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(-) Description

Title :  STRUCTURE OF SMALL-MOLECULE INHIBITOR OF GLMU FROM HAEMOPHILUS INFLUENZAE REVEALS AN ALLOSTERIC BINDING SITE
 
Authors :  I. Mochalkin, S. Lightle, L. Mcdowell
Date :  28 Sep 07  (Deposition) - 15 Jan 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Glmu, Inhibitor, Magnesium, Cell Shape, Peptidoglycan Synthesis, Allosteric, Transferase, Active Site, Metal-Binding, Cell Wall Biogenesis/Degradation, Multifunctional Enzyme, Nucleotidyltransferase, Acyltransferase, Uridyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Mochalkin, S. Lightle, L. Narasimhan, D. Bornemeier, M. Melnick, S. Vanderroest, L. Mcdowell
Structure Of A Small-Molecule Inhibitor Complexed With Glmu From Haemophilus Influenzae Reveals An Allosteric Binding Site.
Protein Sci. V. 17 577 2008
PubMed-ID: 18218712  |  Reference-DOI: 10.1110/PS.073271408

(-) Compounds

Molecule 1 - BIFUNCTIONAL PROTEIN GLMU
    Chains: A
    EC Number: 2.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 727
    Synonym: GLMU FROM HAEMOPHILIS INFLUENZAE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 12)

Asymmetric Unit (5, 12)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2P211Ligand/Ion4-CHLORO-N-(3-METHOXYPROPYL)-N-[(3S)-1-(2-PHENYLETHYL)PIPERIDIN-3-YL]BENZAMIDE
3PG42Ligand/IonTETRAETHYLENE GLYCOL
4PGE1Ligand/IonTRIETHYLENE GLYCOL
5SO46Ligand/IonSULFATE ION
Biological Unit 1 (4, 30)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2P213Ligand/Ion4-CHLORO-N-(3-METHOXYPROPYL)-N-[(3S)-1-(2-PHENYLETHYL)PIPERIDIN-3-YL]BENZAMIDE
3PG46Ligand/IonTETRAETHYLENE GLYCOL
4PGE3Ligand/IonTRIETHYLENE GLYCOL
5SO418Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:139 , ASN A:169 , VAL A:223 , GLU A:224 , GLY A:225 , GLN A:231 , LEU A:235 , SO4 A:1458 , HOH A:2280BINDING SITE FOR RESIDUE P21 A1454
02AC2SOFTWARELYS A:360 , ASN A:362 , HIS A:363 , HOH A:2225 , HOH A:2281 , HOH A:2282BINDING SITE FOR RESIDUE SO4 A1455
03AC3SOFTWARELYS A:15 , HIS A:57 , GLY A:58BINDING SITE FOR RESIDUE SO4 A1456
04AC4SOFTWAREASN A:377 , ARG A:451 , HOH A:2221 , HOH A:2284BINDING SITE FOR RESIDUE SO4 A1457
05AC5SOFTWAREASN A:227 , GLN A:231 , P21 A:1454BINDING SITE FOR RESIDUE SO4 A1458
06AC6SOFTWAREHIS A:57 , GLU A:78 , GLN A:79 , HOH A:2285BINDING SITE FOR RESIDUE SO4 A1459
07AC7SOFTWAREARG A:331 , ARG A:333 , PRO A:334 , HOH A:2290 , HOH A:2291BINDING SITE FOR RESIDUE SO4 A1465
08AC8SOFTWAREGLU A:49 , ASN A:50 , GLN A:70 , VAL A:71 , ASN A:72 , PHE A:92 , TYR A:387 , HOH A:2023 , HOH A:2024 , HOH A:2286BINDING SITE FOR RESIDUE PG4 A1460
09AC9SOFTWAREASN A:72 , ASN A:386 , ASP A:388 , PHE A:402 , ALA A:423 , HOH A:2252 , HOH A:2287 , HOH A:2288BINDING SITE FOR RESIDUE PG4 A1461
10BC1SOFTWAREVAL A:153 , ASP A:157 , ASN A:159 , GLN A:162 , ASN A:189 , ASN A:191 , ALA A:192 , GLY A:194 , HOH A:2289BINDING SITE FOR RESIDUE PGE A1462
11BC2SOFTWAREASP A:406 , HOH A:2244BINDING SITE FOR RESIDUE MG A1463
12BC3SOFTWAREASP A:406 , HOH A:2228BINDING SITE FOR RESIDUE MG A1464

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VD4)

(-) Cis Peptide Bonds  (2, 2)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VD4)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEXAPEP_TRANSFERASESPS00101 Hexapeptide-repeat containing-transferases signature.GLMU_HAEIN403-431  1A:403-431
Biological Unit 1 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEXAPEP_TRANSFERASESPS00101 Hexapeptide-repeat containing-transferases signature.GLMU_HAEIN403-431  3A:403-431

(-) Exons   (0, 0)

(no "Exon" information available for 2VD4)

(-) 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 d2vd4a1 A:4-251 automated matches                                                                                                                                                                                                                       d2vd4a2 A:252-453 automated matches                                                                                                                                                                        SCOP domains
               CATH domains 2vd4A01 A:4-227 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                    2vd4A02 A:228-453 Hexapeptide repeat proteins                                                                                                                                                                                      CATH domains
           Pfam domains (1) ----NTP_transf_3-2vd4A01 A:8-258                                                                                                                                                                                                                               ---------------------------------------------------------------------------------------------------------------------------------------Hexapep-2vd4A02 A:394-429           ------------------------ Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Hexapep-2vd4A03 A:394-429           ------------------------ Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Hexapep-2vd4A04 A:394-429           ------------------------ Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Hexapep-2vd4A05 A:394-429           ------------------------ Pfam domains (4)
         Sec.struct. author ..eeeeee....hhhhh...hhhh.ee..eehhhhhhhhhhhh....eeeee..hhhhhhhhh.....eeee.....hhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhh....eeeeeee........eeeee..eeeeeehhhhhhhhhhh..eeeeeeeeeehhhhhhhhh...........hhhhhhhhhhhh...eeeee...hhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.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
                 2vd4 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)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 5)

Asymmetric Unit
(-)
Clan: GT-A (172)
(-)
Clan: no clan defined [family: Hexapep] (52)

(-) 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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  GLMU_HAEIN | P43889
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 Related Entries

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

UniProtKB/Swiss-Prot
        GLMU_HAEIN | P43889: 2v0h 2v0i 2v0j 2v0k 2v0l 2w0v 2w0w 4e1k 4knr 4knx 4kpx 4kpz 4kql

(-) Related Entries Specified in the PDB File

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)