2V0H - JenaLib

Title :   CHARACTERIZATION OF SUBSTRATE BINDING AND CATALYSIS OF THE POTENTIAL ANTIBACTERIAL TARGET N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE (GLMU)

Authors :   I. Mochalkin, S. Lightle, J. F. Ohren, N. Y. Chirgadze

Date :   14 May 07 (Deposition) - 15 Jan 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.79

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

Keywords :   Glmu, Cell Wall, Magnesium, Cell Shape, Transferase, Peptidoglycan Synthesis, Associative Mechanism, Multifunctional Enzyme, Nucleotidyltransferase, Uridylation, Metal-Binding, Acyltransferase, (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. Mochalkin, S. Lightle, Y. Zhu, J. F. Ohren, C. Spessard, N. Y. Chirgadze, C. Banotai, M. Melnick, L. Mcdowell
Characterization Of Substrate Binding And Catalysis In The Potential Antibacterial Target N- Acetylglucosamine-1-Phosphate Uridyltransferase (Glmu).
Protein Sci. V. 16 2657 2007
PubMed-ID: 18029420 | Reference-DOI: 10.1110/PS.073135107

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 11)

Sites (11, 11)

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	VAL A:153 , ASP A:157 , ASN A:159 , GLN A:162 , ASN A:191 , ALA A:192 , GLY A:194 , HOH A:2477 , HOH A:2478	BINDING SITE FOR RESIDUE PEG A1454
02	AC2	SOFTWARE	ASN A:50 , GLN A:70 , VAL A:71 , ASN A:72 , PRO A:412 , HOH A:2057 , HOH A:2479 , HOH A:2480 , HOH A:2481	BINDING SITE FOR RESIDUE PEG A1455
03	AC3	SOFTWARE	ASN A:169	BINDING SITE FOR RESIDUE PEG A1456
04	AC4	SOFTWARE	ASN A:386 , TYR A:387 , ASP A:388 , PHE A:402 , ALA A:423 , HOH A:2482 , HOH A:2483	BINDING SITE FOR RESIDUE PEG A1457
05	AC5	SOFTWARE	ASN A:377 , ARG A:451 , HOH A:2380 , HOH A:2383 , HOH A:2397 , HOH A:2405 , HOH A:2484	BINDING SITE FOR RESIDUE SO4 A1458
06	AC6	SOFTWARE	LYS A:360 , ASN A:362 , HIS A:363 , HOH A:2384 , HOH A:2386 , HOH A:2485 , HOH A:2486	BINDING SITE FOR RESIDUE SO4 A1459
07	AC7	SOFTWARE	LYS A:310 , ARG A:331 , ARG A:333 , PRO A:334 , HOH A:2487 , HOH A:2488 , HOH A:2489 , HOH A:2490	BINDING SITE FOR RESIDUE SO4 A1460
08	AC8	SOFTWARE	HIS A:57 , GLU A:78 , GLN A:79 , HOH A:2491	BINDING SITE FOR RESIDUE SO4 A1461
09	AC9	SOFTWARE	LYS A:15 , HIS A:57 , GLY A:58 , HOH A:2492 , HOH A:2493 , HOH A:2495	BINDING SITE FOR RESIDUE SO4 A1462
10	BC1	SOFTWARE	ASP A:406 , HOH A:2496	BINDING SITE FOR RESIDUE CO A1463
11	BC2	SOFTWARE	ASP A:406 , HOH A:2497	BINDING SITE FOR RESIDUE CO A1464

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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:450
 aligned with GLMU_HAEIN | P43889 from UniProtKB/Swiss-Prot  Length:456

    Alignment length:450
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453
           GLMU_HAEIN     4 KALSAVILAAGKGTRMYSDLPKVLHTIAGKPMVKHVIDTAHQLGSENIHLIYGHGGDLMRTHLANEQVNWVLQTEQLGTAHAVQQAAPFFKDNENIVVLYGDAPLITKETLEKLIEAKPENGIALLTVNLDNPTGYGRIIRENGNVVAIVEQKDANAEQLNIKEVNTGVMVSDGASFKKWLARVGNNNAQGEYYLTDLIALANQDNCQVVAVQATDVMEVEGANNRLQLAALERYFQNKQASKLLLEGVMIYDPARFDLRGTLEHGKDVEIDVNVIIEGNVKLGDRVKIGTGCVLKNVVIGNDVEIKPYSVLEDSIVGEKAAIGPFSRLRPGAELAAETHVGNFVEIKKSTVGKGSKVNHLTYVGDSEIGSNCNIGAGVITCNYDGANKFKTIIGDDVFVGSDTQLVAPVKVANGATIGAGTTITRDVGENELVITRVAQRHIQGWQRPI 453
               SCOP domains d2v0ha1 A:4-251 automated matches                                                                                                                                                                                                                       d2v0ha2 A:252-453 automated matches                                                                                                                                                                        SCOP domains
               CATH domains 2v0hA01 A:4-227 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                    2v0hA02 A:228-453 Hexapeptide repeat proteins                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee....hhhhh...hhhh.ee..eehhhhhhhhhhhh....eeeee..hhhhhhhhh.....eeee.....hhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhh....eeeeeee........eeeee..eeeeee.....hhhhhh..eeeeeeeeeehhhhhhhhh...........hhhhhhhhhhhh...eeeee...hhhhh...hhhhhhhhhhhhhhhhhhhhhhh..ee.hhh..............ee................ee...............ee....eeeeeee....ee...eee..........eeeeeeeee........eeeeeeeee........ee....eeee...............ee....eeee........ee....ee........ee................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HEXAPEP_TRANSFERASES         ---------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2v0h A   4 KALSAVILAAGKGTRMYSDLPKVLHTIAGKPMVKHVIDTAHQLGSENIHLIYGHGGDLMRTHLANEQVNWVLQTEQLGTAHAVQQAAPFFKDNENIVVLYGDAPLITKETLEKLIEAKPENGIALLTVNLDNPTGYGRIIRENGNVVAIVEQKDANAEQLNIKEVNTGVMVSDGASFKKWLARVGNNNAQGEYYLTDLIALANQDNCQVVAVQATDVMEVEGANNRLQLAALERYFQNKQASKLLLEGVMIYDPARFDLRGTLEHGKDVEIDVNVIIEGNVKLGDRVKIGTGCVLKNVVIGNDVEIKPYSVLEDSIVGEKAAIGPFSRLRPGAELAAETHVGNFVEIKKSTVGKGSKVNHLTYVGDSEIGSNCNIGAGVITCNYDGANKFKTIIGDDVFVGSDTQLVAPVKVANGATIGAGTTITRDVGENELVITRVAQRHIQGWQRPI 453
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453

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)

CATH Domains (2, 2)

Pfam Domains (0, 0)

Gene Ontology (17, 17)

Asymmetric Unit(hide GO term definitions)

Chain A (GLMU_HAEIN | P43889)

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.

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