2BLN - JenaLib

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Title :   N-TERMINAL FORMYLTRANSFERASE DOMAIN OF ARNA IN COMPLEX WITH N-5-FORMYLTETRAHYDROFOLATE AND UMP

Authors :   G. J. Williams, S. D. Breazeale, C. R. H. Raetz, J. H. Naismith

Date :   07 Mar 05 (Deposition) - 08 Apr 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.20

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

Keywords :   Transferase, Formyltransferase, L-Ara4N Biosynthesis, Methyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. J. Williams, S. D. Breazeale, C. R. H. Raetz, J. H. Naismith
Structure And Function Of Both Domains Of Arna, A Dual Function Decarboxylase And A Formyltransferase, Involved In 4-Amino-4-Deoxy-L- Arabinose Biosynthesis.
J. Biol. Chem. V. 280 23000 2005
PubMed-ID: 15809294 | Reference-DOI: 10.1074/JBC.M501534200

Molecule 1 - PROTEIN YFBG
	Chains	:	A, B
	EC Number	:	2.1.1.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET24B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	FORMYLTRANSFERASE DOMAIN, RESIDUES 1-305
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Strain	:	W3310
	Synonym	:	UDP-D-GLUCURONATE DEHYDROGENASE ARNA

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	FON	2	Ligand/Ion	FOLINIC ACID
3	U5P	2	Ligand/Ion	URIDINE-5'-MONOPHOSPHATE

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	FON	1	Ligand/Ion	FOLINIC ACID
3	U5P	1	Ligand/Ion	URIDINE-5'-MONOPHOSPHATE

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	FON	1	Ligand/Ion	FOLINIC ACID
3	U5P	1	Ligand/Ion	URIDINE-5'-MONOPHOSPHATE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MET A:11 , TYR A:83 , LEU A:117 , HIS A:162 , HOH A:2126 , HOH A:2293	BINDING SITE FOR RESIDUE ACT A1307
2	AC2	SOFTWARE	MET B:11 , TYR B:83 , LEU B:117 , HIS B:162 , HOH B:2354 , HOH B:2355	BINDING SITE FOR RESIDUE ACT B1307
3	AC3	SOFTWARE	TYR A:84 , HIS A:86 , LEU A:87 , ILE A:88 , LEU A:93 , ASN A:102 , ARG A:114 , MET A:135 , VAL A:136 , ALA A:139 , ASP A:140 , HOH A:2097 , HOH A:2149 , HOH A:2284 , HOH A:2285 , HOH A:2286 , HOH A:2287 , HOH A:2288 , GLU B:194	BINDING SITE FOR RESIDUE FON A1305
4	AC4	SOFTWARE	TYR A:42 , ARG A:85 , ASN A:118 , ARG A:200 , ARG A:201 , THR A:202 , PRO A:203 , VAL A:224 , PRO A:229 , HOH A:2198 , HOH A:2289 , HOH A:2290 , HOH A:2291 , HOH A:2292	BINDING SITE FOR RESIDUE U5P A1306
5	AC5	SOFTWARE	HIS A:211 , SER B:81 , TYR B:84 , HIS B:86 , LEU B:87 , ILE B:88 , LEU B:93 , ASN B:102 , ARG B:114 , MET B:135 , VAL B:136 , ALA B:139 , ASP B:140 , HOH B:2117 , HOH B:2178 , HOH B:2342 , HOH B:2343 , HOH B:2344 , HOH B:2345 , HOH B:2346 , HOH B:2347	BINDING SITE FOR RESIDUE FON B1305
6	AC6	SOFTWARE	HIS B:9 , TYR B:42 , ARG B:85 , ASN B:118 , ARG B:201 , THR B:202 , PRO B:203 , VAL B:224 , PRO B:229 , HOH B:2243 , HOH B:2248 , HOH B:2349 , HOH B:2350 , HOH B:2351 , HOH B:2353	BINDING SITE FOR RESIDUE U5P B1306

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

Asymmetric Unit

No.	Residues
1	Leu A:108	-	Pro A:109
2	Asp A:226	-	Pro A:227
3	Ala A:263	-	Pro A:264
4	Leu B:108	-	Pro B:109
5	Asp B:226	-	Pro B:227
6	Ala B:263	-	Pro B:264

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

(no "PROSITE Motif" information available for 2BLN)

(no "Exon" information available for 2BLN)

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
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Chain A from PDB  Type:PROTEIN  Length:298
 aligned with ARNA_ECOLI | P77398 from UniProtKB/Swiss-Prot  Length:660

    Alignment length:304
                                    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       270       280       290       300    
           ARNA_ECOLI     1 MKTVVFAYHDMGCLGIEALLAAGYEISAIFTHTDNPGEKAFYGSVARLAAERGIPVYAPDNVNHPLWVERIAQLSPDVIFSFYYRHLIYDEILQLAPAGAFNLHGSLLPKYRGRAPLNWVLVNGETETGVTLHRMVKRADAGAIVAQLRIAIAPDDIAITLHHKLCHAARQLLEQTLPAIKHGNILEIAQRENEATCFGRRTPDDSFLEWHKPASVLHNMVRAVADPWPGAFSYVGNQKFTVWSSRVHPHASKAQPGSVISVAPLLIACGDGALEIVTGQAGDGITMQGSQLAQTLGLVQGSRL 304
               SCOP domains d2blna2 A:1-203 Polymyxin resistan      ce protein ArnA, N-terminal domain                                                                                                                                 d2blna1 A:204-304 Polymyxin resistance protein ArnA, domain 2                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeehhhhhhhhhhhhhhh..eeeeee....------...hhhhhhhhhh..ee......hhhhhhhhhhh...eeeee......hhhhhh.....eeeee.......ee.hhhhhhhhh...eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhh.ee...hhhhh......hhhhhhhhhhhh......eeeee..eeeeeeeeeee..........eee...eeee....eeeeeeeee.....eehhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bln A   1 MKTVVFAYHDMGCLGIEALLAAGYEISAIFTHTD------FYGSVARLAAERGIPVYAPDNVNHPLWVERIAQLSPDVIFSFYYRHLIYDEILQLAPAGAFNLHGSLLPKYRGRAPLNWVLVNGETETGVTLHRMVKRADAGAIVAQLRIAIAPDDIAITLHHKLCHAARQLLEQTLPAIKHGNILEIAQRENEATCFGRRTPDDSFLEWHKPASVLHNMVRAVADPWPGAFSYVGNQKFTVWSSRVHPHASKAQPGSVISVAPLLIACGDGALEIVTGQAGDGITMQGSQLAQTLGLVQGSRL 304
                                    10        20        30   |     -|       50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300    
                                                            34     41

Chain B from PDB  Type:PROTEIN  Length:298
 aligned with ARNA_ECOLI | P77398 from UniProtKB/Swiss-Prot  Length:660

    Alignment length:304
                                    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       270       280       290       300    
           ARNA_ECOLI     1 MKTVVFAYHDMGCLGIEALLAAGYEISAIFTHTDNPGEKAFYGSVARLAAERGIPVYAPDNVNHPLWVERIAQLSPDVIFSFYYRHLIYDEILQLAPAGAFNLHGSLLPKYRGRAPLNWVLVNGETETGVTLHRMVKRADAGAIVAQLRIAIAPDDIAITLHHKLCHAARQLLEQTLPAIKHGNILEIAQRENEATCFGRRTPDDSFLEWHKPASVLHNMVRAVADPWPGAFSYVGNQKFTVWSSRVHPHASKAQPGSVISVAPLLIACGDGALEIVTGQAGDGITMQGSQLAQTLGLVQGSRL 304
               SCOP domains d2blnb2 B:1-203 Polymyxin resistan      ce protein ArnA, N-terminal domain                                                                                                                                 d2blnb1 B:204-304 Polymyxin resistance protein ArnA, domain 2                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeehhhhhhhhhhhhhhh..eeeeee....------...hhhhhhhhhh..ee......hhhhhhhhhh....eeeee......hhhhhh.....eeeee.......ee.hhhhhhhhh...eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhh.ee...hhhhh......hhhhhhhhhhhh......eeeee..eeeeeeeeeee..........eee...eeee....eeeeeeeee.....eehhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bln B   1 MKTVVFAYHDMGCLGIEALLAAGYEISAIFTHTD------FYGSVARLAAERGIPVYAPDNVNHPLWVERIAQLSPDVIFSFYYRHLIYDEILQLAPAGAFNLHGSLLPKYRGRAPLNWVLVNGETETGVTLHRMVKRADAGAIVAQLRIAIAPDDIAITLHHKLCHAARQLLEQTLPAIKHGNILEIAQRENEATCFGRRTPDDSFLEWHKPASVLHNMVRAVADPWPGAFSYVGNQKFTVWSSRVHPHASKAQPGSVISVAPLLIACGDGALEIVTGQAGDGITMQGSQLAQTLGLVQGSRL 304
                                    10        20        30   |     -|       50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300    
                                                            34     41

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 2BLN)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (ARNA_ECOLI | P77398)

molecular function
	GO:0070403	NAD+ binding	Interacting selectively and non-covalently with the oxidized form, NAD, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions.
	GO:0099619	UDP-4-amino-4-deoxy-L-arabinose formyltransferase activity	Catalysis of the reaction: 10-formyltetrahydrofolate + UDP-4-amino-4-deoxy-beta-L-arabinopyranose = 5,6,7,8-tetrahydrofolate + UDP-4-deoxy-4-formamido-beta-L-arabinopyranose
	GO:0048040	UDP-glucuronate decarboxylase activity	Catalysis of the reaction: H(+) + UDP-alpha-D-glucuronate = CO(2) + UDP-alpha-D-xylose.
	GO:0099618	UDP-glucuronic acid dehydrogenase activity	Catalytis of the reaction: UDP-glucuronate + NAD+ = UDP-beta-L-threo-pentapyranos-4-ulose + CO2 + NADH + H+
	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:0050662	coenzyme binding	Interacting selectively and non-covalently with a coenzyme, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed.
	GO:0016742	hydroxymethyl-, formyl- and related transferase activity	Catalysis of the transfer of a hydroxymethyl- or formyl group from one compound (donor) to another (acceptor).
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
	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.
biological process
	GO:0033320	UDP-D-xylose biosynthetic process	The chemical reactions and pathways resulting in the formation of UDP-D-xylose, uridinediphosphoxylose, a substance composed of xylose in glycosidic linkage with uridine diphosphate.
	GO:0009058	biosynthetic process	The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
	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:0046493	lipid A metabolic process	The chemical reactions and pathways involving 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: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.
	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:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0046677	response to antibiotic	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

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	Cis Peptide Bonds
		Ala A:263 - Pro A:264	[ RasMol ]
		Ala B:263 - Pro B:264	[ RasMol ]
		Asp A:226 - Pro A:227	[ RasMol ]
		Asp B:226 - Pro B:227	[ RasMol ]
		Leu A:108 - Pro A:109	[ RasMol ]
		Leu B:108 - Pro B:109	[ RasMol ]

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	2bln
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	ARNA_ECOLI \| P77398
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	2.1.1.2
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	ARNA_ECOLI \| P77398	:	1u9j 1yrw 1z73 1z74 1z75 1z7b 1z7e 2bll 4wkg

1u9j	CRYSTAL STRUCTURE OF E. COLI ARNA (PMRI) DECARBOXYLASEDOMAIN
2bll	APO-STRUCTURE OF THE C-TERMINAL DECARBOXYLASE DOMAIN OF ARNA

Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

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