism, Transferase, Arginine Biosynthesis, Amino-Acid Biosynthesis, Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Ramon-Maiques, M. L. Fernandez-Murga, F. Gil-Ortiz, A. Vagin, I. Fita, V. Rubio
Structural Bases Of Feed-Back Control Of Arginine Biosynthesis, Revealed By The Structure Of Two Hexameric N-Acetylglutamate Kinases, From Thermotoga Maritima And Pseudomonas Aeruginosa
J. Mol. Biol. V. 356 695 2006
PubMed-ID: 16376937 | Reference-DOI: 10.1016/J.JMB.2005.11.079

Molecule 1 - ACETYLGLUTAMATE KINASE
	Chains	:	A, B, C
	EC Number	:	2.7.2.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNAGK-TM16
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET-22B
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336
	Synonym	:	NAG KINASE, AGK, N-ACETYL-L-GLUTAMATE 5-PHOSPHOTRANSFERASE

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (2x)	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	ARG	3	Mod. Amino Acid	ARGININE
2	K	1	Ligand/Ion	POTASSIUM ION
3	NLG	3	Ligand/Ion	N-ACETYL-L-GLUTAMATE

Biological Unit 1 (2, 12)

No.	Name	Count	Type	Full Name
1	ARG	6	Mod. Amino Acid	ARGININE
2	K	-1	Ligand/Ion	POTASSIUM ION
3	NLG	6	Ligand/Ion	N-ACETYL-L-GLUTAMATE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:160	BINDING SITE FOR RESIDUE K A1285
2	AC2	SOFTWARE	TYR A:15 , PHE A:19 , LYS A:196 , SER A:214 , GLU A:266 , ILE A:267 , SER A:269 , ARG A:270 , LYS A:271 , GLY A:274 , MET A:276 , HOH A:2015	BINDING SITE FOR RESIDUE ARG A1283
3	AC3	SOFTWARE	TYR B:15 , PHE B:19 , LYS B:196 , SER B:214 , THR B:215 , GLU B:266 , ILE B:267 , SER B:269 , ARG B:270 , LYS B:271 , GLY B:274 , MET B:276 , HOH B:2015	BINDING SITE FOR RESIDUE ARG B1283
4	AC4	SOFTWARE	PHE C:19 , LYS C:196 , SER C:214 , THR C:215 , GLU C:266 , ILE C:267 , SER C:269 , ARG C:270 , LYS C:271 , GLY C:272 , GLY C:274 , MET C:276	BINDING SITE FOR RESIDUE ARG C1283
5	AC5	SOFTWARE	LYS A:27 , GLY A:29 , GLY A:30 , GLY A:61 , GLY A:62 , ASN A:180 , ASP A:182	BINDING SITE FOR RESIDUE NLG A1284
6	AC6	SOFTWARE	LYS B:27 , GLY B:29 , GLY B:30 , GLY B:61 , ASN B:180 , ASP B:182	BINDING SITE FOR RESIDUE NLG B1284
7	AC7	SOFTWARE	LYS C:27 , GLY C:30 , GLY C:61 , GLY C:62 , GLY C:63 , ILE C:179 , ASN C:180	BINDING SITE FOR RESIDUE NLG C1284

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

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

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

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

(no "Exon" information available for 2BTY)

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:283
 aligned with ARGB_THEMA | Q9X2A4 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:283
                                                                                                                                                                                                                                                                                                                   282 
                                    10        20        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 | 
          ARGB_THEMA      1 MRIDTVNVLLEALPYIKEFYGKTFVIKFGGSAMKQENAKKAFIQDIILLKYTGIKPIIVHGGGPAISQMMKDLGIEPVFKNGHRVTDEKTMEIVEMVLVGKINKEIVMNLNLHGGRAVGICGKDSKLIVAEKETKHGDIGYVGKVKKVNPEILHALIENDYIPVIAPVGIGEDGHSYNINADTAAAEIAKSLMAEKLILLTDVDGVLKDGKLISTLTPDEAEELIRDGTVTGGMIPKVECAVSAVRGGVGAVHIINGGLEHAILLEIFSRKGIGTMIKELEG-    -
               SCOP domains d2btya1 A:1-282 N-acetyl-l-glutamate kinase                                                                                                                                                                                                                                               - SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..eeeeeee......hhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee......eeeeee.........eeeeeee.hhhhhhhhhh.eeeeeeeeee....eeee.hhhhhhhhhhhhh..eeeeeee....ee...ee.eeehhhhhhhhhhh.....hhhhhhhhhhhhhhh..eeeeeee....hhhhhhhh.....eeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2bty A    1 MRIDTVNVLLEALPYIKEFYGKTFVIKFGGSAMKQENAKKAFIQDIILLKYTGIKPIIVHGGGPAISQMMKDLGIEPVFKNGHRVTDEKTMEIVEMVLVGKINKEIVMNLNLHGGRAVGICGKDSKLIVAEKETKHGDIGYVGKVKKVNPEILHALIENDYIPVIAPVGIGEDGHSYNINADTAAAEIAKSLMAEKLILLTDVDGVLKDGKLISTLTPDEAEELIRDGTVTGGMIPKVECAVSAVRGGVGAVHIINGGLEHAILLEIFSRKGIGTMIKELEGR 1283
                                    10        20        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 ||
                                                                                                                                                                                                                                                                                                                   282|
                                                                                                                                                                                                                                                                                                                   1283

Chain B from PDB  Type:PROTEIN  Length:283
 aligned with ARGB_THEMA | Q9X2A4 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:283
                                                                                                                                                                                                                                                                                                                   282 
                                    10        20        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 | 
          ARGB_THEMA      1 MRIDTVNVLLEALPYIKEFYGKTFVIKFGGSAMKQENAKKAFIQDIILLKYTGIKPIIVHGGGPAISQMMKDLGIEPVFKNGHRVTDEKTMEIVEMVLVGKINKEIVMNLNLHGGRAVGICGKDSKLIVAEKETKHGDIGYVGKVKKVNPEILHALIENDYIPVIAPVGIGEDGHSYNINADTAAAEIAKSLMAEKLILLTDVDGVLKDGKLISTLTPDEAEELIRDGTVTGGMIPKVECAVSAVRGGVGAVHIINGGLEHAILLEIFSRKGIGTMIKELEG-    -
               SCOP domains d2btyb_ B: automated matches                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..eeeeeee......hhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee......eeeeee.........eeeeeee.hhhhhhhhhh.eeeeeeeeee....eeee.hhhhhhhhhhhhh..eeeeeee....ee...ee.eeehhhhhhhhhhh.....hhhhhhhhhhhhhhh..eeeeeee....hhhhhhhh.....eeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2bty B    1 MRIDTVNVLLEALPYIKEFYGKTFVIKFGGSAMKQENAKKAFIQDIILLKYTGIKPIIVHGGGPAISQMMKDLGIEPVFKNGHRVTDEKTMEIVEMVLVGKINKEIVMNLNLHGGRAVGICGKDSKLIVAEKETKHGDIGYVGKVKKVNPEILHALIENDYIPVIAPVGIGEDGHSYNINADTAAAEIAKSLMAEKLILLTDVDGVLKDGKLISTLTPDEAEELIRDGTVTGGMIPKVECAVSAVRGGVGAVHIINGGLEHAILLEIFSRKGIGTMIKELEGR 1283
                                    10        20        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 ||
                                                                                                                                                                                                                                                                                                                   282|
                                                                                                                                                                                                                                                                                                                   1283

Chain C from PDB  Type:PROTEIN  Length:283
 aligned with ARGB_THEMA | Q9X2A4 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:283
                                                                                                                                                                                                                                                                                                                   282 
                                    10        20        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 | 
          ARGB_THEMA      1 MRIDTVNVLLEALPYIKEFYGKTFVIKFGGSAMKQENAKKAFIQDIILLKYTGIKPIIVHGGGPAISQMMKDLGIEPVFKNGHRVTDEKTMEIVEMVLVGKINKEIVMNLNLHGGRAVGICGKDSKLIVAEKETKHGDIGYVGKVKKVNPEILHALIENDYIPVIAPVGIGEDGHSYNINADTAAAEIAKSLMAEKLILLTDVDGVLKDGKLISTLTPDEAEELIRDGTVTGGMIPKVECAVSAVRGGVGAVHIINGGLEHAILLEIFSRKGIGTMIKELEG-    -
               SCOP domains d2btyc_ C: automated matches                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..eeeeeee......hhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee......eeeeee.........eeeeeee.hhhhhhhhhh.eeeeeeeeee....eeee.hhhhhhhhhhhhh..eeeeeee....ee...ee.eeehhhhhhhhhhh.....hhhhhhhhhhhhhhh..eeeeeee....hhhhhhhh.....eeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2bty C    1 MRIDTVNVLLEALPYIKEFYGKTFVIKFGGSAMKQENAKKAFIQDIILLKYTGIKPIIVHGGGPAISQMMKDLGIEPVFKNGHRVTDEKTMEIVEMVLVGKINKEIVMNLNLHGGRAVGICGKDSKLIVAEKETKHGDIGYVGKVKKVNPEILHALIENDYIPVIAPVGIGEDGHSYNINADTAAAEIAKSLMAEKLILLTDVDGVLKDGKLISTLTPDEAEELIRDGTVTGGMIPKVECAVSAVRGGVGAVHIINGGLEHAILLEIFSRKGIGTMIKELEGR 1283
                                    10        20        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 ||
                                                                                                                                                                                                                                                                                                                   282|
                                                                                                                                                                                                                                                                                                                   1283

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Carbamate kinase-like (63)

Superfamily: Carbamate kinase-like (63)

Family: N-acetyl-l-glutamate kinase (13)

Protein domain: automated matches (5)

Thermotoga maritima [TaxId: 2336] (1)

1a	d2btyb_	B:
1b	d2btyc_	C:

Protein domain: N-acetyl-l-glutamate kinase (8)

Thermotoga maritima [TaxId: 2336] (1)

d2btya1

A:1-282

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (ARGB_THEMA | Q9X2A4)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003991	acetylglutamate kinase activity	Catalysis of the reaction: ATP + N-acetyl-L-glutamate = ADP + N-acetyl-L-glutamate-5-phosphate.
	GO:0034618	arginine binding	Interacting selectively and non-covalently with 2-amino-5-(carbamimidamido)pentanoic acid.
	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.
biological process
	GO:0006526	arginine biosynthetic process	The chemical reactions and pathways resulting in the formation of arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	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:0006561	proline biosynthetic process	The chemical reactions and pathways resulting in the formation of proline (pyrrolidine-2-carboxylic acid), a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric 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
		ARG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		K	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NLG	[ 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 ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2bty)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2bty
		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
	ARGB_THEMA \| Q9X2A4
		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)
	2.7.2.8
		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

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	ARGB_THEMA \| Q9X2A4
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 2BTY)

(no "Related Entries Specified in the PDB File" available for 2BTY)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 3)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (13, 13)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File