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Description

Title :   STRUCTURE OF E. COLI LPXA WITH A BOUND PEPTIDE THAT IS COMPETITIVE WITH ACYL-ACP

Authors :   A. H. Williams, R. M. Immormino, D. T. Gewirth, C. R. Raetz

Date :   17 Aug 05 (Deposition) - 27 Jun 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Lpxa, Peptide Inhibitor, Acyl Acp, Acp, Udp-Glcnac, Lipid A, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. H. Williams, R. M. Immormino, D. T. Gewirth, C. R. Raetz
Structure Of Udp-N-Acetylglucosamine Acyltransferase With A Bound Antibacterial Pentadecapeptide.
Proc. Natl. Acad. Sci. Usa V. 103 10877 2006
PubMed-ID: 16835299 | Reference-DOI: 10.1073/PNAS.0604465103

Compounds

Molecule 1 - ACYL-[ACYL-CARRIER-PROTEIN]--UDP-N-ACETYLGLUCOSAMINE O- ACYLTRANSFERASE
	Chains	:	A
	EC Number	:	2.3.1.129
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PPET23C-LPXA(1-262) PT01
	Expression System Strain	:	BL21(DE3)PLYSE
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	LPXA
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	UDP-N-ACETYLGLUCOSAMINE ACYLTRANSFERASE

Molecule 2 - PEPTIDE INHIBITOR
	Chains	:	X
	Engineered	:	YES
	Synthetic	:	YES

Structural Features

Chains, Units

		1	2
Asymmetric Unit	:	A	X
Biological Unit 1 (3x)	:	A	X

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 27)

Asymmetric Unit (2, 27)

No.	Name	Count	Type	Full Name
1	DMS	22	Ligand/Ion	DIMETHYL SULFOXIDE
2	PO4	5	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 81)

No.	Name	Count	Type	Full Name
1	DMS	66	Ligand/Ion	DIMETHYL SULFOXIDE
2	PO4	15	Ligand/Ion	PHOSPHATE ION

Sites (27, 27)

Asymmetric Unit (27, 27)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:100 , ARG A:216 , LYS A:220 , PO4 A:302 , HOH A:453 , HOH A:540 , HOH A:542 , HOH A:613 , HOH A:689	BINDING SITE FOR RESIDUE PO4 A 301
02	AC2	SOFTWARE	PRO A:34 , ASN A:51 , GLY A:52 , PO4 A:301 , HOH A:431 , HOH A:488 , HOH A:517 , HOH A:518 , HOH A:605 , HOH A:660	BINDING SITE FOR RESIDUE PO4 A 302
03	AC3	SOFTWARE	LYS A:76 , GLN A:104 , LYS A:203 , HOH A:536 , HOH A:572 , HOH A:598 , TRP X:4 , ARG X:15	BINDING SITE FOR RESIDUE PO4 A 303
04	AC4	SOFTWARE	LEU A:75 , ASP A:114 , ARG A:132 , CYS A:133	BINDING SITE FOR RESIDUE PO4 A 304
05	AC5	SOFTWARE	ILE A:13 , VAL A:14 , GLU A:16	BINDING SITE FOR RESIDUE DMS A 401
06	AC6	SOFTWARE	ILE A:56 , ILE A:86 , DMS A:405	BINDING SITE FOR RESIDUE DMS A 402
07	AC7	SOFTWARE	GLY A:17 , PRO A:34 , HIS A:35 , VAL A:36 , GLU A:37	BINDING SITE FOR RESIDUE DMS A 403
08	AC8	SOFTWARE	ASN A:23 , HIS A:25 , GLY A:41 , ASN A:217 , LEU A:239 , TYR A:243 , DMS A:408	BINDING SITE FOR RESIDUE DMS A 404
09	AC9	SOFTWARE	ASP A:88 , DMS A:402	BINDING SITE FOR RESIDUE DMS A 405
10	BC1	SOFTWARE	ASP A:148 , ARG A:255	BINDING SITE FOR RESIDUE DMS A 406
11	BC2	SOFTWARE	HIS A:25 , HOH A:549	BINDING SITE FOR RESIDUE DMS A 407
12	BC3	SOFTWARE	GLY A:41 , ASP A:59 , ASN A:60 , GLU A:210 , THR A:213 , TYR A:243 , DMS A:404	BINDING SITE FOR RESIDUE DMS A 408
13	BC4	SOFTWARE	HIS A:144 , SER A:146 , PHE A:162 , THR A:257 , DMS A:412	BINDING SITE FOR RESIDUE DMS A 409
14	BC5	SOFTWARE	PHE A:7 , VAL A:8	BINDING SITE FOR RESIDUE DMS A 410
15	BC6	SOFTWARE	ASP A:148 , ASP A:149	BINDING SITE FOR RESIDUE DMS A 411
16	BC7	SOFTWARE	ASP A:126 , THR A:128 , VAL A:145 , SER A:146 , DMS A:409 , HOH A:450 , HOH A:703	BINDING SITE FOR RESIDUE DMS A 412
17	BC8	SOFTWARE	LYS A:4 , ALA A:6 , GLU A:238 , HOH A:530	BINDING SITE FOR RESIDUE DMS A 413
18	BC9	SOFTWARE	MET A:1 , ASP A:3 , ILE A:20	BINDING SITE FOR RESIDUE DMS A 414
19	CC1	SOFTWARE	ASP A:3 , LYS A:4	BINDING SITE FOR RESIDUE DMS A 415
20	CC2	SOFTWARE	GLU A:15 , PRO A:28 , HOH A:491 , HOH A:549	BINDING SITE FOR RESIDUE DMS A 416
21	CC3	SOFTWARE	ASN A:131 , ARG A:132 , PHE A:150 , HOH A:625	BINDING SITE FOR RESIDUE DMS A 417
22	CC4	SOFTWARE	PRO A:194 , TYR A:219	BINDING SITE FOR RESIDUE DMS A 418
23	CC5	SOFTWARE	ARG A:205 , GLU A:245 , HOH A:445	BINDING SITE FOR RESIDUE DMS A 419
24	CC6	SOFTWARE	HIS A:25 , VAL A:43 , LYS A:45 , HOH A:695	BINDING SITE FOR RESIDUE DMS A 420
25	CC7	SOFTWARE	GLN A:73 , ARG A:91 , ARG A:93 , LEU A:116 , HOH A:524	BINDING SITE FOR RESIDUE DMS A 421
26	CC8	SOFTWARE	ALA A:78 , PHE A:207 , ARG A:209	BINDING SITE FOR RESIDUE DMS A 422
27	CC9	SOFTWARE	GLN A:73 , ASP A:74 , LEU A:75 , LYS A:76 , GLN A:161 , LEU X:6 , PRO X:8 , HOH X:28	BINDING SITE FOR RESIDUE PO4 X 305

SS Bonds (0, 0)

(no "SS Bond" information available for 2AQ9)

Cis Peptide Bonds (1, 1)

Asymmetric Unit

No.	Residues
1	Asn A:190	-	His A:191

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

Asymmetric Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LPXA_ECOLI_001 *	G	189	S	LPXA_ECOLI	---	---	A	G	189	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LPXA_ECOLI_001 *	G	189	S	LPXA_ECOLI	---	---	A	G	189	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (1, 2)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HEXAPEP_TRANSFERASES	PS00101	Hexapeptide-repeat containing-transferases signature.	LPXA_ECOLI	20-48 153-181	2	A:20-48 A:153-181

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HEXAPEP_TRANSFERASES	PS00101	Hexapeptide-repeat containing-transferases signature.	LPXA_ECOLI	20-48 153-181	6	A:20-48 A:153-181

Exons (0, 0)

(no "Exon" information available for 2AQ9)

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:262
 aligned with LPXA_ECOLI | P0A722 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:262
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260  
           LPXA_ECOLI     1 MIDKSAFVHPTAIVEEGASIGANAHIGPFCIVGPHVEIGEGTVLKSHVVVNGHTKIGRDNEIYQFASIGEVNQDLKYAGEPTRVEIGDRNRIRESVTIHRGTVQGGGLTKVGSDNLLMINAHIAHDCTVGNRCILANNATLAGHVSVDDFAIIGGMTAVHQFCIIGAHVMVGGCSGVAQDVPPYVIAQGNHATPFGVNIEGLKRRGFSREAITAIRNAYKLIYRSGKTLDEVKPEIAELAETYPEVKAFTDFFARSTRGLIR 262
               SCOP domains d2aq9a_ A: UDP N-acetylglucosamine acyltransferase                                                                                                                                                                                                                     SCOP domains
               CATH domains 2aq9A01 A:1-196 Hexapeptide repeat proteins                                                                                                                                                         2aq9A02 A:197-262  [code=1.20.1180.10, no name defined]            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eee...eee...eee..eeee..eeee..eeee..eeee..eeee..eeee..eeee..eeee..eeeee............eeeee..eeee..eeee.......eeeeee..eeee..eeee..eeee..eeee..eeee..eeee..eeee..eeee..eeee..eeee..eee.......eeee....eeee.hhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------HEXAPEP_TRANSFERASES         --------------------------------------------------------------------------------------------------------HEXAPEP_TRANSFERASES         --------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aq9 A   1 MIDKSAFVHPTAIVEEGASIGANAHIGPFCIVGPHVEIGEGTVLKSHVVVNGHTKIGRDNEIYQFASIGEVNQDLKYAGEPTRVEIGDRNRIRESVTIHRGTVQGGGLTKVGSDNLLMINAHIAHDCTVGNRCILANNATLAGHVSVDDFAIIGGMTAVHQFCIIGAHVMVGGCSGVAQDVPPYVIAQGNHATPFGVNIEGLKRRGFSREAITAIRNAYKLIYRSGKTLDEVKPEIAELAETYPEVKAFTDFFARSTRGLIR 262
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260

Chain X from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author .eee....eee. Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 2aq9 X   4 WMLDPIAGKWSR  15
                                    13

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 (1, 1)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Single-stranded left-handed beta-helix (154)

Superfamily: Trimeric LpxA-like enzymes (147)

Family: UDP N-acetylglucosamine acyltransferase (7)

Protein domain: UDP N-acetylglucosamine acyltransferase (7)

Escherichia coli, gene lpxA [TaxId: 562] (6)

d2aq9a_

CATH Domains (2, 2)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Udp N-acetylglucosamine O-acyltransferase; Domain 2 (10)

Homologous Superfamily: [code=1.20.1180.10, no name defined] (10)

Escherichia coli k12. Organism_taxid: 83333. Strain: k12. (2)

2aq9A02

A:197-262

Class: Mainly Beta (13760)

Architecture: 3 Solenoid (196)

Topology: UDP N-Acetylglucosamine Acyltransferase; domain 1 (90)

Homologous Superfamily: Hexapeptide repeat proteins (85)

Escherichia coli k12. Organism_taxid: 83333. Strain: k12. (2)

2aq9A01

A:1-196

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 2AQ9)

Gene Ontology (9, 9)

Asymmetric Unit(hide GO term definitions)

Chain A (LPXA_ECOLI | P0A722)

molecular function
	GO:0008780	acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase activity	Catalysis of the reaction: (R)-3-hydroxytetradecanoyl-[acyl-carrier protein] + UDP-N-acetylglucosamine = [acyl-carrier protein] + UDP-3-O-(3-hydroxytetradecanoyl)-N-acetylglucosamine.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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: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:0008610	lipid biosynthetic process	The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	LPXA_ECOLI \| P0A722	:	1lxa 2jf2 2jf3 2qia 2qiv 4j09

Related Entries Specified in the PDB File

1lxa	UDP N-ACETYLGLUCOSAMINE ACYLTRANSFERASE (STRUCTURE OF APO LPXA)