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(-) Description

Title :  ACETYLGLUTAMATE KINASE FROM ESCHERICHIA COLI COMPLEXED WITH MGADP AND N-ACETYL-L-GLUTAMATE
 
Authors :  F. Gil-Ortiz, S. Ramon-Maiques, I. Fita, V. Rubio
Date :  23 May 03  (Deposition) - 31 Jul 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Kinase, N-Acetyl-L-Glutamate Kinase, Amino Acid Kinase, Phosphoryl N-Acetyl-L-Glutamate 5-Phosphotransferase, Nag Kinase, Group Transfer, Arginine Metabolism, X-Ray Diffraction (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Gil-Ortiz, S. Ramon-Maiques, I. Fita, V. Rubio
The Course Of Phosphorus In The Reaction Of N-Acetyl-L-Glutamate Kinase, Determined From The Structures Of Crystalline Complexes, Including A Complex With An Alf(4)(-) Transition State Mimic
J. Mol. Biol. V. 331 231 2003
PubMed-ID: 12875848  |  Reference-DOI: 10.1016/S0022-2836(03)00716-2

(-) Compounds

Molecule 1 - ACETYLGLUTAMATE KINASE
    Chains: A
    EC Number: 2.7.2.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNAGK24
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET-15B TYPE PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: BL21(DE3)
    Synonym: NAG KINASE, AGK, N-ACETYL-L-GLUTAMATE 5-PHOSPHOTRANSFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric Unit (4, 4)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
3MG1Ligand/IonMAGNESIUM ION
4NLG1Ligand/IonN-ACETYL-L-GLUTAMATE
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
4NLG2Ligand/IonN-ACETYL-L-GLUTAMATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:63 , THR A:211 , ASP A:212 , HOH A:2035 , HOH A:2141BINDING SITE FOR RESIDUE ACT A1261
2AC2SOFTWAREADP A:1259 , HOH A:2090 , HOH A:2137 , HOH A:2138 , HOH A:2139BINDING SITE FOR RESIDUE MG A1262
3AC3SOFTWARELYS A:8 , GLY A:10 , GLY A:11 , SER A:180 , ASP A:181 , VAL A:182 , GLY A:184 , ILE A:185 , LEU A:186 , ILE A:209 , ILE A:210 , THR A:211 , ASP A:212 , GLY A:213 , MET A:214 , LYS A:217 , MG A:1262 , HOH A:2090 , HOH A:2099 , HOH A:2135 , HOH A:2136 , HOH A:2137 , HOH A:2138BINDING SITE FOR RESIDUE ADP A1259
4AC4SOFTWAREGLY A:43 , GLY A:44 , GLY A:45 , LEU A:65 , ARG A:66 , LEU A:80 , SER A:147 , ASN A:158 , VAL A:159 , ASN A:160 , ALA A:161 , HOH A:2135 , HOH A:2138 , HOH A:2139 , HOH A:2140BINDING SITE FOR RESIDUE NLG A1260

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OHA)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1OHA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OHA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OHA)

(-) Exons   (0, 0)

(no "Exon" information available for 1OHA)

(-) Sequences/Alignments

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:258
 aligned with ARGB_ECO57 | P0A6C9 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_ECO57     1 MMNPLIIKLGGVLLDSEEALERLFSALVNYRESHQRPLVIVHGGGCVVDELMKGLNLPVKKKNGLRVTPADQIDIITGALAGTANKTLLAWAKKHQIAAVGLFLGDGDSVKVTQLDEELGHVGLAQPGSPKLINSLLENGYLPVVSSIGVTDEGQLMNVNADQAATALAATLGADLILLSDVSGILDGKGQRIAEMTAAKAEQLIEQGIITDGMIVKVNAALDAARTLGRPVDIASWRHAEQLPALFNGMPMGTRILA 258
               SCOP domains d1ohaa_ A: N-acetyl-l-glutamate kinase                                                                                                                                                                                                                             SCOP domains
               CATH domains 1ohaA00 A:1-258  [code=3.40.1160.10, no name defined]                                                                                                                                                                                                              CATH domains
               Pfam domains --AA_kinase-1ohaA01 A:3-236                                                                                                                                                                                                                 ---------------------- Pfam domains
         Sec.struct. author ...eeeeee.hhhhhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhh....eee..eee....hhhhhhhhhhhhhhhhhhhhhhhh..eeeee........eeee.......eeeee...hhhhhhhhhh..eeee.eeee....eeee.hhhhhhhhhhhhhh.eeeeee.....ee...ee.eeehhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhh.....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1oha 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 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 d1ohaa_ A: N-acetyl-l-glutamate kinase                                                                                                                                                                                                                             SCOP domains
               CATH domains 1ohaA00 A:1-258  [code=3.40.1160.10, no name defined]                                                                                                                                                                                                              CATH domains
               Pfam domains --AA_kinase-1ohaA01 A:3-236                                                                                                                                                                                                                 ---------------------- Pfam domains
         Sec.struct. author ...eeeeee.hhhhhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhh....eee..eee....hhhhhhhhhhhhhhhhhhhhhhhh..eeeee........eeee.......eeeee...hhhhhhhhhh..eeee.eeee....eeee.hhhhhhhhhhhhhh.eeeeee.....ee...ee.eeehhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhh.....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1oha 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
   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  (1, 1)

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

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: AA_kinase] (20)

(-) Gene Ontology  (11, 20)

Asymmetric Unit(hide GO term definitions)
Chain A   (ARGB_ECO57 | P0A6C9)
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: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: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.

Chain A   (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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ARGB_ECO57 | P0A6C9: 1gs5 1gsj 1oh9 1ohb
        ARGB_ECOLI | P0A6C8: 1gs5 1gsj 1oh9 1ohb 2wxb 2x2w

(-) Related Entries Specified in the PDB File

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-
1ohb N-ACETYL-L-GLUTAMATE KINASE FROM ESCHERICHIA COLI COMPLEXED WITH ADP AND SULPHATE