1Q6R - JenaLib

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Title :   STRUCTURE OF 3-KETO-L-GULONATE 6-PHOSPHATE DECARBOXYLASE WITH BOUND L-XYLULOSE 5-PHOSPHATE

Authors :   E. L. Wise, W. S. Yew, J. A. Gerlt, I. Rayment

Date :   13 Aug 03 (Deposition) - 28 Oct 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.76

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

Keywords :   Beta Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. L. Wise, W. S. Yew, J. A. Gerlt, I. Rayment
Structural Evidence For A 1, 2-Enediolate Intermediate In The Reaction Catalyzed By 3-Keto-L-Gulonate 6-Phosphate Decarboxylase, A Member Of The Orotidine 5'-Monophosphate Decarboxylase Suprafamily
Biochemistry V. 42 12133 2003
PubMed-ID: 14567674 | Reference-DOI: 10.1021/BI0348819
(for further references see the PDB file header)

Molecule 1 - 3-KETO-L-GULONATE 6-PHOSPHATE DECARBOXYLASE
	Chains	:	A, B
	EC Number	:	4.1.2.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	PROBABLE HEXULOSE-6-PHOSPHATE SYNTHASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	LX1	2	Ligand/Ion	L-XYLULOSE 5-PHOSPHATE
2	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	LX1	2	Ligand/Ion	L-XYLULOSE 5-PHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	LX1	4	Ligand/Ion	L-XYLULOSE 5-PHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:33 , ASP A:62 , LX1 A:7301 , HOH A:7410 , HOH A:7442	BINDING SITE FOR RESIDUE MG A 7300
2	AC2	SOFTWARE	GLU B:33 , ASP B:62 , LX1 B:9301 , HOH B:9384 , HOH B:9453	BINDING SITE FOR RESIDUE MG B 9300
3	AC3	SOFTWARE	ALA A:9 , ASP A:11 , GLU A:33 , ASP A:62 , LYS A:64 , HIS A:136 , THR A:169 , GLY A:171 , ILE A:189 , GLY A:191 , ARG A:192 , MG A:7300 , HOH A:7303 , HOH A:7308 , HOH A:7312 , HOH A:7326 , HOH A:7396 , HOH A:7410 , HOH A:7442	BINDING SITE FOR RESIDUE LX1 A 7301
4	AC4	SOFTWARE	ALA B:9 , ASP B:11 , GLU B:33 , ASP B:62 , LYS B:64 , HIS B:136 , THR B:169 , GLY B:170 , GLY B:171 , GLY B:191 , ARG B:192 , MG B:9300 , HOH B:9303 , HOH B:9314 , HOH B:9316 , HOH B:9384 , HOH B:9385 , HOH B:9453	BINDING SITE FOR RESIDUE LX1 B 9301

Asymmetric Unit

No.	Residues
1	A:89	-	B:89

(no "Cis Peptide Bond" information available for 1Q6R)

(no "SAP(SNP)/Variant" information available for 1Q6R)

(no "PROSITE Motif" information available for 1Q6R)

(no "Exon" information available for 1Q6R)

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:214
 aligned with ULAD_ECOLI | P39304 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:214
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211    
           ULAD_ECOLI     2 SLPMLQVALDNQTMDSAYETTRLIAEEVDIIEVGTILCVGEGVRAVRDLKALYPHKIVLADAKIADAGKILSRMCFEANADWVTVICCADINTAKGALDVAKEFNGDVQIELTGYWTWEQAQQWRDAGIGQVVYHRSRDAQAAGVAWGEADITAIKRLSDMGFKVTVTGGLALEDLPLFKGIPIHVFIAGRSIRDAASPVEAARQFKRSIAELW 215
               SCOP domains d1q6ra_ A: 3-keto-L-gulonate 6-phosphate decarboxylase                                                                                                                                                                 SCOP domains
               CATH domains 1q6rA00 A:2-215 Aldolase class I                                                                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...hhhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhh..eeeee.hhhhhhh....hhhhhhhhhhhhhh..eeeee...hhhhhhhhh.....eeeehhhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q6r A   2 SLPMLQVALDNQTMDSAYETTRLIAEEVDIIEVGTILCVGEGVRAVRDLKALYPHKIVLADAKIADAGKILSRMCFEANADWVTVICCADINTAKGALDVAKEFNGDVQIELTGYWTWEQAQQWRDAGIGQVVYHRSRDAQAAGVAWGEADITAIKRLSDMGFKVTVTGGLALEDLPLFKGIPIHVFIAGRSIRDAASPVEAARQFKRSIAELW 215
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

Chain B from PDB  Type:PROTEIN  Length:215
 aligned with ULAD_ECOLI | P39304 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:215
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     
           ULAD_ECOLI     2 SLPMLQVALDNQTMDSAYETTRLIAEEVDIIEVGTILCVGEGVRAVRDLKALYPHKIVLADAKIADAGKILSRMCFEANADWVTVICCADINTAKGALDVAKEFNGDVQIELTGYWTWEQAQQWRDAGIGQVVYHRSRDAQAAGVAWGEADITAIKRLSDMGFKVTVTGGLALEDLPLFKGIPIHVFIAGRSIRDAASPVEAARQFKRSIAELWG 216
               SCOP domains d1q6rb_ B: 3-keto-L-gulonate 6-phosphate decarboxylase                                                                                                                                                                  SCOP domains
               CATH domains 1q6rB00 B:2-216 Aldolase class I                                                                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...hhhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhh...eeeee.hhhhhhh....hhhhhhhhhhhhhh..eeeee...hhhhhhhhh.....eeeehhhhhh..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q6r B   2 SLPMLQVALDNQTMDSAYETTRLIAEEVDIIEVGTILCVGEGVRAVRDLKALYPHKIVLADAKIADAGKILSRMCFEANADWVTVICCADINTAKGALDVAKEFNGDVQIELTGYWTWEQAQQWRDAGIGQVVYHRSRDAQAAGVAWGEADITAIKRLSDMGFKVTVTGGLALEDLPLFKGIPIHVFIAGRSIRDAASPVEAARQFKRSIAELWG 216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Ribulose-phoshate binding barrel (356)

Family: Decarboxylase (172)

Protein domain: 3-keto-L-gulonate 6-phosphate decarboxylase (17)

Escherichia coli [TaxId: 562] (14)

1a	d1q6ra_	A:
1b	d1q6rb_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Escherichia coli. Organism_taxid: 562. (44)

1a	1q6rB00	B:2-216
1b	1q6rA00	A:2-215

(no "Pfam Domain" information available for 1Q6R)

Asymmetric Unit(hide GO term definitions)

Chain A,B (ULAD_ECOLI | P39304)

molecular function
	GO:0033982	3-dehydro-L-gulonate-6-phosphate decarboxylase activity	Catalysis of the reaction: 3-dehydro-L-gulonate 6-phosphate + H(+) = L-xylulose 5-phosphate + CO(2).
	GO:0016831	carboxy-lyase activity	Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
	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:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	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:0004590	orotidine-5'-phosphate decarboxylase activity	Catalysis of the reaction: H(+) + orotidine 5'-phosphate = CO(2) + UMP.
biological process
	GO:0006207	'de novo' pyrimidine nucleobase biosynthetic process	The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
	GO:0019854	L-ascorbic acid catabolic process	The chemical reactions and pathways resulting in the breakdown of L-ascorbic acid; L-ascorbic acid ionizes to give L-ascorbate, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate, which is required as a cofactor in the oxidation of prolyl residues to hydroxyprolyl, and other reactions.
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	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.

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	ULAD_ECOLI \| P39304	:	1kv8 1kw1 1q6l 1q6o 1q6q 1so3 1so4 1so5 1so6 1xbv 1xbx 1xby 1xbz

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Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (1, 1)

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