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Title :   ACETYLGLUTAMATE KINASE FROM ESCHERICHIA COLI BOUND TO N-ACETYL-L-GLUTAMYL-5-PHOSPHATE

Authors :   F. Gil-Ortiz, V. Rubio

Date :   18 Jan 10 (Deposition) - 19 May 10 (Release) - 20 Mar 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Arginine Biosynthesis, Transferase, Atp-Binding, Nucleotide-Binding, Amino-Acid Biosynthesis, Amino Acid Kinase Family (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Gil-Ortiz, S. Ramon-Maiques, M. L. Fernandez-Murga, I. Fita, V. Rubio
Two Crystal Structures Of Escherichia Coli N- Acetyl-L-Glutamate Kinase Demonstrate The Cycling Between Open And Closed Conformations.
J. Mol. Biol. V. 399 476 2010
PubMed-ID: 20403363 | Reference-DOI: 10.1016/J.JMB.2010.04.025

Molecule 1 - ACETYLGLUTAMATE KINASE
	Chains	:	A, B
	EC Number	:	2.7.2.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15-B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	469008
	Strain	:	BL21(DE3)
	Synonym	:	N-ACETYL-L-GLUTAMATE KINASE, NAG KINASE, AGK, N- ACETYL-L-GLUTAMATE 5-PHOSPHOTRANSFERASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION
2	X2W	2	Ligand/Ion	N-ACETYL-L-GLUTAMYL 5-PHOSPHATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:10 , GLY A:11 , VAL A:12 , SER A:180 , LYS A:217 , X2W A:1259	BINDING SITE FOR RESIDUE SO4 A1260
2	AC2	SOFTWARE	GLY B:11 , VAL B:12 , SER B:180 , ASP B:181 , LYS B:217 , HOH B:2066 , HOH B:2091 , HOH B:2092	BINDING SITE FOR RESIDUE SO4 B1260
3	AC3	SOFTWARE	LYS A:8 , LEU A:9 , GLY A:10 , GLY A:11 , GLY A:43 , GLY A:44 , GLY A:45 , ARG A:66 , ASN A:158 , ALA A:161 , SO4 A:1260 , HOH A:2065	BINDING SITE FOR RESIDUE X2W A1259
4	AC4	SOFTWARE	LYS B:8 , GLY B:10 , GLY B:11 , GLY B:43 , GLY B:44 , GLY B:45 , LEU B:65 , ARG B:66 , ASN B:158 , ALA B:161 , HOH B:2089 , HOH B:2090	BINDING SITE FOR RESIDUE X2W B1259

(no "SS Bond" information available for 2X2W)

(no "Cis Peptide Bond" information available for 2X2W)

(no "SAP(SNP)/Variant" information available for 2X2W)

(no "PROSITE Motif" information available for 2X2W)

(no "Exon" information available for 2X2W)

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:258
 aligned with ARGB_ECOLI | P0A6C8 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:258
                                    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        
           ARGB_ECOLI     1 MMNPLIIKLGGVLLDSEEALERLFSALVNYRESHQRPLVIVHGGGCVVDELMKGLNLPVKKKNGLRVTPADQIDIITGALAGTANKTLLAWAKKHQIAAVGLFLGDGDSVKVTQLDEELGHVGLAQPGSPKLINSLLENGYLPVVSSIGVTDEGQLMNVNADQAATALAATLGADLILLSDVSGILDGKGQRIAEMTAAKAEQLIEQGIITDGMIVKVNAALDAARTLGRPVDIASWRHAEQLPALFNGMPMGTRILA 258
               SCOP domains d2x2wa_ A: automated matches                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2x2wA00 A:1-258  [code=3.40.1160.10, no name defined]                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeehhhhhhhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhh..eeeeee......eeeee.......eeeee...hhhhhhhhhh..eeeee..ee....eeee.hhhhhhhhhhhhh.eeeeee..............eeehhhhhhhh........hhhhhhhhhhhhhhhh..eeeee......hhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2x2w A   1 MMNPLIIKLGGVLLDSEEALERLFSALVNYRESHQRPLVIVHGGGCVVDELMKGLNLPVKKKNGLRVTPADQIDIITGALAGTANKTLLAWAKKHQIAAVGLFLGDGDSVKVTQLDEELGHVGLAQPGSPKLINSLLENGYLPVVSSIGVTDEGQLMNVNADQAATALAATLGADLILLSDVSGILDGKGQRIAEMTAAKAEQLIEQGIITDGMIVKVNAALDAARTLGRPVDIASWRHAEQLPALFNGMPMGTRILA 258
                                    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

Chain B from PDB  Type:PROTEIN  Length:258
 aligned with ARGB_ECOLI | P0A6C8 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:258
                                    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        
           ARGB_ECOLI     1 MMNPLIIKLGGVLLDSEEALERLFSALVNYRESHQRPLVIVHGGGCVVDELMKGLNLPVKKKNGLRVTPADQIDIITGALAGTANKTLLAWAKKHQIAAVGLFLGDGDSVKVTQLDEELGHVGLAQPGSPKLINSLLENGYLPVVSSIGVTDEGQLMNVNADQAATALAATLGADLILLSDVSGILDGKGQRIAEMTAAKAEQLIEQGIITDGMIVKVNAALDAARTLGRPVDIASWRHAEQLPALFNGMPMGTRILA 258
               SCOP domains d2x2wb_ B: automated matches                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2x2wB00 B:1-258  [code=3.40.1160.10, no name defined]                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee......hhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhh....ee...ee.....hhhhhhhhhhhhhhhhhhhhhhhh...eeee.......eeeee.......eeeee...hhhhhhhhhh.eeeeee.eeee...eeee.hhhhhhhhhhhhh.eeeeeee.............eeehhhhhhhhhhh....hhhhhhhhhhhhhhhhh..eeeee......hhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2x2w B   1 MMNPLIIKLGGVLLDSEEALERLFSALVNYRESHQRPLVIVHGGGCVVDELMKGLNLPVKKKNGLRVTPADQIDIITGALAGTANKTLLAWAKKHQIAAVGLFLGDGDSVKVTQLDEELGHVGLAQPGSPKLINSLLENGYLPVVSSIGVTDEGQLMNVNADQAATALAATLGADLILLSDVSGILDGKGQRIAEMTAAKAEQLIEQGIITDGMIVKVNAALDAARTLGRPVDIASWRHAEQLPALFNGMPMGTRILA 258
                                    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

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) (23833)

Fold: Carbamate kinase-like (63)

Superfamily: Carbamate kinase-like (63)

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

Protein domain: automated matches (5)

Escherichia coli [TaxId: 469008] (2)

1a	d2x2wa_	A:
1b	d2x2wb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Carbamate kinase (24)

Homologous Superfamily: [code=3.40.1160.10, no name defined] (24)

Escherichia coli. Organism_taxid: 469008. Strain: bl21(de3). (2)

1a	2x2wA00	A:1-258
1b	2x2wB00	B:1-258

(no "Pfam Domain" information available for 2X2W)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (ARGB_ECOLI | P0A6C8)

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: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:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	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.

Asymmetric/Biological Unit
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	2.7.2.8
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UniProtKB/Swiss-Prot
	ARGB_ECOLI \| P0A6C8	:	1gs5 1gsj 1oh9 1oha 1ohb 2wxb

1gs5	N-ACETYL-L-GLUTAMATE KINASE FROM ESCHERICHIA COLI COMPLEXED WITH ITS SUBSTRATE N- ACETYLGLUTAMATE AND ITS SUBSTRATE ANALOG AMPPMP
1gsj	SELENOMETHIONINE SUBSTITUTED N-ACETYL-L- GLUTAMATE KINASE FROM ESCHERICHIA COLI COMPLEXED WITH ITS SUBSTRATE N-ACETYL-L- GLUTAMATE AND ITS SUBSTRATE ANALOG AMPPNP
1oh9	ACETYLGLUTAMATE KINASE FROM ESCHERICHIA COLI COMPLEXED WITH MGADP, N-ACETYL-L-GLUTAMATE AND THE TRANSITION-STATE MIMIC ALF4-
1oha	ACETYLGLUTAMATE KINASE FROM ESCHERICHIA COLI COMPLEXED WITH MGADP AND N-ACETYL-L- GLUTAMATE
1ohb	ACETYLGLUTAMATE KINASE FROM ESCHERICHIA COLI COMPLEXED WITH ADP AND SULPHATE
2wxb	ACETYLGLUTAMATE KINASE FROM ESCHERICHIA COLI FREE OF SUBSTRATES

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 2)

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Gene Ontology (11, 11)

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