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(-) Description

Title :  CRYSTAL STRUCTURE OF GLMU FROM MYCOBACTERIUM TUBERCULOSIS, LIGAND-FREE FORM
 
Authors :  Z. Zhang, C. J. Squire, E. N. Baker
Date :  27 May 08  (Deposition) - 10 Mar 09  (Release) - 16 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Glmu, Uridyltransferase, Acetyltransferase, Acyltransferase, Cell Shape, Cell Wall Biogenesis/Degradation, Magnesium, Metal-Binding, Multifunctional Enzyme, Nucleotidyltransferase, Peptidoglycan Synthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Z. Zhang, E. M. Bulloch, R. D. Bunker, E. N. Baker, C. J. Squire
Structure And Function Of Glmu From Mycobacterium Tuberculosis.
Acta Crystallogr. , Sect. D V. 65 275 2009
PubMed-ID: 19237750  |  Reference-DOI: 10.1107/S0907444909001036

(-) Compounds

Molecule 1 - BIFUNCTIONAL PROTEIN GLMU
    ChainsA
    EC Number2.7.7.23, 2.3.1.157
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPDEST17
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneGLMU, RV1018C, MT1046
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS
    Organism Taxid1773
    Synonym[INCLUDES: UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE (EC 2.7.7.23) (N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE)

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (3x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3D98)

(-) Sites  (0, 0)

(no "Site" information available for 3D98)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D98)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Gly A:5 -Asp A:6
2Asn A:203 -Ala A:204
3Gly A:305 -Pro A:306
4Gly A:338 -Pro A:339
5Gly A:390 -Ala A:391

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D98)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3D98)

(-) Exons   (0, 0)

(no "Exon" information available for 3D98)

(-) 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:390
 aligned with GLMU_MYCTO | P9WMN2 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:390
                                    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       371       381       391
           GLMU_MYCTO     2 TFPGDTAVLVLAAGPGTRMRSDTPKVLHTLAGRSMLSHVLHAIAKLAPQRLIVVLGHDHQRIAPLVGELADTLGRTIDVALQDRPLGTGHAVLCGLSALPDDYAGNVVVTSGDTPLLDADTLADLIATHRAVSAAVTVLTTTLDDPFGYGRILRTQDHEVMAIVEQTDATPSQREIREVNAGVYAFDIAALRSALSRLSSNNAQQELYLTDVIAILRSDGQTVHASHVDDSALVAGVNNRVQLAELASELNRRVVAAHQLAGVTVVDPATTWIDVDVTIGRDTVIHPGTQLLGRTQIGGRCVVGPDTTLTDVAVGDGASVVRTHGSSSSIGDGAAVGPFTYLRPGTALGADGKLGAFVEVKNSTIGTGTKVPHLTYVGDADIGEYSNIGA 391
               SCOP domains d3d98a1 A:2-263 N-acetylglucosamine 1-phosphate uridyltransferase GlmU, N-terminal domain                                                                                                                                                                             d3d98a2 A:264-391 N-acetylglucosamine 1-phosphate uridyltransferase GlmU, C-terminal domain                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee....hhhhh...hhhh.ee..eehhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhh.........eeeee......hhhhhhhhhhhhhhh...eeeeeee........eeee.....eeeeehhhhh..hhhhh.eeeeeeeeehhhhhhhhhh.............hhhhhhhhhh...eeeee..hhhhh....hhhhhhhhhhhhhhhhhhhhhhh..ee.hhh.eee....ee....ee...eeee...ee....ee...eeeeeeee....ee..eeeeeeee....ee...eee...eee....eeeeeeeee..ee....eeeeeeeee..ee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3d98 A   2 TFPGDTAVLVLAAGPGTRMRSDTPKVLHTLAGRSMLSHVLHAIAKLAPQRLIVVLGHDHQRIAPLVGELADTLGRTIDVALQDRPLGTGHAVLCGLSALPDDYAGNVVVTSGDTPLLDADTLADLIATHRAVSAAVTVLTTTLDDPFGYGRILRTQDHEVMAIVEQTDATPSQREIREVNAGVYAFDIAALRSALSRLSSNNAQQELYLTDVIAILRSDGQTVHASHVDDSALVAGVNNRVQLAELASELNRRVVAAHQLAGVTVVDPATTWIDVDVTIGRDTVIHPGTQLLGRTQIGGRCVVGPDTTLTDVAVGDGASVVRTHGSSSSIGDGAAVGPFTYLRPGTALGADGKLGAFVEVKNSTIGTGTKVPHLTYVGDADIGEYSNIGA 391
                                    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       371       381       391

Chain A from PDB  Type:PROTEIN  Length:390
 aligned with GLMU_MYCTU | P9WMN3 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:390
                                    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       371       381       391
           GLMU_MYCTU     2 TFPGDTAVLVLAAGPGTRMRSDTPKVLHTLAGRSMLSHVLHAIAKLAPQRLIVVLGHDHQRIAPLVGELADTLGRTIDVALQDRPLGTGHAVLCGLSALPDDYAGNVVVTSGDTPLLDADTLADLIATHRAVSAAVTVLTTTLDDPFGYGRILRTQDHEVMAIVEQTDATPSQREIREVNAGVYAFDIAALRSALSRLSSNNAQQELYLTDVIAILRSDGQTVHASHVDDSALVAGVNNRVQLAELASELNRRVVAAHQLAGVTVVDPATTWIDVDVTIGRDTVIHPGTQLLGRTQIGGRCVVGPDTTLTDVAVGDGASVVRTHGSSSSIGDGAAVGPFTYLRPGTALGADGKLGAFVEVKNSTIGTGTKVPHLTYVGDADIGEYSNIGA 391
               SCOP domains d3d98a1 A:2-263 N-acetylglucosamine 1-phosphate uridyltransferase GlmU, N-terminal domain                                                                                                                                                                             d3d98a2 A:264-391 N-acetylglucosamine 1-phosphate uridyltransferase GlmU, C-terminal domain                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee....hhhhh...hhhh.ee..eehhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhh.........eeeee......hhhhhhhhhhhhhhh...eeeeeee........eeee.....eeeeehhhhh..hhhhh.eeeeeeeeehhhhhhhhhh.............hhhhhhhhhh...eeeee..hhhhh....hhhhhhhhhhhhhhhhhhhhhhh..ee.hhh.eee....ee....ee...eeee...ee....ee...eeeeeeee....ee..eeeeeeee....ee...eee...eee....eeeeeeeee..ee....eeeeeeeee..ee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3d98 A   2 TFPGDTAVLVLAAGPGTRMRSDTPKVLHTLAGRSMLSHVLHAIAKLAPQRLIVVLGHDHQRIAPLVGELADTLGRTIDVALQDRPLGTGHAVLCGLSALPDDYAGNVVVTSGDTPLLDADTLADLIATHRAVSAAVTVLTTTLDDPFGYGRILRTQDHEVMAIVEQTDATPSQREIREVNAGVYAFDIAALRSALSRLSSNNAQQELYLTDVIAILRSDGQTVHASHVDDSALVAGVNNRVQLAELASELNRRVVAAHQLAGVTVVDPATTWIDVDVTIGRDTVIHPGTQLLGRTQIGGRCVVGPDTTLTDVAVGDGASVVRTHGSSSSIGDGAAVGPFTYLRPGTALGADGKLGAFVEVKNSTIGTGTKVPHLTYVGDADIGEYSNIGA 391
                                    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       371       381       391

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3D98)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D98)

(-) Gene Ontology  (19, 36)

Asymmetric Unit(hide GO term definitions)
Chain A   (GLMU_MYCTO | P9WMN2)
molecular function
    GO:0003977    UDP-N-acetylglucosamine diphosphorylase activity    Catalysis of the reaction: N-acetyl-alpha-D-glucosamine 1-phosphate + UTP = diphosphate + UDP-N-acetyl-alpha-D-glucosamine.
    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:0019134    glucosamine-1-phosphate N-acetyltransferase activity    Catalysis of the reaction: alpha-D-glucosamine 1-phosphate + acetyl-CoA = N-acetyl-alpha-D-glucosamine 1-phosphate + CoA + H(+).
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    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.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
    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:0000902    cell morphogenesis    The developmental process in which the size or shape of a cell is generated and organized.
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0009245    lipid A biosynthetic process    The chemical reactions and pathways resulting in the formation of lipid A, the glycolipid group of bacterial lipopolysaccharides, consisting of four to six fatty acyl chains linked to two glucosamine residues. Further modifications of the backbone are common.
    GO:0009103    lipopolysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.
    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.
    GO:0009252    peptidoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A   (GLMU_MYCTU | P9WMN3)
molecular function
    GO:0003977    UDP-N-acetylglucosamine diphosphorylase activity    Catalysis of the reaction: N-acetyl-alpha-D-glucosamine 1-phosphate + UTP = diphosphate + UDP-N-acetyl-alpha-D-glucosamine.
    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:0019134    glucosamine-1-phosphate N-acetyltransferase activity    Catalysis of the reaction: alpha-D-glucosamine 1-phosphate + acetyl-CoA = N-acetyl-alpha-D-glucosamine 1-phosphate + CoA + H(+).
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    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.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
    GO:0070569    uridylyltransferase activity    Catalysis of the transfer of an uridylyl group to an acceptor.
biological process
    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:0000902    cell morphogenesis    The developmental process in which the size or shape of a cell is generated and organized.
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    GO:0009245    lipid A biosynthetic process    The chemical reactions and pathways resulting in the formation of lipid A, the glycolipid group of bacterial lipopolysaccharides, consisting of four to six fatty acyl chains linked to two glucosamine residues. Further modifications of the backbone are common.
    GO:0009103    lipopolysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.
    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.
    GO:0009252    peptidoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GLMU_MYCTO | P9WMN22qkx 3d8v 3dj4 3foq 3spt 3st8 4g3p 4g3q 4g3s 4g87 4hcq 4k6r
        GLMU_MYCTU | P9WMN32qkx 3d8v 3dj4 3foq 3spt 3st8 4g3p 4g3q 4g3s 4g87 4hcq 4k6r

(-) Related Entries Specified in the PDB File

2qkx CRYSTAL STRUCTURE OF GLMU FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH N-ACETYL GLUCOSAMINE 1-PHOSPHATE
3d8v CRYSTAL STRUCTURE OF GLMU FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE