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(-) Description

Title :  GLUCOSAMINE-6-PHOSPHATE DEAMINASE FROM E.COLI, R CONFORMER. COMPLEXED WITH THE ALLOSTERIC ACTIVATOR N-ACETYL-GLUCOSAMINE-6-PHOSPHATE AT 2.2 A RESOLUTION
 
Authors :  E. Rudino-Pinera, S. Morales-Arrieta, S. P. Rojas-Trejo, E. Horjales
Date :  07 Sep 00  (Deposition) - 04 Jan 02  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Allosteric Enzyme, Entropic Effects, Aldose-Ketose Isomerase, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Rudino-Pinera, S. Morales-Arrieta, S. P. Rojas-Trejo, E. Horjale
Structural Flexibility, An Essential Component Of The Allosteric Activation In Escherichia Coli Glucosamine-6-Phosphate Deaminase.
Acta Crystallogr. , Sect. D V. 58 10 2002
PubMed-ID: 11752775  |  Reference-DOI: 10.1107/S0907444901016699
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUCOSAMINE-6-PHOSPHATE DEAMINASE
    ChainsA, B
    EC Number5.3.1.10
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTZ18-R
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    Other DetailsCOMPLEXED WITH N-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE
    SynonymGLUCOSAMINE-6-PHOSPHATE DEAMINASE, GNPDA, GLCN6P DEAMINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (3x)AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
116G2Ligand/IonN-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
116G6Ligand/IonN-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:1 , SER A:151 , SER A:152 , ARG A:158 , ILE A:159 , LYS A:160 , THR A:161 , HOH A:1283 , HOH A:1284 , HOH A:1326BINDING SITE FOR RESIDUE 16G A 1267
2AC2SOFTWAREMET B:1 , SER B:151 , SER B:152 , ARG B:158 , ILE B:159 , LYS B:160 , THR B:161 , HOH B:2598 , HOH B:2624 , HOH B:2625 , HOH B:2682BINDING SITE FOR RESIDUE 16G B 2567

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1FRZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLC_GALNAC_ISOMERASEPS01161 Glucosamine/galactosamine-6-phosphate isomerases signature.NAGB_ECOLI125-143
 
  2A:125-143
B:125-143
Biological Unit 1 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLC_GALNAC_ISOMERASEPS01161 Glucosamine/galactosamine-6-phosphate isomerases signature.NAGB_ECOLI125-143
 
  6A:125-143
B:125-143

(-) Exons   (0, 0)

(no "Exon" information available for 1FRZ)

(-) 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:266
 aligned with NAGB_ECOLI | P0A759 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:266
                                    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      
           NAGB_ECOLI     1 MRLIPLTTAEQVGKWAARHIVNRINAFKPTADRPFVLGLPTGGTPMTTYKALVEMHKAGQVSFKHVVTFNMDEYVGLPKEHPESYYSFMHRNFFDHVDIPAENINLLNGNAPDIDAECRQYEEKIRSYGKIHLFMGGVGNDGHIAFNEPASSLASRTRIKTLTHDTRVANSRFFDNDVNQVPKYALTVGVGTLLDAEEVMILVLGSQKALALQAAVEGCVNHMWTISCLQLHPKAIMVCDEPSTMELKVKTLRYFNELEAENIKGL 266
               SCOP domains d1frza_ A: Glucosamine 6-phosphate deaminase/isomerase NagB                                                                                                                                                                                                                SCOP domains
               CATH domains 1frzA00 A:1-266  [code=3.40.50.1360, no name defined]                                                                                                                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..hhhhhhhhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhhhh.......eeeee.eee.........hhhhhhhhhhhhhh..hhh.ee.......hhhhhhhhhhhhhhhhh...eeee.....................eeee.hhhhhhhhhhhh..hhhhh..eeee.hhhhhhh...eeeee.hhhhhhhhhhhhhh.....hhhhhhhhh..eeeee.hhhhh..hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------GLC_GALNAC_ISOMERAS--------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1frz A   1 MRLIPLTTAEQVGKWAARHIVNRINAFKPTADRPFVLGLPTGGTPMTTYKALVEMHKAGQVSFKHVVTFNMDEYVGLPKEHPESYYSFMHRNFFDHVDIPAENINLLNGNAPDIDAECRQYEEKIRSYGKIHLFMGGVGNDGHIAFNEPASSLASRTRIKTLTHDTRVANSRFFDNDVNQVPKYALTVGVGTLLDAEEVMILVLGSQKALALQAAVEGCVNHMWTISCLQLHPKAIMVCDEPSTMELKVKTLRYFNELEAENIKGL 266
                                    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      

Chain B from PDB  Type:PROTEIN  Length:266
 aligned with NAGB_ECOLI | P0A759 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:266
                                    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      
           NAGB_ECOLI     1 MRLIPLTTAEQVGKWAARHIVNRINAFKPTADRPFVLGLPTGGTPMTTYKALVEMHKAGQVSFKHVVTFNMDEYVGLPKEHPESYYSFMHRNFFDHVDIPAENINLLNGNAPDIDAECRQYEEKIRSYGKIHLFMGGVGNDGHIAFNEPASSLASRTRIKTLTHDTRVANSRFFDNDVNQVPKYALTVGVGTLLDAEEVMILVLGSQKALALQAAVEGCVNHMWTISCLQLHPKAIMVCDEPSTMELKVKTLRYFNELEAENIKGL 266
               SCOP domains d1frzb_ B: Glucosamine 6-phosphate deaminase/isomerase NagB                                                                                                                                                                                                                SCOP domains
               CATH domains 1frzB00 B:1-266  [code=3.40.50.1360, no name defined]                                                                                                                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..hhhhhhhhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhhhh.......eeeee.eee.........hhhhhhhhhhhhhh..hhh.ee.......hhhhhhhhhhhhhhhhh...eeee.....................eeee.hhhhhhhhhhhhh.hhhhh..eeee.hhhhhhh...eeeee.hhhhhhhhhhhhh......hhhhhhhhh..eeeee.hhhhh..hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------GLC_GALNAC_ISOMERAS--------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1frz B   1 MRLIPLTTAEQVGKWAARHIVNRINAFKPTADRPFVLGLPTGGTPMTTYKALVEMHKAGQVSFKHVVTFNMDEYVGLPKEHPESYYSFMHRNFFDHVDIPAENINLLNGNAPDIDAECRQYEEKIRSYGKIHLFMGGVGNDGHIAFNEPASSLASRTRIKTLTHDTRVANSRFFDNDVNQVPKYALTVGVGTLLDAEEVMILVLGSQKALALQAAVEGCVNHMWTISCLQLHPKAIMVCDEPSTMELKVKTLRYFNELEAENIKGL 266
                                    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      

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NAGB_ECOLI | P0A759)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
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:0006048    UDP-N-acetylglucosamine biosynthetic process    The chemical reactions and pathways resulting in the formation of UDP-N-acetylglucosamine, a substance composed of N-acetylglucosamine, a common structural unit of oligosaccharides, in glycosidic linkage with uridine diphosphate.
    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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NAGB_ECOLI | P0A7591cd5 1dea 1fqo 1fs5 1fs6 1fsf 1hor 1hot 1jt9 2wu1

(-) Related Entries Specified in the PDB File

1cd5 1CD5 CONTAINS THE SAME PROTEIN IN THE T CONFORMER
1d9t CONTAINS THE HUMAN ENZYME IN THE R CONFORMER COMPLEXED WITH SULPHATE IONS AND THE ALLOSTERIC ACTIVATOR
1dea CONTAINS THE SAME R CONFORMER PROTEIN COMPLEXED WITH INORGANIC PHOSPHATE
1fqo CONTAINS THE SAME MOLECULE COMPLEXED WITH THE SUBSTRATE OF THE REVERSE REACTION FRUCTOSE-6-PHOSPHATE
1hor CONTAINS THE SAME R CONFORMER PROTEIN COMPLEXED WITH BOTH PHOSPHATE IONS AND THE COMPETITIVE INHIBITOR 2-DEOXY-2- AMINO-GLUCITOL-6-PHOSPHATE
1hot CONTAINS THE SAME R CONFORMER PROTEIN COMPLEXED WITH BOTH PHOSPHATE IONS AND THE ALLOSTERIC ACTIVATOR N-ACETYL- GLUCOSAMINE-6-PHOSPHATE