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(-) Description

Title :  THE CRYSTAL STRUCTURE OF SMU.665 FROM STREPTOCOCCUS MUTANS UA159
 
Authors :  X. -D. Su, X. Liu, C. W. Wu
Date :  30 Dec 09  (Deposition) - 05 Jan 11  (Release) - 05 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.06
Chains :  Asym./Biol. Unit :  A
Keywords :  Argb, Smu. 665, Amino-Acid Biosynthesis, Arginine Biosynthesis, Atp- Binding, Kinase, Nucleotide-Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. -D. Su, X. Liu, C. W. Wu
The Crystal Structure Of Smu. 665 From Streptococcus Mutans Ua159
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ACETYLGLUTAMATE KINASE
    Chains: A
    EC Number: 2.7.2.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SMU.665
    Organism Scientific: STREPTOCOCCUS MUTANS
    Organism Taxid: 210007
    Strain: UA159
    Synonym: SMU.665, NAG KINASE, AGK, N-ACETYL-L-GLUTAMATE 5- PHOSPHOTRANSFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3NLG1Ligand/IonN-ACETYL-L-GLUTAMATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:8 , GLY A:10 , GLY A:11 , THR A:179 , ASN A:180 , GLY A:183 , LEU A:185 , VAL A:207 , THR A:209 , GLY A:211 , MET A:212 , LYS A:215 , MG A:248 , HOH A:250 , HOH A:252 , HOH A:273 , HOH A:275 , HOH A:297 , HOH A:308BINDING SITE FOR RESIDUE ADP A 246
2AC2SOFTWAREGLY A:40 , GLY A:41 , GLY A:42 , ILE A:45 , ARG A:63 , SER A:145 , ASN A:156 , ILE A:157 , ASN A:158 , ALA A:159 , HOH A:262 , HOH A:286BINDING SITE FOR RESIDUE NLG A 247
3AC3SOFTWAREADP A:246 , HOH A:262 , HOH A:273 , HOH A:274 , HOH A:275BINDING SITE FOR RESIDUE MG A 248

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3L86)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3L86)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3L86)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3L86)

(-) Exons   (0, 0)

(no "Exon" information available for 3L86)

(-) 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:245
 aligned with ARGB_STRMU | Q8DV44 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
           ARGB_STRMU     1 MKDIIVIKIGGVASQQLSGDFLSQIKNWQDAGKQLVIVHGGGFAINKLMEENQVPVKKINGLRVTSKDDMVLVSHALLDLVGKNLQEKLRQAGVSCQQLKSDIKHVVAADYLDKDTYGYVGDVTHINKRVIEEFLENRQIPILASLGYSKEGDMLNINADYLATAVAVALAADKLILMTNVKGVLENGAVLEKITSHQVQEKIDTAVITAGMIPKIESAAKTVAAGVGQVLIGDNLLTGTLITAD 245
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --AA_kinase-3l86A01 A:3-234                                                                                                                                                                                                               ----------- Pfam domains
         Sec.struct. author ...eeeeee..hhhhh.hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh.....ee..ee..hhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.hhhhhh.eeeee.hhhhhh..eeeeeehhhhhhhhhhh..eeeee.eee.....eee.hhhhhhhhhhhhh...eeeee......ee..ee..eee...hhhhhhh.....hhhhhhhhhhhhhhh...eeeee......eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l86 A   1 MKDIIVIKIGGVASQQLSGDFLSQIKNWQDAGKQLVIVHGGGFAINKLMEENQVPVKKINGLRVTSKDDMVLVSHALLDLVGKNLQEKLRQAGVSCQQLKSDIKHVVAADYLDKDTYGYVGDVTHINKRVIEEFLENRQIPILASLGYSKEGDMLNINADYLATAVAVALAADKLILMTNVKGVLENGAVLEKITSHQVQEKIDTAVITAGMIPKIESAAKTVAAGVGQVLIGDNLLTGTLITAD 245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
   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  (0, 0)

(no "SCOP Domain" information available for 3L86)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3L86)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ARGB_STRMU | Q8DV44)
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.
    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.

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  3l86
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