2JF2 - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   NUCLEOTIDE SUBSTRATE BINDING BY UDP-N-ACETYLGLUCOSAMINE ACYLTRANSFERASE

Authors :   V. Ulaganathan, L. Buetow, W. N. Hunter

Date :   25 Jan 07 (Deposition) - 24 Apr 07 (Release) - 04 Dec 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Lipid A Biosynthesis, Transferase, Acyltransferase, Lipid Synthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Ulaganathan, L. Buetow, W. N. Hunter
Nucleotide Substrate Recognition By Udp-N- Acetylglucosamine Acyltransferase (Lpxa) In The First Step Of Lipid A Biosynthesis.
J. Mol. Biol. V. 369 305 2007
PubMed-ID: 17434525 | Reference-DOI: 10.1016/J.JMB.2007.03.039

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 Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET15B
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	UDP-N-ACETYLGLUCOSAMINE ACYLTRANSFERASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
2	PEG	3	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:220 , ARG A:224 , HOH A:2106 , HOH A:2193 , HOH A:2392 , HOH A:2393 , HOH A:2394 , HOH A:2395 , HOH A:2398	BINDING SITE FOR RESIDUE EDO A1264
2	AC2	SOFTWARE	GLY A:79 , GLY A:196 , VAL A:197 , ILE A:199 , ARG A:216 , HOH A:2278 , HOH A:2391 , HOH A:2392 , HOH A:2397	BINDING SITE FOR RESIDUE PEG A1263

(no "SS Bond" information available for 2JF2)

Asymmetric Unit

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

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)

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

(no "Exon" information available for 2JF2)

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:264
 aligned with LPXA_ECOLI | P0A722 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:264
                              1                                                                                                                                                                                                                                                                     
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258    
           LPXA_ECOLI     - --MIDKSAFVHPTAIVEEGASIGANAHIGPFCIVGPHVEIGEGTVLKSHVVVNGHTKIGRDNEIYQFASIGEVNQDLKYAGEPTRVEIGDRNRIRESVTIHRGTVQGGGLTKVGSDNLLMINAHIAHDCTVGNRCILANNATLAGHVSVDDFAIIGGMTAVHQFCIIGAHVMVGGCSGVAQDVPPYVIAQGNHATPFGVNIEGLKRRGFSREAITAIRNAYKLIYRSGKTLDEVKPEIAELAETYPEVKAFTDFFARSTRGLIR 262
               SCOP domains d2jf2a_ A: UDP N-acetylglucosamine acyltransferase                                                                                                                                                                                                                       SCOP domains
               CATH domains 2jf2A01 A:-1-196 Hexapeptide repeat proteins                                                                                                                                                          2jf2A02 A:197-262  [code=1.20.1180.10, no name defined]            CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------Hexapep-2jf2A02 A:108-143           ------------------------------------Acetyltransf_11-2jf2A01 A:180-262                                                   Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------Hexapep-2jf2A03 A:108-143           ----------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------Hexapep-2jf2A04 A:108-143           ----------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------------------------------------------------Hexapep-2jf2A05 A:108-143           ----------------------------------------------------------------------------------------------------------------------- Pfam domains (4)
           Pfam domains (5) -------------------------------------------------------------------------------------------------------------Hexapep-2jf2A06 A:108-143           ----------------------------------------------------------------------------------------------------------------------- Pfam domains (5)
         Sec.struct. author ........ee....ee....ee....ee....ee...eee....ee....ee..eeee....ee....eeee............eeee....ee....eee........eeee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee.......eeee....eeeeehhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------HEXAPEP_TRANSFERASES         --------------------------------------------------------------------------------------------------------HEXAPEP_TRANSFERASES         --------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2jf2 A  -1 GSMIDKSAFVHPTAIVEEGASIGANAHIGPFCIVGPHVEIGEGTVLKSHVVVNGHTKIGRDNEIYQFASIGEVNQDLKYAGEPTRVEIGDRNRIRESVTIHRGTVQGGGLTKVGSDNLLMINAHIAHDCTVGNRCILANNATLAGHVSVDDFAIIGGMTAVHQFCIIGAHVMVGGCSGVAQDVPPYVIAQGNHATPFGVNIEGLKRRGFSREAITAIRNAYKLIYRSGKTLDEVKPEIAELAETYPEVKAFTDFFARSTRGLIR 262
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258

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 '\|'

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)

d2jf2a_

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Acetyltransf_11] (6)

Family: Acetyltransf_11 (6)

Escherichia coli (strain K12) (5)

Acetyltransf_11-2jf2A01

A:180-262

Clan: no clan defined [family: Hexapep] (52)

Family: Hexapep (52)

Escherichia coli (strain K12) (13)

2a	Hexapep-2jf2A02	A:108-143
2b	Hexapep-2jf2A03	A:108-143
2c	Hexapep-2jf2A04	A:108-143
2d	Hexapep-2jf2A05	A:108-143
2e	Hexapep-2jf2A06	A:108-143

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.

Asymmetric Unit
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	Cis Peptide Bonds
		Asn A:190 - His A:191	[ RasMol ]

Biological Unit
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		Biological Unit 1	[ Jena3D ]

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	2.3.1.129
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	LPXA_ECOLI \| P0A722	:	1lxa 2aq9 2jf3 2qia 2qiv 4j09

1lxa	UDP N-ACETYLGLUCOSAMINE ACYLTRANSFERASE
2aq9	STRUCTURE OF E. COLI LPXA WITH A BOUND PEPTIDE THAT ISCOMPETITIVE WITH ACYL-ACP
2jf3	NUCLEOTIDE SUBSTRATE BINDING BY UDP-N- ACETYLGLUCOSAMINE ACYLTRANSFERASE

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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Gene Ontology (9, 9)

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