3I3A - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURAL BASIS FOR THE SUGAR NUCLEOTIDE AND ACYL CHAIN SELECTIVITY OF LEPTOSPIRA INTERROGANS LPXA

Authors :   A. H. Williams

Date :   30 Jun 09 (Deposition) - 01 Sep 09 (Release) - 08 Sep 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.12

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (3x)
Biol. Unit 2: B  (3x)
Biol. Unit 3: C  (3x)

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

Reference :   L. I. Robins, A. H. Williams, C. R. Raetz
Structural Basis For The Sugar Nucleotide And Acyl-Chain Selectivity Of Leptospira Interrogans Lpxa.
Biochemistry V. 48 6191 2009
PubMed-ID: 19456129 | Reference-DOI: 10.1021/BI900629E
(for further references see the PDB file header)

Molecule 1 - ACYL-[ACYL-CARRIER-PROTEIN]--UDP-N- ACETYLGLUCOSAMINE O-ACYLTRANSFERASE
	Chains	:	A, B, C
	EC Number	:	2.3.1.129
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET30A
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	LA3949, LA_3949, LPXA
	Organism Scientific	:	LEPTOSPIRA INTERROGANS
	Organism Taxid	:	173
	Strain	:	K-12

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (3x)	:	A
Biological Unit 2 (3x)	:		B
Biological Unit 3 (3x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	S2N	3	Ligand/Ion	S-[2-({N-[(2R)-2-HYDROXY-4-{[(S)-HYDROXY(METHOXY)PHOSPHORYL]OXY}-3,3-DIMETHYLBUTANOYL]-BETA-ALANYL}AMINO)ETHYL] (3R)-3-HYDROXYDODECANETHIOATE

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	S2N	3	Ligand/Ion	S-[2-({N-[(2R)-2-HYDROXY-4-{[(S)-HYDROXY(METHOXY)PHOSPHORYL]OXY}-3,3-DIMETHYLBUTANOYL]-BETA-ALANYL}AMINO)ETHYL] (3R)-3-HYDROXYDODECANETHIOATE

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	S2N	3	Ligand/Ion	S-[2-({N-[(2R)-2-HYDROXY-4-{[(S)-HYDROXY(METHOXY)PHOSPHORYL]OXY}-3,3-DIMETHYLBUTANOYL]-BETA-ALANYL}AMINO)ETHYL] (3R)-3-HYDROXYDODECANETHIOATE

Biological Unit 3 (1, 3)

No.	Name	Count	Type	Full Name
1	S2N	3	Ligand/Ion	S-[2-({N-[(2R)-2-HYDROXY-4-{[(S)-HYDROXY(METHOXY)PHOSPHORYL]OXY}-3,3-DIMETHYLBUTANOYL]-BETA-ALANYL}AMINO)ETHYL] (3R)-3-HYDROXYDODECANETHIOATE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:68 , MET A:113 , HIS A:117 , ALA A:137 , GLY A:138 , PHE A:147 , SER A:149 , VAL A:154 , HIS A:155 , GLN A:156 , MET A:165 , ALA A:167 , GLY A:168 , LYS A:171 , VAL A:173 , THR A:181 , ASP A:183 , ARG A:253 , ARG A:259 , HOH A:262 , HOH A:394 , GLY B:221	BINDING SITE FOR RESIDUE S2N A 260
2	AC2	SOFTWARE	SER A:220 , GLY A:221 , GLN B:68 , MET B:113 , HIS B:117 , ALA B:137 , GLY B:138 , PHE B:147 , SER B:149 , HIS B:155 , GLN B:156 , ALA B:167 , GLY B:168 , LYS B:171 , ARG B:253 , HOH B:309	BINDING SITE FOR RESIDUE S2N B 260
3	AC3	SOFTWARE	GLN C:68 , HIS C:117 , ALA C:137 , GLY C:138 , PHE C:147 , SER C:149 , HIS C:155 , GLN C:156 , ALA C:167 , GLY C:168 , LYS C:171 , ASP C:183 , VAL C:190 , HIS C:219 , GLY C:221 , ARG C:253 , ARG C:259 , HOH C:311	BINDING SITE FOR RESIDUE S2N C 260

(no "SS Bond" information available for 3I3A)

Asymmetric Unit

No.	Residues
1	Asn A:185	-	Pro A:186
2	Asn B:185	-	Pro B:186
3	Pro B:204	-	Glu B:205
4	Asn C:185	-	Pro C:186

(no "SAP(SNP)/Variant" information available for 3I3A)

(no "PROSITE Motif" information available for 3I3A)

(no "Exon" information available for 3I3A)

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:259
 aligned with Q8EZA6_LEPIN | Q8EZA6 from UniProtKB/TrEMBL  Length:259

    Alignment length:259
                                    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         
         Q8EZA6_LEPIN     1 MKIHPTAIIDPKAELHESVEVGPYSIIEGNVSIQEGTIIEGHVKICAGSEIGKFNRFHQGAVIGVMPQDLGFNQQLLTKTVIGDHNIFREYSNIHKGTKEDSPTVIGNKNYFMGNSHVGHDCILGNNNILTHGAVLAGHVTLGNFAFISGLVAVHQFCFVGDYSMVAGLAKVVQDVPPYSTVDGNPSTVVGLNSVGMKRAGFSPEVRNAIKHAYKVIYHSGISTRKALDELEASGNLIEQVKYIIKFFRDSDRGVTNHR 259
               SCOP domains d3i3aa_ A: automated matches                                                                                                                                                                                                                                        SCOP domains
               CATH domains 3i3aA01 A:1-191 Hexapeptide repeat proteins                                                                                                                                                    3i3aA02 A:192-259  [code=1.20.1180.10, no name defined]              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee....ee....ee....ee....ee....ee....ee....ee...eee....ee....eeee..............eee....ee....ee.........eee....ee....ee....ee....ee....ee....ee....ee...eee....ee....ee...eee.......eeee....eeeee.hhhhhhh...hhhhhhhhhhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i3a A   1 MKIHPTAIIDPKAELHESVEVGPYSIIEGNVSIQEGTIIEGHVKICAGSEIGKFNRFHQGAVIGVMPQDLGFNQQLLTKTVIGDHNIFREYSNIHKGTKEDSPTVIGNKNYFMGNSHVGHDCILGNNNILTHGAVLAGHVTLGNFAFISGLVAVHQFCFVGDYSMVAGLAKVVQDVPPYSTVDGNPSTVVGLNSVGMKRAGFSPEVRNAIKHAYKVIYHSGISTRKALDELEASGNLIEQVKYIIKFFRDSDRGVTNHR 259
                                    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

Chain B from PDB  Type:PROTEIN  Length:259
 aligned with Q8EZA6_LEPIN | Q8EZA6 from UniProtKB/TrEMBL  Length:259

    Alignment length:259
                                    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         
         Q8EZA6_LEPIN     1 MKIHPTAIIDPKAELHESVEVGPYSIIEGNVSIQEGTIIEGHVKICAGSEIGKFNRFHQGAVIGVMPQDLGFNQQLLTKTVIGDHNIFREYSNIHKGTKEDSPTVIGNKNYFMGNSHVGHDCILGNNNILTHGAVLAGHVTLGNFAFISGLVAVHQFCFVGDYSMVAGLAKVVQDVPPYSTVDGNPSTVVGLNSVGMKRAGFSPEVRNAIKHAYKVIYHSGISTRKALDELEASGNLIEQVKYIIKFFRDSDRGVTNHR 259
               SCOP domains d3i3ab_ B: automated matches                                                                                                                                                                                                                                        SCOP domains
               CATH domains 3i3aB01 B:1-191 Hexapeptide repeat proteins                                                                                                                                                    3i3aB02 B:192-259  [code=1.20.1180.10, no name defined]              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee....ee....ee....ee....ee....ee....ee....ee...eee....ee....eeee..............eee....ee....ee.........eee....ee....ee....ee....ee....ee....ee....ee...eee....ee....ee...eee.......eeee....eeeee.hhhhhhh...hhhhhhhhhhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i3a B   1 MKIHPTAIIDPKAELHESVEVGPYSIIEGNVSIQEGTIIEGHVKICAGSEIGKFNRFHQGAVIGVMPQDLGFNQQLLTKTVIGDHNIFREYSNIHKGTKEDSPTVIGNKNYFMGNSHVGHDCILGNNNILTHGAVLAGHVTLGNFAFISGLVAVHQFCFVGDYSMVAGLAKVVQDVPPYSTVDGNPSTVVGLNSVGMKRAGFSPEVRNAIKHAYKVIYHSGISTRKALDELEASGNLIEQVKYIIKFFRDSDRGVTNHR 259
                                    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

Chain C from PDB  Type:PROTEIN  Length:259
 aligned with Q8EZA6_LEPIN | Q8EZA6 from UniProtKB/TrEMBL  Length:259

    Alignment length:259
                                    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         
         Q8EZA6_LEPIN     1 MKIHPTAIIDPKAELHESVEVGPYSIIEGNVSIQEGTIIEGHVKICAGSEIGKFNRFHQGAVIGVMPQDLGFNQQLLTKTVIGDHNIFREYSNIHKGTKEDSPTVIGNKNYFMGNSHVGHDCILGNNNILTHGAVLAGHVTLGNFAFISGLVAVHQFCFVGDYSMVAGLAKVVQDVPPYSTVDGNPSTVVGLNSVGMKRAGFSPEVRNAIKHAYKVIYHSGISTRKALDELEASGNLIEQVKYIIKFFRDSDRGVTNHR 259
               SCOP domains d3i3ac_ C: automated matches                                                                                                                                                                                                                                        SCOP domains
               CATH domains 3i3aC01 C:1-191 Hexapeptide repeat proteins                                                                                                                                                    3i3aC02 C:192-259  [code=1.20.1180.10, no name defined]              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee....ee....ee....ee....ee....ee....ee....ee...eee....ee....eeee..............eee....ee....ee.........eee....ee....ee....ee....ee....ee....ee....ee...eee....ee....ee...eee.......eeee....eeeee.hhhhhhh...hhhhhhhhhhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i3a C   1 MKIHPTAIIDPKAELHESVEVGPYSIIEGNVSIQEGTIIEGHVKICAGSEIGKFNRFHQGAVIGVMPQDLGFNQQLLTKTVIGDHNIFREYSNIHKGTKEDSPTVIGNKNYFMGNSHVGHDCILGNNNILTHGAVLAGHVTLGNFAFISGLVAVHQFCFVGDYSMVAGLAKVVQDVPPYSTVDGNPSTVVGLNSVGMKRAGFSPEVRNAIKHAYKVIYHSGISTRKALDELEASGNLIEQVKYIIKFFRDSDRGVTNHR 259
                                    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

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: automated matches (55)

Protein domain: automated matches (55)

Leptospira interrogans [TaxId: 173] (3)

1a	d3i3aa_	A:
1b	d3i3ab_	B:
1c	d3i3ac_	C:

(no "Pfam Domain" information available for 3I3A)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (Q8EZA6_LEPIN | Q8EZA6)

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: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.

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	Cis Peptide Bonds
		Asn A:185 - Pro A:186	[ RasMol ]
		Asn B:185 - Pro B:186	[ RasMol ]
		Asn C:185 - Pro C:186	[ RasMol ]
		Pro B:204 - Glu B:205	[ RasMol ]

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	2.3.1.129
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	Q8EZA6_LEPIN \| Q8EZA6	:	3hsq 3i3x

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3i3x

Description

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Ligands, Modified Residues, Ions (1, 3)

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