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Title :   CRYSTAL STRUCTURE OF GLMU FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE.

Authors :   S. K. Verma, B. Prakash

Date :   22 Jun 08 (Deposition) - 19 May 09 (Release) - 19 May 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.38

Chains :   Asym. Unit : A
Biol. Unit 1: A  (3x)

Keywords :   Acetyltransferase, Bifunctional, Pyrophosphorylase, Rossmann-Like Fold, Left-Handed-Beta-Helix, Trimer, Cell Shape, Cell Wall Biogenesis/Degradation, Cytoplasm, Magnesium, Metal-Binding, Multifunctional Enzyme, Nucleotidyltransferase, Peptidoglycan Synthesis, Transferase, Acyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Parikh, S. K. Verma, S. Khan, B. Prakash, V. K. Nandicoori
Pknb-Mediated Phosphorylation Of A Novel Substrate, N-Acetylglucosamine-1-Phosphate Uridyltransferase, Modulates Its Acetyltransferase Activity.
J. Mol. Biol. V. 386 451 2009
PubMed-ID: 19121323 | Reference-DOI: 10.1016/J.JMB.2008.12.031
(for further references see the PDB file header)

Molecule 1 - BIFUNCTIONAL PROTEIN GLMU
	Chains	:	A
	EC Number	:	2.7.7.23, 2.3.1.157
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQEII
	Expression System Strain	:	DH5ALPHA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GLMU, RV1018C, MT1046
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Strain	:	H37RV
	Synonym	:	UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE, N- ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE, GLUCOSAMINE-1-PHOSPHATE N-ACETYLTRANSFERASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	CO	1	Ligand/Ion	COBALT (II) ION
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	UD1	1	Ligand/Ion	URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	UD1	3	Ligand/Ion	URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:114 , ASN A:239 , HOH A:4120 , HOH A:4133	BINDING SITE FOR RESIDUE MG A 496
2	AC2	SOFTWARE	PHE A:340	BINDING SITE FOR RESIDUE CO A 497
3	AC3	SOFTWARE	LEU A:12 , ALA A:13 , ALA A:14 , GLY A:15 , LYS A:26 , GLN A:83 , PRO A:86 , LEU A:87 , GLY A:88 , THR A:89 , ALA A:92 , SER A:112 , GLY A:113 , ASP A:114 , TYR A:150 , GLY A:151 , GLU A:166 , ASN A:181 , ALA A:182 , THR A:211 , ASN A:239 , HOH A:4001 , HOH A:4019 , HOH A:4066 , HOH A:4076 , HOH A:4120 , HOH A:4133	BINDING SITE FOR RESIDUE UD1 A 4000

(no "SS Bond" information available for 3DJ4)

Asymmetric Unit

No.	Residues
1	Gly A:338	-	Pro A:339
2	Ala A:422	-	Pro A:423
3	Ala A:471	-	Gln A:472

(no "SAP(SNP)/Variant" information available for 3DJ4)

(no "PROSITE Motif" information available for 3DJ4)

(no "Exon" information available for 3DJ4)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:462
 aligned with GLMU_MYCTO | P9WMN2 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:469
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465         
           GLMU_MYCTO     6 DTAVLVLAAGPGTRMRSDTPKVLHTLAGRSMLSHVLHAIAKLAPQRLIVVLGHDHQRIAPLVGELADTLGRTIDVALQDRPLGTGHAVLCGLSALPDDYAGNVVVTSGDTPLLDADTLADLIATHRAVSAAVTVLTTTLDDPFGYGRILRTQDHEVMAIVEQTDATPSQREIREVNAGVYAFDIAALRSALSRLSSNNAQQELYLTDVIAILRSDGQTVHASHVDDSALVAGVNNRVQLAELASELNRRVVAAHQLAGVTVVDPATTWIDVDVTIGRDTVIHPGTQLLGRTQIGGRCVVGPDTTLTDVAVGDGASVVRTHGSSSSIGDGAAVGPFTYLRPGTALGADGKLGAFVEVKNSTIGTGTKVPHLTYVGDADIGEYSNIGASSVFVNYDGTSKRRTTVGSHVRTGSDTMFVAPVTIGDGAYTGAGTVVREDVPPGALAVSAGPQRNIENWVQRKRPGSPAAQAS 474
               SCOP domains d3dj4a1 A:6-263 automated matches                                                                                                                                                                                                                                 d3dj4a2 A:264-474 automated matches                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhh...hhhh.ee..eehhhhhhhhhhhhh..eeeeee..hhhhhh....hhhhhh....eeee.....hhhhhhhhhhh........eeeeee......hhhhhhhhhhhhhhh...eeeeeee........eeee.....eeeee.............eeeeeeeeeehhhhhhhhh...........hhhhhhhhhhhh...eeeee..hhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..ee.hhh.eee....ee....ee...eeee...ee....ee....eeeeeee....ee..eeeeeeee....ee...eee....ee....eeee.eeee..ee....eeee..eee.eee....ee....eee.-------.eee....ee....eee...ee....ee....ee........ee..........hhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dj4 A   6 DTAVLVLAAGPGTRMRSDTPKVLHTLAGRSMLSHVLHAIAKLAPQRLIVVLGHDHQRIAPLVGELADTLGRTIDVALQDRPLGTGHAVLCGLSALPDDYAGNVVVTSGDTPLLDADTLADLIATHRAVSAAVTVLTTTLDDPFGYGRILRTQDHEVMAIVEQTDATPSQREIREVNAGVYAFDIAALRSALSRLSSNNAQQELYLTDVIAILRSDGQTVHASHVDDSALVAGVNNRVQLAELASELNRRVVAAHQLAGVTVVDPATTWIDVDVTIGRDTVIHPGTQLLGRTQIGGRCVVGPDTTLTDVAVGDGASVVRTHGSSSSIGDGAAVGPFTYLRPGTALGADGKLGAFVEVKNSTIGTGTKVPHLTYVGDADIGEYSNIGASSVFVN-------RTTVGSHVRTGSDTMFVAPVTIGDGAYTGAGTVVREDVPPGALAVSAGPQRNIENWVQRKRPGSPAAQAS 474
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395 |     405       415       425       435       445       455       465         
                                                                                                                                                                                                                                                                                                                                                                                                                                 397     405

Chain A from PDB  Type:PROTEIN  Length:462
 aligned with GLMU_MYCTU | P9WMN3 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:469
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465         
           GLMU_MYCTU     6 DTAVLVLAAGPGTRMRSDTPKVLHTLAGRSMLSHVLHAIAKLAPQRLIVVLGHDHQRIAPLVGELADTLGRTIDVALQDRPLGTGHAVLCGLSALPDDYAGNVVVTSGDTPLLDADTLADLIATHRAVSAAVTVLTTTLDDPFGYGRILRTQDHEVMAIVEQTDATPSQREIREVNAGVYAFDIAALRSALSRLSSNNAQQELYLTDVIAILRSDGQTVHASHVDDSALVAGVNNRVQLAELASELNRRVVAAHQLAGVTVVDPATTWIDVDVTIGRDTVIHPGTQLLGRTQIGGRCVVGPDTTLTDVAVGDGASVVRTHGSSSSIGDGAAVGPFTYLRPGTALGADGKLGAFVEVKNSTIGTGTKVPHLTYVGDADIGEYSNIGASSVFVNYDGTSKRRTTVGSHVRTGSDTMFVAPVTIGDGAYTGAGTVVREDVPPGALAVSAGPQRNIENWVQRKRPGSPAAQAS 474
               SCOP domains d3dj4a1 A:6-263 automated matches                                                                                                                                                                                                                                 d3dj4a2 A:264-474 automated matches                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhh...hhhh.ee..eehhhhhhhhhhhhh..eeeeee..hhhhhh....hhhhhh....eeee.....hhhhhhhhhhh........eeeeee......hhhhhhhhhhhhhhh...eeeeeee........eeee.....eeeee.............eeeeeeeeeehhhhhhhhh...........hhhhhhhhhhhh...eeeee..hhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..ee.hhh.eee....ee....ee...eeee...ee....ee....eeeeeee....ee..eeeeeeee....ee...eee....ee....eeee.eeee..ee....eeee..eee.eee....ee....eee.-------.eee....ee....eee...ee....ee....ee........ee..........hhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dj4 A   6 DTAVLVLAAGPGTRMRSDTPKVLHTLAGRSMLSHVLHAIAKLAPQRLIVVLGHDHQRIAPLVGELADTLGRTIDVALQDRPLGTGHAVLCGLSALPDDYAGNVVVTSGDTPLLDADTLADLIATHRAVSAAVTVLTTTLDDPFGYGRILRTQDHEVMAIVEQTDATPSQREIREVNAGVYAFDIAALRSALSRLSSNNAQQELYLTDVIAILRSDGQTVHASHVDDSALVAGVNNRVQLAELASELNRRVVAAHQLAGVTVVDPATTWIDVDVTIGRDTVIHPGTQLLGRTQIGGRCVVGPDTTLTDVAVGDGASVVRTHGSSSSIGDGAAVGPFTYLRPGTALGADGKLGAFVEVKNSTIGTGTKVPHLTYVGDADIGEYSNIGASSVFVN-------RTTVGSHVRTGSDTMFVAPVTIGDGAYTGAGTVVREDVPPGALAVSAGPQRNIENWVQRKRPGSPAAQAS 474
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395 |     405       415       425       435       445       455       465         
                                                                                                                                                                                                                                                                                                                                                                                                                                 397     405

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 '\|'

(no "CATH Domain" information available for 3DJ4)

(no "Pfam Domain" information available for 3DJ4)

Asymmetric Unit(hide GO term definitions)

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.

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.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:422 - Pro A:423	[ RasMol ]
		Ala A:471 - Gln A:472	[ RasMol ]
		Gly A:338 - Pro A:339	[ RasMol ]

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	3dj4
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	GLMU_MYCTO \| P9WMN2
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	2.7.7.23
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3diu	CRYSTAL STRUCTURE OF GLMU FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH UMPPNP AND N-ACETYLGLUCOSAMINE-1-PHOSPHATE.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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