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(-) Description

Title :  CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA 1,6-ANHYDRO-N-ACTETYLMURAMIC ACID KINASE (ANMK) BOUND TO ADENOSINE DIPHOSPHATE
 
Authors :  J. P. Bacik, D. R. Martin, B. L. Mark
Date :  14 Jan 11  (Deposition) - 02 Feb 11  (Release) - 20 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.23
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Acetate And Sugar Kinases, Hsp70, Actin Superfamily, Kinase, 1, 6- Anhydro-N-Actetylmuramic Acid Binding, Glycoside Hydrolase, Atp- Binding, Carbohydrate Metabolism, Peptidoglycan Recycling, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. P. Bacik, G. E. Whitworth, K. A. Stubbs, A. K. Yadav, D. R. Martin, B. A. Bailey-Elkin, D. J. Vocadlo, B. L. Mark
Molecular Basis Of 1, 6-Anhydro Bond Cleavage And Phosphoryl Transfer By Pseudomonas Aeruginosa 1, 6-Anhydro-N-Acetylmuramic Acid Kinase.
J. Biol. Chem. V. 286 12283 2011
PubMed-ID: 21288904  |  Reference-DOI: 10.1074/JBC.M110.198317

(-) Compounds

Molecule 1 - ANHYDRO-N-ACETYLMURAMIC ACID KINASE
    Chains: A, B
    EC Number: 2.7.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ANMK, PA0666
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: ANHMURNAC KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:10 , THR A:11 , SER A:12 , ASP A:14 , GLY A:164 , GLY A:165 , ASN A:187 , ASP A:191 , PHE A:202 , ASP A:203 , ARG A:204 , ASP A:205 , GLY A:291 , GLY A:292 , HOH A:404BINDING SITE FOR RESIDUE ADP A 601
2AC2SOFTWAREARG A:129 , ALA A:140 , PRO A:141 , LEU A:142 , VAL A:143 , GLU A:326BINDING SITE FOR RESIDUE SO4 A 372
3AC3SOFTWAREGLY B:10 , THR B:11 , SER B:12 , ASP B:14 , GLY B:164 , GLY B:165 , ASN B:187 , ASP B:191 , PHE B:202 , ASP B:203 , ASP B:205 , GLY B:291 , GLY B:292 , PHE B:295 , ASN B:296 , HOH B:421BINDING SITE FOR RESIDUE ADP B 602
4AC4SOFTWAREARG B:129 , LEU B:142 , VAL B:143 , ASN B:168 , GLU B:326 , HOH B:442BINDING SITE FOR RESIDUE SO4 B 372

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:140 -Pro A:141
2Ala B:140 -Pro B:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3QBW)

(-) 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:347
 aligned with ANMK_PSEAE | Q9I5Q5 from UniProtKB/Swiss-Prot  Length:363

    Alignment length:361
                                    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       361 
           ANMK_PSEAE     2 PRYLGLMSGTSLDGMDIVLIEQGDRTTLLASHYLPMPAGLREDILALCVPGPDEIARAAEVEQRWVALAAQGVRELLLQQQMSPDEVRAIGSHGQTIRHEPARHFTVQIGNPALLAELTGIDVVADFRRRDVAAGGQGAPLVPAFHQALFGDDDTSRAVLNIGGFSNVSLLSPGKPVRGFDCGPGNVLMDAWIHHQRGEHFDRDGAWAASGQVNHALLASLLADEFFAARGPKSTGRERFNLPWLQEHLARHPALPAADIQATLLELSARSISESLLDAQPDCEEVLVCGGGAFNTALMKRLAMLMPEARVASTDEYGIPPAWMEGMAFAWLAHRFLERLPGNCPDVTGALGPRTLGALYP 362
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....eeeeeeeee...eeeeeeeeee..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh....hhh..eeee..eeeeee....eeeee..hhhhhhhh...eee...hhhhh.........hhhhhhhh-----.eeeeee..eeeeee.------eeeeeee..hhhhhhhhhh..................hhhhhhhh..hhhh.............hhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh...---eeee.hhhh.hhhhhhhhhh....eeeehhhh......hhhhhhhhhhhhhh.......hhhh.........eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qbw A   2 PRYLGLMSGTSLDGMDIVLIEQGDRTTLLASHYLPMPAGLREDILALCVPGPDEIARAAEVEQRWVALAAQGVRELLLQQQMSPDEVRAIGSHGQTIRHEPARHFTVQIGNPALLAELTGIDVVADFRRRDVAAGGQGAPLVPAFHQALF-----SRAVLNIGGFSNVSLL------RGFDCGPGNVLMDAWIHHQRGEHFDRDGAWAASGQVNHALLASLLADEFFAARGPKSTGRERFNLPWLQEHLARHPALPAADIQATLLELSARSISESLLDAQPD---VLVCGGGAFNTALMKRLAMLMPEARVASTDEYGIPPAWMEGMAFAWLAHRFLERLPGNCPDVTGALGPRTLGALYP 362
                                    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       361 
                                                                                                                                                                               151   157            172    179                                                                                                     283 287                                                                           


Chain B from PDB  Type:PROTEIN  Length:356
 aligned with ANMK_PSEAE | Q9I5Q5 from UniProtKB/Swiss-Prot  Length:363

    Alignment length:363
                                                                                                                                                                                                                                                                                                                                                                                                   363 
                                    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       361 | 
           ANMK_PSEAE     2 PRYLGLMSGTSLDGMDIVLIEQGDRTTLLASHYLPMPAGLREDILALCVPGPDEIARAAEVEQRWVALAAQGVRELLLQQQMSPDEVRAIGSHGQTIRHEPARHFTVQIGNPALLAELTGIDVVADFRRRDVAAGGQGAPLVPAFHQALFGDDDTSRAVLNIGGFSNVSLLSPGKPVRGFDCGPGNVLMDAWIHHQRGEHFDRDGAWAASGQVNHALLASLLADEFFAARGPKSTGRERFNLPWLQEHLARHPALPAADIQATLLELSARSISESLLDAQPDCEEVLVCGGGAFNTALMKRLAMLMPEARVASTDEYGIPPAWMEGMAFAWLAHRFLERLPGNCPDVTGALGPRTLGALYPA-   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) UPF0075-3qbwB01 B:2-363                                                                                                                                                                                                                                                                                                                                                   - Pfam domains (1)
           Pfam domains (2) UPF0075-3qbwB02 B:2-363                                                                                                                                                                                                                                                                                                                                                   - Pfam domains (2)
         Sec.struct. author .eeeeeee.....eeeeeeeee...eeeeeeeeee..hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh....hhh..eeee..eeeeee....eeeee..hhhhhhhh...eee...hhhhh.........hhhhhhhh.---..eeeeee..eeeeeee......eeeeeee..hhhhhhhhhhh.................hhhhhhhh..hhhh.............hhhhhhhh.----..hhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhh.hhhhhhhhhh....eeeehhhh...hhhhhhhhhhhhhhhhh.......hhhh.........eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qbw B   2 PRYLGLMSGTSLDGMDIVLIEQGDRTTLLASHYLPMPAGLREDILALCVPGPDEIARAAEVEQRWVALAAQGVRELLLQQQMSPDEVRAIGSHGQTIRHEPARHFTVQIGNPALLAELTGIDVVADFRRRDVAAGGQGAPLVPAFHQALFG---TSRAVLNIGGFSNVSLLSPGKPVRGFDCGPGNVLMDAWIHHQRGEHFDRDGAWAASGQVNHALLASLLADEFFAARGPKSTGRERFNLPWLQEHLA----LPAADIQATLLELSARSISESLLDAQPDCEEVLVCGGGAFNTALMKRLAMLMPEARVASTDEYGIPPAWMEGMAFAWLAHRFLERLPGNCPDVTGALGPRTLGALYPAG 364
                                    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       361   
                                                                                                                                                                                152 156                                                                                            251  256
   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 3QBW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Actin_ATPase (173)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ANMK_PSEAE | Q9I5Q5)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0016773    phosphotransferase activity, alcohol group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
    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:0097175    1,6-anhydro-N-acetyl-beta-muramic acid catabolic process    The chemical reactions and pathways resulting in the breakdown of 1,6-anhydro-N-acetylmuramic acid, the 1,6-anhydro-derivative of N-acetyl-beta-muramic acid.
    GO:0006040    amino sugar metabolic process    The chemical reactions and pathways involving any amino sugar, sugars containing an amino group in place of a hydroxyl group.
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0009254    peptidoglycan turnover    The continual breakdown and regeneration of peptidoglycan required to maintain the cell wall.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ANMK_PSEAE | Q9I5Q5: 3qbx 4mo4 4mo5

(-) Related Entries Specified in the PDB File

3qbx