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Title :   CRYSTAL STRUCTURE OF THE C123S 2-METHYLISOCITRATE LYASE MUTANT FROM ESCHERICHIA COLI IN COMPLEX WITH THE INHIBITOR ISOCITRATE

Authors :   S. Liu, Z. Lu, Y. Han, E. Melamud, D. Dunaway-Mariano, O. Herzberg

Date :   16 Sep 04 (Deposition) - 01 Mar 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   2-Methylisocitrate Lyase/Inhibitor Complex, Isocitrate, Isocitrate Lyase Superfamily (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
(for further references see the PDB file header)

Molecule 1 - PROBABLE METHYLISOCITRATE LYASE
	Chains	:	A, B, C, D
	EC Number	:	4.1.3.30
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET3C
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PRPB
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	2-METHYLISOCITRATE LYASE

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 6)

No.	Name	Count	Type	Full Name
1	ICT	3	Ligand/Ion	ISOCITRIC ACID
2	MG	3	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:85 , ICT A:1105 , HOH A:1360 , HOH A:1361 , HOH A:1362	BINDING SITE FOR RESIDUE MG A 1101
2	AC2	SOFTWARE	ASP B:85 , ICT B:1205 , HOH B:1465 , HOH B:1466 , HOH B:1467	BINDING SITE FOR RESIDUE MG B 1201
3	AC3	SOFTWARE	ASP D:85 , ICT D:1405 , HOH D:1633 , HOH D:1634 , HOH D:1635	BINDING SITE FOR RESIDUE MG D 1401
4	AC4	SOFTWARE	SER A:45 , GLY A:46 , GLY A:47 , ASP A:85 , SER A:123 , GLY A:124 , HIS A:125 , ARG A:158 , GLU A:188 , ASN A:210 , THR A:212 , PRO A:236 , ARG A:241 , MG A:1101 , HOH A:1360 , ARG B:270	BINDING SITE FOR RESIDUE ICT A 1105
5	AC5	SOFTWARE	ARG A:270 , SER B:45 , GLY B:46 , GLY B:47 , ASP B:85 , SER B:123 , GLY B:124 , HIS B:125 , ARG B:158 , GLU B:188 , ASN B:210 , THR B:212 , PRO B:236 , ARG B:241 , MG B:1201 , HOH B:1230 , HOH B:1465	BINDING SITE FOR RESIDUE ICT B 1205
6	AC6	SOFTWARE	ARG C:270 , SER D:45 , GLY D:46 , GLY D:47 , ASP D:85 , SER D:123 , GLY D:124 , HIS D:125 , ARG D:158 , GLU D:188 , ASN D:210 , THR D:212 , PRO D:236 , ARG D:241 , MG D:1401 , HOH D:1436 , HOH D:1633	BINDING SITE FOR RESIDUE ICT D 1405

(no "SS Bond" information available for 1XG4)

Asymmetric/Biological Unit

No.	Residues
1	Asn A:18	-	Pro A:19
2	Asn B:18	-	Pro B:19
3	Asn C:18	-	Pro C:19
4	Asn D:18	-	Pro D:19

(no "SAP(SNP)/Variant" information available for 1XG4)

Asymmetric/Biological Unit (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:121-126 B:121-126 C:121-126 D:121-126

(no "Exon" information available for 1XG4)

Asymmetric/Biological 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:287
 aligned with PRPB_ECOLI | P77541 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:287
                                    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       
           PRPB_ECOLI     2 SLHSPGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGAKRCGHRPNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAVEGLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEKLDN 288
               SCOP domains d1xg4a_ A: 2-methylisocitrate lyase                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1xg4A00 A:2-288 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..eeeee..hhhhhhhhhhh....eeehhhhhhhh..........hhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhh..eeeee.................hhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh...eee..........hhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------ISOCIT------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xg4 A   2 SLHSPGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGAKRSGHRPNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAVEGLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEKLDN 288
                                    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

Chain B from PDB  Type:PROTEIN  Length:286
 aligned with PRPB_ECOLI | P77541 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:286
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282      
           PRPB_ECOLI     3 LHSPGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGAKRCGHRPNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAVEGLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEKLDN 288
               SCOP domains d1xg4b_ B: 2-methylisocitrate lyase                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1xg4B00 B:3-288 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..eeeee..hhhhhhhhhhh....eeehhhhhhhh..........hhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhh..eeeee.................hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh...eee..........hhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------ISOCIT------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xg4 B   3 LHSPGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGAKRSGHRPNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAVEGLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEKLDN 288
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282

Chain C from PDB  Type:PROTEIN  Length:287
 aligned with PRPB_ECOLI | P77541 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:287
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       
           PRPB_ECOLI     3 LHSPGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGAKRCGHRPNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAVEGLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEKLDNL 289
               SCOP domains d1xg4c_ C: 2-methylisocitrate lyase                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1xg4C00 C:3-289 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..eeeee..hhhhhhhhhhh....eeehhhhhhhh..........hhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhh..eeeee.................hhhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh...eee..........hhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------ISOCIT------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xg4 C   3 LHSPGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGAKRSGHRPNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAVEGLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEKLDNL 289
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282

Chain D from PDB  Type:PROTEIN  Length:283
 aligned with PRPB_ECOLI | P77541 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:283
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282   
           PRPB_ECOLI     3 LHSPGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGAKRCGHRPNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAVEGLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEK 285
               SCOP domains d1xg4d_ D: 2-methylisocitrate lyase                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1xg4D00 D:3-285 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                                                         CATH domains
           Pfam domains (1) -------PEP_mutase-1xg4D01 D:10-255                                                                                                                                                                                                                           ------------------------------ Pfam domains (1)
           Pfam domains (2) -------PEP_mutase-1xg4D02 D:10-255                                                                                                                                                                                                                           ------------------------------ Pfam domains (2)
           Pfam domains (3) -------PEP_mutase-1xg4D03 D:10-255                                                                                                                                                                                                                           ------------------------------ Pfam domains (3)
           Pfam domains (4) -------PEP_mutase-1xg4D04 D:10-255                                                                                                                                                                                                                           ------------------------------ Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhh..eeeee..hhhhhhhhhhh....eeehhhhhhhh..........hhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhh..eeeee.................hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh...eee..........hhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------ISOCIT--------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xg4 D   3 LHSPGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGAKRSGHRPNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAVEGLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEK 285
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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	d1xg4a_	A:
1b	d1xg4b_	B:
1c	d1xg4c_	C:
1d	d1xg4d_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

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	1xg4D00	D:3-285
1b	1xg4B00	B:3-288
1c	1xg4A00	A:2-288
1d	1xg4C00	C:3-289

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PK_TIM (63)

Family: PEP_mutase (13)

Escherichia coli (strain K12) (4)

1a	PEP_mutase-1xg4D01	D:10-255
1b	PEP_mutase-1xg4D02	D:10-255
1c	PEP_mutase-1xg4D03	D:10-255
1d	PEP_mutase-1xg4D04	D:10-255

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (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.

Asymmetric/Biological Unit
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	1xg4
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	PRPB_ECOLI \| P77541	:	1mum 1mzx 1oqf 1xg3

1oqf	NATIVE PRPB APO STRUCTURE
1xg3	SAME PROTEIN IN COMPLEX WITH THE REACTION PRODUCT, MG(II)- PYRUVATE AND SUCCINATE

Description

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Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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