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(-) Description

Title :  STRUCTURE AND KINETICS OF A MONOMERIC GLUCOSAMINE-6-PHOSPHATE DEAMINASE: MISSING LINK OF THE NAGB SUPERFAMILY
 
Authors :  F. Vincent, G. J. Davies, J. A. Brannigan
Date :  21 Feb 05  (Deposition) - 09 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Substrate Inhibition, Fructose-6-Phosphate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Vincent, G. J. Davies, J. A. Brannigan
Structure And Kinetics Of A Monomeric Glucosamine 6-Phosphate Deaminase: Missing Link Of The Nagb Superfamily
J. Biol. Chem. V. 280 19649 2005
PubMed-ID: 15755726  |  Reference-DOI: 10.1074/JBC.M502131200

(-) Compounds

Molecule 1 - GLUCOSAMINE-6-PHOSPHATE DEAMINASE
    Chains: A, B
    EC Number: 3.5.99.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Strain: IG20
    Synonym: GLUCOSAMINE-6-PHOSPHATE ISOMERASE 1, GLCN6P DEAMINASE 1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1PGA2Ligand/Ion2-PHOSPHOGLYCOLIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PGA1Ligand/Ion2-PHOSPHOGLYCOLIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1PGA1Ligand/Ion2-PHOSPHOGLYCOLIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:37 , GLY A:38 , THR A:39 , ILE A:133 , HIS A:138 , LYS A:202 , HOH A:2024 , HOH A:2110 , HOH A:2116 , HOH A:2140 , HOH A:2177 , HOH A:2178BINDING SITE FOR RESIDUE PGA A1242
2AC2SOFTWAREGLY B:37 , GLY B:38 , THR B:39 , GLY B:132 , ILE B:133 , HIS B:138 , ARG B:167 , LYS B:202 , HOH B:2034 , HOH B:2140 , HOH B:2196 , HOH B:2197 , HOH B:2198 , HOH B:2199BINDING SITE FOR RESIDUE PGA B1243

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2BKV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLC_GALNAC_ISOMERASEPS01161 Glucosamine/galactosamine-6-phosphate isomerases signature.NAGB_BACSU120-138
 		  2A:120-138
B:120-138
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLC_GALNAC_ISOMERASEPS01161 Glucosamine/galactosamine-6-phosphate isomerases signature.NAGB_BACSU120-138
 		  1A:120-138
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLC_GALNAC_ISOMERASEPS01161 Glucosamine/galactosamine-6-phosphate isomerases signature.NAGB_BACSU120-138
 		  1-
B:120-138

(-) Exons   (0, 0)

(no "Exon" information available for 2BKV)

(-) 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:241
 aligned with NAGB_BACSU | O35000 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:241
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240 
           NAGB_BACSU     1 MKVMECQTYEELSQIAARITADTIKEKPDAVLGLATGGTPEGTYRQLIRLHQTENLSFQNITTVNLDEYAGLSSDDPNSYHFYMNDRFFQHIDSKPSRHFIPNGNADDLEAECRRYEQLVDSLGDTDIQLLGIGRNGHIGFNEPGTSFKSRTHVVTLNEQTRQANARYFPSIDSVPKKALTMGIQTILSSKRILLLISGKSKAEAVRKLLEGNISEDFPASALHLHSDVTVLIDREAASLR 241
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2bkvA00 A:1-241  [code=3.40.50.1360, no name defined]                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhh.......eeee.eee.........hhhhhhhhhhhhhh..hhh.ee.......hhhhhhhhhhhhhhhh....eeee.....................eeee.hhhhhhhhhhhh.hhhhh..eeee.hhhhhhh...eeeee.hhhhhhhhhhhhhh.....hhhhhhhhh..eeeeee.hhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------GLC_GALNAC_ISOMERAS------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bkv A   1 MKVMECQTYEELSQIAARITADTIKEKPDAVLGLATGGTPEGTYRQLIRLHQTENLSFQNITTVNLDEYAGLSSDDPNSYHFYMNDRFFQHIDSKPSRHFIPNGNADDLEAECRRYEQLVDSLGDTDIQLLGIGRNGHIGFNEPGTSFKSRTHVVTLNEQTRQANARYFPSIDSVPKKALTMGIQTILSSKRILLLISGKSKAEAVRKLLEGNISEDFPASALHLHSDVTVLIDREAASLR 241
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240 


Chain B from PDB  Type:PROTEIN  Length:242
 aligned with NAGB_BACSU | O35000 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:242
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240  
           NAGB_BACSU     1 MKVMECQTYEELSQIAARITADTIKEKPDAVLGLATGGTPEGTYRQLIRLHQTENLSFQNITTVNLDEYAGLSSDDPNSYHFYMNDRFFQHIDSKPSRHFIPNGNADDLEAECRRYEQLVDSLGDTDIQLLGIGRNGHIGFNEPGTSFKSRTHVVTLNEQTRQANARYFPSIDSVPKKALTMGIQTILSSKRILLLISGKSKAEAVRKLLEGNISEDFPASALHLHSDVTVLIDREAASLRP 242
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2bkvB00 B:1-242  [code=3.40.50.1360, no name defined]                                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhh......eeee.eee.........hhhhhhhhhhhhhh..hhh.ee.......hhhhhhhhhhhhhhhhh...eeee.....................eeee.hhhhhhhhhhhh.hhhhh..eeee.hhhhhhh...eeeee.hhhhhhhhhhhhhh.....hhhhhhhhh..eeeeee.hhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------GLC_GALNAC_ISOMERAS-------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bkv B   1 MKVMECQTYEELSQIAARITADTIKEKPDAVLGLATGGTPEGTYRQLIRLHQTENLSFQNITTVNLDEYAGLSSDDPNSYHFYMNDRFFQHIDSKPSRHFIPNGNADDLEAECRRYEQLVDSLGDTDIQLLGIGRNGHIGFNEPGTSFKSRTHVVTLNEQTRQANARYFPSIDSVPKKALTMGIQTILSSKRILLLISGKSKAEAVRKLLEGNISEDFPASALHLHSDVTVLIDREAASLRP 242
                                    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 2BKV)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BKV)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NAGB_BACSU | O35000)
molecular function
    GO:0004342    glucosamine-6-phosphate deaminase activity    Catalysis of the reaction: D-glucosamine 6-phosphate + H(2)O = beta-D-fructose 6-phosphate + NH(4)(+).
    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.
biological process
    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.

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 Related Entries

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        NAGB_BACSU | O35000: 2bkx

(-) Related Entries Specified in the PDB File

2bkx STRUCTURE AND KINETICS OF A MONOMERIC GLUCOSAMINE-6-PHOSPHATE DEAMINASE: MISSING LINK OF THE NAGB SUPERFAMILY