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(-) Description

Title :  CRYSTAL STRUCTURE OF N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE (TM0814) FROM THERMOTOGA MARITIMA AT 2.5 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  15 Oct 02  (Deposition) - 18 Dec 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Tm0814, N-Acetylglucosamine-6- Phosphate Deacetylase, Jcsg, Psi, Protein Structure Initiative, Joint Center For Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of N-Acetylglucosamine-6-Phosphate Deacetylase (Tm0814) From Thermotoga Maritima At 2. 5 A Resolution
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) 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: TM0814
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 20)

Asymmetric/Biological Unit (2, 20)
No.NameCountTypeFull Name
1FE2Ligand/IonFE (III) ION
2MSE18Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:115 , HIS A:176 , HIS A:197 , HOH A:408 , HOH A:491BINDING SITE FOR RESIDUE FE A 401
2AC2SOFTWAREGLU B:115 , HIS B:176 , HIS B:197 , HOH B:405 , HOH B:407BINDING SITE FOR RESIDUE FE B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1O12)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Gly A:116 -Pro A:117
2Ser A:145 -Pro A:146
3Phe A:198 -Pro A:199
4Gly B:116 -Pro B:117
5Ser B:145 -Pro B:146
6Phe B:198 -Pro B:199

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1O12)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1O12)

(-) Exons   (0, 0)

(no "Exon" information available for 1O12)

(-) 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:364
 aligned with Q9WZS1_THEMA | Q9WZS1 from UniProtKB/TrEMBL  Length:364

    Alignment length:364
                                    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    
         Q9WZS1_THEMA     1 MIVEKVLIVDPIDGEFTGDVEIEEGKIVKVEKRECIPRGVLMPGFVDPHIHGVVGADTMNCDFSEMEEFLYSQGVTTFLATTVSTSLEKMKEILRKARDYILENPSTSLLGVHLEGPYISKEKKGAHSEKHIRPPSERELSEIDSPAKMLTFAPEIESSELLLRLVKRDIVLSAGHSIATFEEFMKFYKEGVKRITHFPNGLKPLHHREIGITGAGLLLDDVKLELICDGVHLSREMVKLVYKVKKANGIVLVTDSISAAGLKDGTTTLGDLVVKVKDGVPRLEDGTLAGSTLFFSQAVKNFRKFTGCSITELAKVSSYNSCVELGLDDRGRIAEGTRADLVLLDEDLNVVMTIKEGEVVFRSR 364
               SCOP domains d1o12a1 A:1-43,A:332-364                   d1o12a2 A:44-331 N-acetylglucosamine-6-phosphate deacetylase, NagA, catalytic domain                                                                                                                                                                                                            d1o12a1 A:1-43,A:332-364          SCOP domains
               CATH domains -1o12A01 A:2-43,A:332-364                  1o12A02 A:44-331 Metal-dependent hydrolases                                                                                                                                                                                                                                                     1o12A01 A:2-43,A:332-364          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee...eeeeeeeeee..eeeeeee.......eeee.eeeeee.ee..ee....hhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhh....eeeeeee....hhhhh...........hhhhhh.....eeeeee.....hhhhhhhhhhhh.eeee.....hhhhhhhhhh....ee..............hhhhhhhhhh...eeeee......hhhhhhhhhhhhh...eeee............eee....eeeee..eee...........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...............eeee.....eeeeee..eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o12 A   1 mIVEKVLIVDPIDGEFTGDVEIEEGKIVKVEKRECIPRGVLmPGFVDPHIHGVVGADTmNCDFSEmEEFLYSQGVTTFLATTVSTSLEKmKEILRKARDYILENPSTSLLGVHLEGPYISKEKKGAHSEKHIRPPSERELSEIDSPAKmLTFAPEIESSELLLRLVKRDIVLSAGHSIATFEEFmKFYKEGVKRITHFPNGLKPLHHREIGITGAGLLLDDVKLELICDGVHLSREmVKLVYKVKKANGIVLVTDSISAAGLKDGTTTLGDLVVKVKDGVPRLEDGTLAGSTLFFSQAVKNFRKFTGCSITELAKVSSYNSCVELGLDDRGRIAEGTRADLVLLDEDLNVVmTIKEGEVVFRSR 364
                            |       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    
                            |                                       42-MSE           59-MSE 66-MSE                  90-MSE                                                    149-MSE                             185-MSE                                             237-MSE                                                                                                            352-MSE        
                            1-MSE                                                                                                                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:364
 aligned with Q9WZS1_THEMA | Q9WZS1 from UniProtKB/TrEMBL  Length:364

    Alignment length:364
                                    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    
         Q9WZS1_THEMA     1 MIVEKVLIVDPIDGEFTGDVEIEEGKIVKVEKRECIPRGVLMPGFVDPHIHGVVGADTMNCDFSEMEEFLYSQGVTTFLATTVSTSLEKMKEILRKARDYILENPSTSLLGVHLEGPYISKEKKGAHSEKHIRPPSERELSEIDSPAKMLTFAPEIESSELLLRLVKRDIVLSAGHSIATFEEFMKFYKEGVKRITHFPNGLKPLHHREIGITGAGLLLDDVKLELICDGVHLSREMVKLVYKVKKANGIVLVTDSISAAGLKDGTTTLGDLVVKVKDGVPRLEDGTLAGSTLFFSQAVKNFRKFTGCSITELAKVSSYNSCVELGLDDRGRIAEGTRADLVLLDEDLNVVMTIKEGEVVFRSR 364
               SCOP domains d1o12b1 B:1-43,B:332-364                   d1o12b2 B:44-331 N-acetylglucosamine-6-phosphate deacetylase, NagA, catalytic domain                                                                                                                                                                                                            d1o12b1 B:1-43,B:332-364          SCOP domains
               CATH domains -1o12B01 B:2-40,B:331-364               1o12B02 B:41-330 Metal-dependent hydrolases                                                                                                                                                                                                                                                       1o12B01 B:2-40,B:331-364           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee...eeeeeeeeee..eeeeeee.......eeee.eeeeee.ee..ee....hhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhh....eeeeeee....................hhhhhhh....eeeeee.....hhhhhhhhhhhh.eeee.....hhhhhhhhhhh...ee..............hhhhhhhhhh...eeeee......hhhhhhhhhhhhh...eeee...........eeeee..eeeeee..eee...........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..............eeee.....eeeeee..eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o12 B   1 mIVEKVLIVDPIDGEFTGDVEIEEGKIVKVEKRECIPRGVLmPGFVDPHIHGVVGADTmNCDFSEmEEFLYSQGVTTFLATTVSTSLEKmKEILRKARDYILENPSTSLLGVHLEGPYISKEKKGAHSEKHIRPPSERELSEIDSPAKmLTFAPEIESSELLLRLVKRDIVLSAGHSIATFEEFmKFYKEGVKRITHFPNGLKPLHHREIGITGAGLLLDDVKLELICDGVHLSREmVKLVYKVKKANGIVLVTDSISAAGLKDGTTTLGDLVVKVKDGVPRLEDGTLAGSTLFFSQAVKNFRKFTGCSITELAKVSSYNSCVELGLDDRGRIAEGTRADLVLLDEDLNVVmTIKEGEVVFRSR 364
                            |       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    
                            1-MSE                                   42-MSE           59-MSE 66-MSE                  90-MSE                                                    149-MSE                             185-MSE                                             237-MSE                                                                                                            352-MSE
   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  (0, 0)

(no "Pfam Domain" information available for 1O12)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9WZS1_THEMA | Q9WZS1)
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.
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: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.

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