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Biol. Unit 1 - sites (Jmol Viewer)

Title :   ACTIVE SITE LOOP DYNAMICS OF A CLASS IIA FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE FROM M. TUBERCULOSIS

Authors :   S. D. Pegan, A. D. Mesecar

Date :   20 Jan 12 (Deposition) - 23 Jan 13 (Release) - 26 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.58

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Class Ii Fructose-1, 6-Bisphosphate Aldolase, Zinc Enzyme, Dihydroxyacetone, Glyceraldehyde-3-Phosphate, Aldol Condensation, Glycolysis, Lyase, Metal-Binding, Phosphoglycolohydroxamate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. D. Pegan, K. Rukseree, G. C. Capodagli, E. A. Baker, O. Krasnykh, S. G. Franzblau, A. D. Mesecar
Active Site Loop Dynamics Of A Class Iia Fructose 1, 6-Bisphosphate Aldolase From Mycobacterium Tuberculosis.
Biochemistry V. 52 912 2013
PubMed-ID: 23298222 | Reference-DOI: 10.1021/BI300928U

Molecule 1 - FRUCTOSE-BISPHOSPHATE ALDOLASE
	Chains	:	A
	EC Number	:	4.1.2.13
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET17B
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	FBA, MT0379, MTCY13E10.25C, RV0363C
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Strain	:	H37RV
	Synonym	:	FBP ALDOLASE, FBPA, FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 6)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	NA	1	Ligand/Ion	SODIUM ION
3	P6G	1	Ligand/Ion	HEXAETHYLENE GLYCOL
4	PGH	1	Ligand/Ion	PHOSPHOGLYCOLOHYDROXAMIC ACID
5	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 12)

No.	Name	Count	Type	Full Name
1	ACT	4	Ligand/Ion	ACETATE ION
2	NA	-1	Ligand/Ion	SODIUM ION
3	P6G	4	Ligand/Ion	HEXAETHYLENE GLYCOL
4	PGH	4	Ligand/Ion	PHOSPHOGLYCOLOHYDROXAMIC ACID
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:211 , GLY A:213 , GLY A:253 , SER A:255 , PGH A:404 , HOH A:588	BINDING SITE FOR RESIDUE NA A 401
2	AC2	SOFTWARE	HIS A:96 , HIS A:212 , HIS A:252 , PGH A:404	BINDING SITE FOR RESIDUE ZN A 402
3	AC3	SOFTWARE	GLU A:198 , HIS A:199 , HIS A:344 , HIS A:346 , HOH A:992	BINDING SITE FOR RESIDUE ZN A 403
4	AC4	SOFTWARE	ASN A:27 , ASP A:95 , HIS A:96 , HIS A:212 , GLY A:213 , HIS A:252 , GLY A:253 , GLY A:254 , SER A:255 , ASN A:274 , VAL A:275 , ASP A:276 , THR A:277 , NA A:401 , ZN A:402 , HOH A:557 , HOH A:823	BINDING SITE FOR RESIDUE PGH A 404
5	AC5	SOFTWARE	LEU A:13 , GLY A:14 , LYS A:17 , LYS A:201 , ASP A:248 , P6G A:406 , HOH A:829 , HOH A:866	BINDING SITE FOR RESIDUE ACT A 405
6	AC6	SOFTWARE	ALA A:10 , GLU A:11 , ASP A:138 , LYS A:189 , ALA A:196 , GLY A:197 , LYS A:201 , TYR A:202 , ACT A:405 , HOH A:646 , HOH A:866 , HOH A:935 , HOH A:960 , HOH A:969	BINDING SITE FOR RESIDUE P6G A 406

(no "SS Bond" information available for 4DEL)

(no "Cis Peptide Bond" information available for 4DEL)

(no "SAP(SNP)/Variant" information available for 4DEL)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALDOLASE_CLASS_II_1	PS00602	Fructose-bisphosphate aldolase class-II signature 1.	ALF_MYCTO	86-97	1	A:86-97
1	ALDOLASE_CLASS_II_1	PS00602	Fructose-bisphosphate aldolase class-II signature 1.	ALF_MYCTU	86-97	1	A:86-97
2	ALDOLASE_CLASS_II_2	PS00806	Fructose-bisphosphate aldolase class-II signature 2.	ALF_MYCTO	158-169	1	A:158-169
2	ALDOLASE_CLASS_II_2	PS00806	Fructose-bisphosphate aldolase class-II signature 2.	ALF_MYCTU	158-169	1	A:158-169

Biological Unit 1 (2, 16)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALDOLASE_CLASS_II_1	PS00602	Fructose-bisphosphate aldolase class-II signature 1.	ALF_MYCTO	86-97	4	A:86-97
1	ALDOLASE_CLASS_II_1	PS00602	Fructose-bisphosphate aldolase class-II signature 1.	ALF_MYCTU	86-97	4	A:86-97
2	ALDOLASE_CLASS_II_2	PS00806	Fructose-bisphosphate aldolase class-II signature 2.	ALF_MYCTO	158-169	4	A:158-169
2	ALDOLASE_CLASS_II_2	PS00806	Fructose-bisphosphate aldolase class-II signature 2.	ALF_MYCTU	158-169	4	A:158-169

(no "Exon" information available for 4DEL)

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:345
 aligned with ALF_MYCTO | P9WQA2 from UniProtKB/Swiss-Prot  Length:344

    Alignment length:345
                                                                                                                                                                                                                                                                                                                                                                                344  
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341  |  
            ALF_MYCTO     2 PIATPEVYAEMLGQAKQNSYAFPAINCTSSETVNAAIKGFADAGSDGIIQFSTGGAEFGSGLGVKDMVTGAVALAEFTHVIAAKYPVNVALHTDHCPKDKLDSYVRPLLAISAQRVSKGGNPLFQSHMWDGSAVPIDENLAIAQELLKAAAAAKIILEIEIGVVGGEEDGVANEINEKLYTSPEDFEKTIEALGAGEHGKYLLAATFGNVHGVYKPGNVKLRPDILAQGQQVAAAKLGLPADAKPFDFVFHGGSGSLKSEIEEALRYGVVKMNVDTDTQYAFTRPIAGHMFTNYDGVLKVDGEVGVKKVYDPRSYLKKAEASMSQRVVQACNDLHCAGKSLTH--   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh...eeeeehhhhhhhhh.....hhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhhhhhhhhh.......eeee.....hhhhhhhhhhhhhhhhhhh..eeeeee....eee..eee..hhhhh.hhhhhhhhhhhhh......eeeee.................hhhhhhhhhhhhhhhh.........eee......hhhhhhhhhhh.eeeeeehhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------------ALDOLASE_CLA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------ALDOLASE_CLA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4del A   2 PIATPEVYAEMLGQAKQNSYAFPAINCTSSETVNAAIKGFADAGSDGIIQFSTGGAEFGSGLGVKDMVTGAVALAEFTHVIAAKYPVNVALHTDHCPKDKLDSYVRPLLAISAQRVSKGGNPLFQSHMWDGSAVPIDENLAIAQELLKAAAAAKIILEIEIGVVGGEEDGVANEINEKLYTSPEDFEKTIEALGAGEHGKYLLAATFGNVHGVYKPGNVKLRPDILAQGQQVAAAKLGLPADAKPFDFVFHGGSGSLKSEIEEALRYGVVKMNVDTDTQYAFTRPIAGHMFTNYDGVLKVDGEVGVKKVYDPRSYLKKAEASMSQRVVQACNDLHCAGKSLTHHH 346
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341

Chain A from PDB  Type:PROTEIN  Length:345
 aligned with ALF_MYCTU | P9WQA3 from UniProtKB/Swiss-Prot  Length:344

    Alignment length:345
                                                                                                                                                                                                                                                                                                                                                                                344  
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341  |  
            ALF_MYCTU     2 PIATPEVYAEMLGQAKQNSYAFPAINCTSSETVNAAIKGFADAGSDGIIQFSTGGAEFGSGLGVKDMVTGAVALAEFTHVIAAKYPVNVALHTDHCPKDKLDSYVRPLLAISAQRVSKGGNPLFQSHMWDGSAVPIDENLAIAQELLKAAAAAKIILEIEIGVVGGEEDGVANEINEKLYTSPEDFEKTIEALGAGEHGKYLLAATFGNVHGVYKPGNVKLRPDILAQGQQVAAAKLGLPADAKPFDFVFHGGSGSLKSEIEEALRYGVVKMNVDTDTQYAFTRPIAGHMFTNYDGVLKVDGEVGVKKVYDPRSYLKKAEASMSQRVVQACNDLHCAGKSLTH--   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh...eeeeehhhhhhhhh.....hhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhhhhhhhhh.......eeee.....hhhhhhhhhhhhhhhhhhh..eeeeee....eee..eee..hhhhh.hhhhhhhhhhhhh......eeeee.................hhhhhhhhhhhhhhhh.........eee......hhhhhhhhhhh.eeeeeehhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------------------------------------ALDOLASE_CLA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------ALDOLASE_CLA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4del A   2 PIATPEVYAEMLGQAKQNSYAFPAINCTSSETVNAAIKGFADAGSDGIIQFSTGGAEFGSGLGVKDMVTGAVALAEFTHVIAAKYPVNVALHTDHCPKDKLDSYVRPLLAISAQRVSKGGNPLFQSHMWDGSAVPIDENLAIAQELLKAAAAAKIILEIEIGVVGGEEDGVANEINEKLYTSPEDFEKTIEALGAGEHGKYLLAATFGNVHGVYKPGNVKLRPDILAQGQQVAAAKLGLPADAKPFDFVFHGGSGSLKSEIEEALRYGVVKMNVDTDTQYAFTRPIAGHMFTNYDGVLKVDGEVGVKKVYDPRSYLKKAEASMSQRVVQACNDLHCAGKSLTHHH 346
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341

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 "SCOP Domain" information available for 4DEL)

(no "CATH Domain" information available for 4DEL)

(no "Pfam Domain" information available for 4DEL)

Asymmetric Unit(hide GO term definitions)

Chain A (ALF_MYCTO | P9WQA2)

molecular function
	GO:0016832	aldehyde-lyase activity	Catalysis of the cleavage of a C-C bond in a molecule containing a hydroxyl group and a carbonyl group to form two smaller molecules, each being an aldehyde or a ketone.
	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:0004332	fructose-bisphosphate aldolase activity	Catalysis of the reaction: D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde-3-phosphate.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	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:0006096	glycolytic process	The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.

Chain A (ALF_MYCTU | P9WQA3)

molecular function
	GO:0016832	aldehyde-lyase activity	Catalysis of the cleavage of a C-C bond in a molecule containing a hydroxyl group and a carbonyl group to form two smaller molecules, each being an aldehyde or a ketone.
	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:0004332	fructose-bisphosphate aldolase activity	Catalysis of the reaction: D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde-3-phosphate.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	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:0006094	gluconeogenesis	The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
	GO:0006096	glycolytic process	The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
cellular component
	GO:0005618	cell wall	The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric Unit
	Complete Structure
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4del)

Biological Unit
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		Biological Unit 1	[ Jena3D ]

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	4del
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	ALF_MYCTU \| P9WQA3
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	4.1.2.13
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UniProtKB/Swiss-Prot
	ALF_MYCTO \| P9WQA2	:	3ekl 3ekz 3elf 4a21 4a22 4def 4lv4
	ALF_MYCTU \| P9WQA3	:	3ekl 3ekz 3elf 4a21 4a22 4def 4lv4

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Gene Ontology (13, 21)

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Related Entries Specified in the PDB File