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(-) Description

Title :  CRYSTAL STRUCTURE OF N-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE DEACETYLASE D273N MUTANT COMPLEXED WITH N-ACETYL PHOSPHONAMIDATE-D-GLUCOSAMINE-6-PHOSPHATE
 
Authors :  A. A. Fedorov, E. V. Fedorov, R. S. Hall, F. M. Raushel, S. C. Almo
Date :  14 Mar 07  (Deposition) - 24 Jul 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase, Aminohydrolase, (Beta/Alpha)8-Barrel, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. S. Hall, S. Brown, A. A. Fedorov, E. V. Fedorov, C. Xu, P. C. Babbitt, S. C. Almo, F. M. Raushel
Structural Diversity Within The Mononuclear And Binuclear Active Sites Of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase.
Biochemistry V. 46 7953 2007
PubMed-ID: 17567048  |  Reference-DOI: 10.1021/BI700544C

(-) Compounds

Molecule 1 - N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE
    Chains: A, B
    EC Number: 3.5.1.25
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NAGA, B0677, JW0663
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: GLCNAC 6-P DEACETYLASE

 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
1NNG2Ligand/Ion2-DEOXY-2-{[(S)-HYDROXY(METHYL)PHOSPHORYL]AMINO}-6-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE
2ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:131 , HIS A:195 , HIS A:216 , NNG A:411BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWAREGLU B:131 , HIS B:195 , HIS B:216 , NNG B:411BINDING SITE FOR RESIDUE ZN B 401
3AC3SOFTWAREASN A:61 , GLU A:131 , GLY A:141 , THR A:142 , HIS A:143 , HIS A:195 , HIS A:216 , ASN A:219 , ALA A:220 , HIS A:251 , ASN A:273 , THR A:305 , LEU A:306 , GLY A:308 , ZN A:401 , HOH A:476 , HOH A:513 , HOH A:549 , HOH A:587 , ARG B:227BINDING SITE FOR RESIDUE NNG A 411
4AC4SOFTWAREARG A:227 , ASN B:61 , GLU B:131 , GLY B:141 , THR B:142 , HIS B:143 , HIS B:195 , HIS B:216 , ASN B:219 , ALA B:220 , HIS B:251 , ASN B:273 , LEU B:306 , GLY B:308 , ZN B:401 , HOH B:516 , HOH B:525 , HOH B:536 , HOH B:540BINDING SITE FOR RESIDUE NNG B 411

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P53)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:132 -Pro A:133
2Gly B:132 -Pro B:133

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2P53)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2P53)

(-) Exons   (0, 0)

(no "Exon" information available for 2P53)

(-) 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:382
 aligned with NAGA_ECOLI | P0AF18 from UniProtKB/Swiss-Prot  Length:382

    Alignment length:382
                                    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       290       300       310       320       330       340       350       360       370       380  
           NAGA_ECOLI     1 MYALTQGRIFTGHEFLDDHAVVIADGLIKSVCPVAELPPEIEQRSLNGAILSPGFIDVQLNGCGGVQFNDTAEAVSVETLEIMQKANEKSGCTNYLPTLITTSDELMKQGVRVMREYLAKHPNQALGLHLEGPWLNLVKKGTHNPNFVRKPDAALVDFLCENADVITKVTLAPEMVPAEVISKLANAGIVVSAGHSNATLKEAKAGFRAGITFATHLYNAMPYITGREPGLAGAILDEADIYCGIIADGLHVDYANIRNAKRLKGDKLCLVTDATAPAGANIEQFIFAGKTIYYRNGLCVDENGTLSGSSLTMIEGVRNLVEHCGIALDEVLRMATLYPARAIGVEKRLGTLAAGKVANLTAFTPDFKITKTIVNGNEVVTQ 382
               SCOP domains d2p53a1 A:1-53,A:351-382                             d2p53a2 A:54-350 N-acetylglucosamine-6-phosphate deacetylase, NagA, catalytic domain                                                                                                                                                                                                                     d2p53a1 A:1-53,A:351-382         SCOP domains
               CATH domains 2p53A01 A:1-54,A:345-382 Urease, subunit C, domain 1  2p53A02 A:55-280,A:281-344 Metal-dependent hydrolases                                                                                                                                                                             2p53A02 A:55-280,A:281-344 Metal-dependent hydrolases           2p53A01 A:1-54,A:345-382               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eee....ee..eeeeee..eeeeeee.hhh....eeee....eeee.eeeeee.ee..ee........hhhhhhhhhhhhhhh.eeeeeeeee..hhhhhhhhhhhhhhhhh........eeee....hhhhh...hhhhh...hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhh..ee..............hhhhhhhhhh...eeeee......hhhhhhhhhhhhh..eeee............eeee..eeeeee..eeee..........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh................eeee.....eeeeee..eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p53 A   1 MYALTQGRIFTGHEFLDDHAVVIADGLIKSVCPVAELPPEIEQRSLNGAILSPGFIDVQLNGCGGVQFNDTAEAVSVETLEIMQKANEKSGCTNYLPTLITTSDELMKQGVRVMREYLAKHPNQALGLHLEGPWLNLVKKGTHNPNFVRKPDAALVDFLCENADVITKVTLAPEMVPAEVISKLANAGIVVSAGHSNATLKEAKAGFRAGITFATHLYNAMPYITGREPGLAGAILDEADIYCGIIADGLHVDYANIRNAKRLKGDKLCLVTNATAPAGANIEQFIFAGKTIYYRNGLCVDENGTLSGSSLTMIEGVRNLVEHCGIALDEVLRMATLYPARAIGVEKRLGTLAAGKVANLTAFTPDFKITKTIVNGNEVVTQ 382
                                    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       290       300       310       320       330       340       350       360       370       380  


Chain B from PDB  Type:PROTEIN  Length:382
 aligned with NAGA_ECOLI | P0AF18 from UniProtKB/Swiss-Prot  Length:382

    Alignment length:382
                                    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       290       300       310       320       330       340       350       360       370       380  
           NAGA_ECOLI     1 MYALTQGRIFTGHEFLDDHAVVIADGLIKSVCPVAELPPEIEQRSLNGAILSPGFIDVQLNGCGGVQFNDTAEAVSVETLEIMQKANEKSGCTNYLPTLITTSDELMKQGVRVMREYLAKHPNQALGLHLEGPWLNLVKKGTHNPNFVRKPDAALVDFLCENADVITKVTLAPEMVPAEVISKLANAGIVVSAGHSNATLKEAKAGFRAGITFATHLYNAMPYITGREPGLAGAILDEADIYCGIIADGLHVDYANIRNAKRLKGDKLCLVTDATAPAGANIEQFIFAGKTIYYRNGLCVDENGTLSGSSLTMIEGVRNLVEHCGIALDEVLRMATLYPARAIGVEKRLGTLAAGKVANLTAFTPDFKITKTIVNGNEVVTQ 382
               SCOP domains d2p53b1 B:1-53,B:351-382                             d2p53b2 B:54-350 N-acetylglucosamine-6-phosphate deacetylase, NagA, catalytic domain                                                                                                                                                                                                                     d2p53b1 B:1-53,B:351-382         SCOP domains
               CATH domains 2p53B01 B:1-54,B:345-382 Urease, subunit C, domain 1  2p53B02 B:55-280,B:281-344 Metal-dependent hydrolases                                                                                                                                                                             2p53B02 B:55-280,B:281-344 Metal-dependent hydrolases           2p53B01 B:1-54,B:345-382               CATH domains
           Pfam domains (1) -------------------------------------------------Amidohydro_1-2p53B01 B:50-364                                                                                                                                                                                                                                                                                              ------------------ Pfam domains (1)
           Pfam domains (2) -------------------------------------------------Amidohydro_1-2p53B02 B:50-364                                                                                                                                                                                                                                                                                              ------------------ Pfam domains (2)
         Sec.struct. author .eeee..eee....ee..eeeeee..eeeeeee.hhh.....eee....eeee.eeeeee.ee..ee........hhhhhhhhhhhhhh..eeeeeeeee..hhhhhhhhhhhhhhhhhhh......eeee....hhhhh...........hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhh..ee..............hhhhhhhhhh...eeeee......hhhhhhhhhhhhh..eeee............eeee..eeeeee..eeee..........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh................eeee.....eeeeee..eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p53 B   1 MYALTQGRIFTGHEFLDDHAVVIADGLIKSVCPVAELPPEIEQRSLNGAILSPGFIDVQLNGCGGVQFNDTAEAVSVETLEIMQKANEKSGCTNYLPTLITTSDELMKQGVRVMREYLAKHPNQALGLHLEGPWLNLVKKGTHNPNFVRKPDAALVDFLCENADVITKVTLAPEMVPAEVISKLANAGIVVSAGHSNATLKEAKAGFRAGITFATHLYNAMPYITGREPGLAGAILDEADIYCGIIADGLHVDYANIRNAKRLKGDKLCLVTNATAPAGANIEQFIFAGKTIYYRNGLCVDENGTLSGSSLTMIEGVRNLVEHCGIALDEVLRMATLYPARAIGVEKRLGTLAAGKVANLTAFTPDFKITKTIVNGNEVVTQ 382
                                    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       290       300       310       320       330       340       350       360       370       380
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Amidohydrolase (126)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NAGA_ECOLI | P0AF18)
molecular function
    GO:0008448    N-acetylglucosamine-6-phosphate deacetylase activity    Catalysis of the reaction: N-acetyl-D-glucosamine 6-phosphate + H2O = D-glucosamine 6-phosphate + acetate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016810    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds    Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006046    N-acetylglucosamine catabolic process    The chemical reactions and pathways resulting in the breakdown of N-acetylglucosamine. The D isomer is a common structural unit of glycoproteins in plants, bacteria and animals; it is often the terminal sugar of an oligosaccharide group of a glycoprotein.
    GO:0006044    N-acetylglucosamine metabolic process    The chemical reactions and pathways involving N-acetylglucosamine. The D isomer is a common structural unit of glycoproteins in plants, bacteria and animals; it is often the terminal sugar of an oligosaccharide group of a glycoprotein.
    GO:0019262    N-acetylneuraminate catabolic process    The chemical reactions and pathways resulting in the breakdown of N-acetylneuraminate, the anion of 5-(acetylamino)-3,5-dideoxy-D-glycero-D-galacto-non-3-ulosonic acid.
    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:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NAGA_ECOLI | P0AF18: 1ymy 1yrr 2p50

(-) Related Entries Specified in the PDB File

1ymy APO-FORM OF THE SAME WILD TYPE PROTEIN
2p50 THE SAME WILD TYPE PROTEIN LIGANDED WITH ZN