2W0V - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF GLMU FROM HAEMOPHILUS INFLUENZAE IN COMPLEX WITH QUINAZOLINE INHIBITOR 1

Authors :   I. Mochalkin, M. Melnick

Date :   10 Oct 08 (Deposition) - 17 Nov 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.99

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

Keywords :   Peptidoglycan Synthesis, Glmu, Bacterial, Inhibitor, Magnesium, Cell Shape, Transferase, Active Site, Metal-Binding, Cell Wall Biogenesis/Degradation, Multifunctional Enzyme, Nucleotidyltransferase, Acyltransferase, Uridyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Melnick, I. Mochalkin, S. Lightle, L. Narasimhan, L. Mcdowell, R. Sarver
Discovery And Initial Sar Of Quinazoline Inhibitors Of Glmu From Haemophilus Influenzae
To Be Published
PubMed: search

Molecule 1 - GLUCOSAMINE-1-PHOSPHATE N-ACETYLTRANSFERASE
	Chains	:	A
	EC Number	:	2.3.1.157
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	HAEMOPHILUS INFLUENZAE
	Organism Taxid	:	727
	Synonym	:	N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 10)

No.	Name	Count	Type	Full Name
1	LZR	1	Ligand/Ion	6-(CYCLOPROP-2-EN-1-YLMETHOXY)-2-[6-(CYCLOPROPYLMETHYL)-5-OXO-3,4,5,6-TETRAHYDRO-2,6-NAPHTHYRIDIN-2(1H)-YL]-7-METHOXYQUINAZOLIN-4(3H)-ONE
2	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL
3	PGE	2	Ligand/Ion	TRIETHYLENE GLYCOL
4	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 30)

No.	Name	Count	Type	Full Name
1	LZR	3	Ligand/Ion	6-(CYCLOPROP-2-EN-1-YLMETHOXY)-2-[6-(CYCLOPROPYLMETHYL)-5-OXO-3,4,5,6-TETRAHYDRO-2,6-NAPHTHYRIDIN-2(1H)-YL]-7-METHOXYQUINAZOLIN-4(3H)-ONE
2	PG4	3	Ligand/Ion	TETRAETHYLENE GLYCOL
3	PGE	6	Ligand/Ion	TRIETHYLENE GLYCOL
4	SO4	18	Ligand/Ion	SULFATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LEU A:11 , GLY A:14 , VAL A:26 , GLN A:76 , GLN A:79 , THR A:82 , TYR A:103 , ASP A:105 , TYR A:139 , THR A:170 , VAL A:223 , GLU A:224 , GLY A:225	BINDING SITE FOR RESIDUE LZR A1454
02	AC2	SOFTWARE	ASN A:72 , PHE A:92 , ASN A:386 , ASP A:388 , PHE A:402 , THR A:420 , ALA A:423 , ILE A:438 , HOH A:2243 , HOH A:2272 , HOH A:2273	BINDING SITE FOR RESIDUE PG4 A1455
03	AC3	SOFTWARE	VAL A:153 , ASP A:157 , ASN A:159 , GLN A:162 , ASN A:189 , ASN A:191 , ALA A:192 , GLY A:194	BINDING SITE FOR RESIDUE PGE A1456
04	AC4	SOFTWARE	GLU A:49 , ASN A:50 , GLN A:70 , TYR A:387 , HOH A:2274 , HOH A:2275	BINDING SITE FOR RESIDUE PGE A1457
05	AC5	SOFTWARE	LYS A:360 , ASN A:362 , HIS A:363 , LYS A:392 , HOH A:2216 , HOH A:2276 , HOH A:2277	BINDING SITE FOR RESIDUE SO4 A1458
06	AC6	SOFTWARE	ASN A:377 , HOH A:2278 , HOH A:2279	BINDING SITE FOR RESIDUE SO4 A1459
07	AC7	SOFTWARE	ARG A:331 , ARG A:333 , PRO A:334 , HOH A:2178	BINDING SITE FOR RESIDUE SO4 A1460
08	AC8	SOFTWARE	ASN A:227 , GLN A:231	BINDING SITE FOR RESIDUE SO4 A1461
09	AC9	SOFTWARE	LYS A:357 , ASN A:375	BINDING SITE FOR RESIDUE SO4 A1462
10	BC1	SOFTWARE	GLY A:14 , LYS A:15 , GLY A:16 , THR A:17 , HOH A:2282 , HOH A:2283	BINDING SITE FOR RESIDUE SO4 A1463

(no "SS Bond" information available for 2W0V)

Asymmetric Unit

No.	Residues
1	Gly A:327	-	Pro A:328
2	Ala A:411	-	Pro A:412

(no "SAP(SNP)/Variant" information available for 2W0V)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HEXAPEP_TRANSFERASES	PS00101	Hexapeptide-repeat containing-transferases signature.	GLMU_HAEIN	403-431	1	A:403-431

Biological Unit 1 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HEXAPEP_TRANSFERASES	PS00101	Hexapeptide-repeat containing-transferases signature.	GLMU_HAEIN	403-431	3	A:403-431

(no "Exon" information available for 2W0V)

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:451
 aligned with GLMU_HAEIN | P43889 from UniProtKB/Swiss-Prot  Length:456

    Alignment length:451
                                    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 KALSAVILAAGKGTRMYSDLPKVLHTIAGKPMVKHVIDTAHQLGSENIHLIYGHGGDLMRTHLANEQVNWVLQTEQLGTAHAVQQAAPFFKDNENIVVLYGDAPLITKETLEKLIEAKPENGIALLTVNLDNPTGYGRIIRENGNVVAIVEQKDANAEQLNIKEVNTGVMVSDGASFKKWLARVGNNNAQGEYYLTDLIALANQDNCQVVAVQATDVMEVEGANNRLQLAALERYFQNKQASKLLLEGVMIYDPARFDLRGTLEHGKDVEIDVNVIIEGNVKLGDRVKIGTGCVLKNVVIGNDVEIKPYSVLEDSIVGEKAAIGPFSRLRPGAELAAETHVGNFVEIKKSTVGKGSKVNHLTYVGDSEIGSNCNIGAGVITCNYDGANKFKTIIGDDVFVGSDTQLVAPVKVANGATIGAGTTITRDVGENELVITRVAQRHIQGWQRPIK 454
               SCOP domains d2w0va1 A:4-251 automated matches                                                                                                                                                                                                                       d2w0va2 A:252-454 automated matches                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----NTP_transf_3-2w0vA01 A:8-258                                                                                                                                                                                                                               ---------------------------------------------------------------------------------------------------------------------------------------Hexapep-2w0vA02 A:394-429           ------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Hexapep-2w0vA03 A:394-429           ------------------------- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Hexapep-2w0vA04 A:394-429           ------------------------- Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Hexapep-2w0vA05 A:394-429           ------------------------- Pfam domains (4)
         Sec.struct. author ..eeeeee....hhhhh...hhhh.ee..eehhhhhhhhhhhhh...eeeee..hhhhhhhhh.....eeee.....hhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhh....eeeeeee........eeeee..eeeeeehhhhhhhhhhh..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
                 2w0v A   4 KALSAVILAAGKGTRMYSDLPKVLHTIAGKPMVKHVIDTAHQLGSENIHLIYGHGGDLMRTHLANEQVNWVLQTEQLGTAHAVQQAAPFFKDNENIVVLYGDAPLITKETLEKLIEAKPENGIALLTVNLDNPTGYGRIIRENGNVVAIVEQKDANAEQLNIKEVNTGVMVSDGASFKKWLARVGNNNAQGEYYLTDLIALANQDNCQVVAVQATDVMEVEGANNRLQLAALERYFQNKQASKLLLEGVMIYDPARFDLRGTLEHGKDVEIDVNVIIEGNVKLGDRVKIGTGCVLKNVVIGNDVEIKPYSVLEDSIVGEKAAIGPFSRLRPGAELAAETHVGNFVEIKKSTVGKGSKVNHLTYVGDSEIGSNCNIGAGVITCNYDGANKFKTIIGDDVFVGSDTQLVAPVKVANGATIGAGTTITRDVGENELVITRVAQRHIQGWQRPIK 454
                                    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 '\|'

(no "CATH Domain" information available for 2W0V)

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.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		LZR	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PG4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PGE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala A:411 - Pro A:412	[ RasMol ]
		Gly A:327 - Pro A:328	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2w0v
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	GLMU_HAEIN \| P43889
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.3.1.157
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	GLMU_HAEIN \| P43889
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	GLMU_HAEIN \| P43889	:	2v0h 2v0i 2v0j 2v0k 2v0l 2vd4 2w0w 4e1k 4knr 4knx 4kpx 4kpz 4kql

2v0h	CHARACTERIZATION OF SUBSTRATE BINDING AND CATALYSIS OF THE POTENTIAL ANTIBACTERIAL TARGET N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE (GLMU)
2v0i	CHARACTERIZATION OF SUBSTRATE BINDING AND CATALYSIS OF THE POTENTIAL ANTIBACTERIAL TARGET N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE (GLMU)
2v0j	CHARACTERIZATION OF SUBSTRATE BINDING AND CATALYSIS OF THE POTENTIAL ANTIBACTERIAL TARGET N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE (GLMU)
2v0k	CHARACTERIZATION OF SUBSTRATE BINDING AND CATALYSIS OF THE POTENTIAL ANTIBACTERIAL TARGET N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE (GLMU)
2v0l	CHARACTERIZATION OF SUBSTRATE BINDING AND CATALYSIS OF THE POTENTIAL ANTIBACTERIAL TARGET N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE (GLMU)
2vd4	STRUCTURE OF SMALL-MOLECULE INHIBITOR OF GLMU FROM HAEMOPHILUS INFLUENZAE REVEALS AN ALLOSTERIC BINDING SITE
2w0w	CRYSTAL STRUCTURE OF GLMU FROM HAEMOPHILUS INFLUENZAE IN COMPLEX WITH QUINAZOLINE INHIBITOR 2

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 10)

Sites (10, 10)

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

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (0, 0)

Pfam Domains (2, 5)

Gene Ontology (17, 17)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File