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Title :   CRYSTAL STRUCTURE OF THE 2-METHYLISOCITRATE LYASE

Authors :   S. Liu, Z. Lu, D. Dunaway-Mariano, O. Herzberg, Structure 2 Function (S2F)

Date :   08 Mar 03 (Deposition) - 27 Apr 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.93

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

Keywords :   Structural Genomics, Alpha-Beta Barrel, Swapped Helix Across A Dimer, Structure 2 Function Project, S2F, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Liu, Z. Lu, Y. Han, E. Melamud, D. Dunaway-Mariano, O. Herzberg
Crystal Structures Of 2-Methylisocitrate Lyase In Complex With Product And With Isocitrate Inhibitor Provide Insight Into Lyase Substrate Specificity, Catalysis And Evolution.
Biochemistry V. 44 2949 2005
PubMed-ID: 15723538 | Reference-DOI: 10.1021/BI0479712

Molecule 1 - 2-METHYLISOCITRATE LYASE
	Chains	:	A, B
	EC Number	:	4.1.3.30
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET3C-PRPB
	Expression System Strain	:	BL21 DE3 PLYS S
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PRPB OR B0331
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1OQF)

(no "Site" information available for 1OQF)

(no "SS Bond" information available for 1OQF)

Asymmetric Unit

No.	Residues
1	Asn A:17	-	Pro A:18
2	Asn B:17	-	Pro B:18

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ISOCITRATE_LYASE	PS00161	Isocitrate lyase signature.	PRPB_ECOLI	121-126	2	A:120-125 B:120-125

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ISOCITRATE_LYASE	PS00161	Isocitrate lyase signature.	PRPB_ECOLI	121-126	4	A:120-125 B:120-125

(no "Exon" information available for 1OQF)

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:290
 aligned with PRPB_ECOLI | P77541 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:290
                                    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
           PRPB_ECOLI     2 SLHSPGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGAKRCGHRPNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAVEGLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEKLDNLFA 291
               SCOP domains d1oqfa_ A: 2-methylisocitrate lyase                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1oqfA00 A:1-290 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..eeeee..hhhhhhhhhhh....eeehhhhhhhh..........hhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhh..eeeee.................hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhh....eee..........hhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhh..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------ISOCIT--------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oqf A   1 SLHSPGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGAKRCGHRPNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAVEGLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEKLDNLFA 290
                                    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

Chain B from PDB  Type:PROTEIN  Length:290
 aligned with PRPB_ECOLI | P77541 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:290
                                    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
           PRPB_ECOLI     2 SLHSPGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGAKRCGHRPNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAVEGLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEKLDNLFA 291
               SCOP domains d1oqfb_ B: 2-methylisocitrate lyase                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1oqfB00 B:1-290 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                                                                CATH domains
           Pfam domains (1) --------PEP_mutase-1oqfB01 B:9-254                                                                                                                                                                                                                            ------------------------------------ Pfam domains (1)
           Pfam domains (2) --------PEP_mutase-1oqfB02 B:9-254                                                                                                                                                                                                                            ------------------------------------ Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhh..eeeee..hhhhhhhhhhh....eeehhhhhhhh..........hhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhh..eeeee.................hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhh....eee..........hhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhh.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------ISOCIT--------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oqf B   1 SLHSPGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGAKRCGHRPNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAVEGLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEKLDNLFA 290
                                    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

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: Phosphoenolpyruvate/pyruvate domain (92)

Family: Phosphoenolpyruvate mutase/Isocitrate lyase-like (20)

Protein domain: 2-methylisocitrate lyase (6)

Escherichia coli [TaxId: 562] (4)

1a	d1oqfa_	A:
1b	d1oqfb_	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( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Phosphoenolpyruvate-binding domains (67)

Escherichia coli. Organism_taxid: 562. (5)

1a	1oqfA00	A:1-290
1b	1oqfB00	B:1-290

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PK_TIM (63)

Family: PEP_mutase (13)

Escherichia coli (strain K12) (4)

1a	PEP_mutase-1oqfB01	B:9-254
1b	PEP_mutase-1oqfB02	B:9-254

Asymmetric Unit(hide GO term definitions)

Chain A,B (PRPB_ECOLI | P77541)

molecular function
	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:0046421	methylisocitrate lyase activity	Catalysis of the reaction: (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = pyruvate + succinate.
	GO:0046912	transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer	Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor), with the acyl group being converted into alkyl on transfer.
biological process
	GO:0006097	glyoxylate cycle	A modification of the TCA cycle occurring in some plants and microorganisms, in which isocitrate is cleaved to glyoxylate and succinate. Glyoxylate can then react with acetyl-CoA to form malate.
	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:0019629	propionate catabolic process, 2-methylcitrate cycle	The chemical reactions and pathways resulting in the breakdown of propionate that occurs in the 2-methylcitrate cycle.
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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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Asn A:17 - Pro A:18	[ RasMol ]
		Asn B:17 - Pro B:18	[ RasMol ]

Biological Unit
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		Biological Unit 1	[ Jena3D ]

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	PRPB_ECOLI \| P77541	:	1mum 1mzx 1xg3 1xg4

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