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Title :   CRYSTAL STRUCTURE OF MYCOLIC ACID CYCLOPROPANE SYNTHASE PCAA COMPLEXED WITH S-ADENOSYL-L-HOMOCYSTEINE

Authors :   C. -C. Huang, C. V. Smith, M. S. Glickman, W. R. Jacobs Jr. , J. C. Sacchettini, Tb Structural Genomics Consortium (Tbsgc)

Date :   15 Feb 02 (Deposition) - 06 Mar 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Methyltransferase, S-Adenosyl-L-Homocysteine Cofactor, Alpha/Beta, Structural Genomics, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. -C. Huang, C. V. Smith, M. S. Glickman, W. R. Jacobs Jr. , J. C. Sacchettini
Crystal Structures Of Mycolic Acid Cyclopropane Synthases From Mycobacterium Tuberculosis.
J. Biol. Chem. V. 277 11559 2002
PubMed-ID: 11756461 | Reference-DOI: 10.1074/JBC.M111698200
(for further references see the PDB file header)

Molecule 1 - MYCOLIC ACID SYNTHASE
	Chains	:	A, B
	EC Number	:	2.1.1.79
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET30B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PCAA
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Synonym	:	PCAA CYCLOPROPANE SYNTHASE

		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 (2, 4)

No.	Name	Count	Type	Full Name
1	CO3	2	Ligand/Ion	CARBONATE ION
2	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CO3	1	Ligand/Ion	CARBONATE ION
2	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	CO3	1	Ligand/Ion	CARBONATE ION
2	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:34 , CYS A:35 , GLY A:137 , GLU A:140 , HIS A:167 , ILE A:169 , TYR A:232	BINDING SITE FOR RESIDUE CO3 A 903
2	AC2	SOFTWARE	SER B:34 , CYS B:35 , GLY B:137 , GLU B:140 , HIS B:167 , THR B:168 , ILE B:169	BINDING SITE FOR RESIDUE CO3 B 904
3	AC3	SOFTWARE	THR A:32 , TYR A:33 , SER A:34 , GLY A:72 , GLY A:74 , THR A:94 , LEU A:95 , GLN A:99 , GLY A:122 , TRP A:123 , GLU A:124 , ILE A:136 , GLY A:137 , ALA A:138 , ARG A:146 , HOH A:907 , HOH A:909 , HOH A:973	BINDING SITE FOR RESIDUE SAH A 900
4	AC4	SOFTWARE	THR B:32 , TYR B:33 , SER B:34 , GLY B:72 , GLY B:74 , THR B:94 , LEU B:95 , GLN B:99 , GLY B:122 , TRP B:123 , ILE B:136 , GLY B:137 , ALA B:138 , PHE B:142 , HOH B:905 , HOH B:906 , HOH B:908 , HOH B:911 , HOH B:919	BINDING SITE FOR RESIDUE SAH B 901

(no "SS Bond" information available for 1L1E)

(no "Cis Peptide Bond" information available for 1L1E)

(no "SAP(SNP)/Variant" information available for 1L1E)

(no "PROSITE Motif" information available for 1L1E)

(no "Exon" information available for 1L1E)

Asymmetric Unit

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	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:272
 aligned with CMAS3_MYCTO | P9WPB2 from UniProtKB/Swiss-Prot  Length:287

    Alignment length:272
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285  
          CMAS3_MYCTO    16 YDLSDDFFRLFLDPTQTYSCAYFERDDMTLQEAQIAKIDLALGKLNLEPGMTLLDIGCGWGATMRRAIEKYDVNVVGLTLSENQAGHVQKMFDQMDTPRSRRVLLEGWEKFDEPVDRIVSIGAFEHFGHQRYHHFFEVTHRTLPADGKMLLHTIVRPTFKEGREKGLTLTHELVHFTKFILAEIFPGGWLPSIPTVHEYAEKVGFRVTAVQSLQLHYARTLDMWATALEANKDQAIAIQSQTVYDRYMKYLTGCAKLFRQGYTDVDQFTLEK 287
               SCOP domains d1l1ea_ A: PccA                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1l1eA00 A:16-287 Vaccinia Virus protein VP39                                                                                                                                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh...................hhhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhh.....eeeee.hhhhh.....eeeee.hhhhhhhhhhhhhhhhhhhhh....eeeeeeee.................hhhhhhhhhhhh.......hhhhhhhhhhh...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l1e A  16 YDLSDDFFRLFLDPTQTYSCAYFERDDMTLQEAQIAKIDLALGKLNLEPGMTLLDIGCGWGATMRRAIEKYDVNVVGLTLSENQAGHVQKMFDQMDTPRSRRVLLEGWEKFDEPVDRIVSIGAFEHFGHQRYHHFFEVTHRTLPADGKMLLHTIVRPTFKEGREKGLTLTHELVHFTKFILAEIFPGGWLPSIPTVHEYAEKVGFRVTAVQSLQLHYARTLDMWATALEANKDQAIAIQSQTVYDRYMKYLTGCAKLFRQGYTDVDQFTLEK 287
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285

Chain A from PDB  Type:PROTEIN  Length:272
 aligned with CMAS3_MYCTU | P9WPB3 from UniProtKB/Swiss-Prot  Length:287

    Alignment length:272
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285  
          CMAS3_MYCTU    16 YDLSDDFFRLFLDPTQTYSCAYFERDDMTLQEAQIAKIDLALGKLNLEPGMTLLDIGCGWGATMRRAIEKYDVNVVGLTLSENQAGHVQKMFDQMDTPRSRRVLLEGWEKFDEPVDRIVSIGAFEHFGHQRYHHFFEVTHRTLPADGKMLLHTIVRPTFKEGREKGLTLTHELVHFTKFILAEIFPGGWLPSIPTVHEYAEKVGFRVTAVQSLQLHYARTLDMWATALEANKDQAIAIQSQTVYDRYMKYLTGCAKLFRQGYTDVDQFTLEK 287
               SCOP domains d1l1ea_ A: PccA                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1l1eA00 A:16-287 Vaccinia Virus protein VP39                                                                                                                                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh...................hhhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhh.....eeeee.hhhhh.....eeeee.hhhhhhhhhhhhhhhhhhhhh....eeeeeeee.................hhhhhhhhhhhh.......hhhhhhhhhhh...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l1e A  16 YDLSDDFFRLFLDPTQTYSCAYFERDDMTLQEAQIAKIDLALGKLNLEPGMTLLDIGCGWGATMRRAIEKYDVNVVGLTLSENQAGHVQKMFDQMDTPRSRRVLLEGWEKFDEPVDRIVSIGAFEHFGHQRYHHFFEVTHRTLPADGKMLLHTIVRPTFKEGREKGLTLTHELVHFTKFILAEIFPGGWLPSIPTVHEYAEKVGFRVTAVQSLQLHYARTLDMWATALEANKDQAIAIQSQTVYDRYMKYLTGCAKLFRQGYTDVDQFTLEK 287
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285

Chain B from PDB  Type:PROTEIN  Length:260
 aligned with CMAS3_MYCTO | P9WPB2 from UniProtKB/Swiss-Prot  Length:287

    Alignment length:272
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285  
          CMAS3_MYCTO    16 YDLSDDFFRLFLDPTQTYSCAYFERDDMTLQEAQIAKIDLALGKLNLEPGMTLLDIGCGWGATMRRAIEKYDVNVVGLTLSENQAGHVQKMFDQMDTPRSRRVLLEGWEKFDEPVDRIVSIGAFEHFGHQRYHHFFEVTHRTLPADGKMLLHTIVRPTFKEGREKGLTLTHELVHFTKFILAEIFPGGWLPSIPTVHEYAEKVGFRVTAVQSLQLHYARTLDMWATALEANKDQAIAIQSQTVYDRYMKYLTGCAKLFRQGYTDVDQFTLEK 287
               SCOP domains d1l1eb_ B: PccA                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1l1eB00 B:16-287 Vaccinia Virus protein VP39                                                                                                                                                                                                                                     CATH domains
           Pfam domains (1) CMAS-1l1eB01 B:16-283                                                                                                                                                                                                                                                       ---- Pfam domains (1)
           Pfam domains (2) CMAS-1l1eB02 B:16-283                                                                                                                                                                                                                                                       ---- Pfam domains (2)
         Sec.struct. author ...hhhhhh...................hhhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhhh.eeeee..hhhhhhhhhhhhh.......eeee..hhhhh.....eeeee.hhhhhh..hhhhhhhhhh.......eeeeeeee.....------------...hhhhhhhhh.......hhhhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l1e B  16 YDLSDDFFRLFLDPTQTYSCAYFERDDMTLQEAQIAKIDLALGKLNLEPGMTLLDIGCGWGATMRRAIEKYDVNVVGLTLSENQAGHVQKMFDQMDTPRSRRVLLEGWEKFDEPVDRIVSIGAFEHFGHQRYHHFFEVTHRTLPADGKMLLHTIVRPTFK------------LVHFTKFILAEIFPGGWLPSIPTVHEYAEKVGFRVTAVQSLQLHYARTLDMWATALEANKDQAIAIQSQTVYDRYMKYLTGCAKLFRQGYTDVDQFTLEK 287
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175         -  |    195       205       215       225       235       245       255       265       275       285  
                                                                                                                                                                                         175          188

Chain B from PDB  Type:PROTEIN  Length:260
 aligned with CMAS3_MYCTU | P9WPB3 from UniProtKB/Swiss-Prot  Length:287

    Alignment length:272
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285  
          CMAS3_MYCTU    16 YDLSDDFFRLFLDPTQTYSCAYFERDDMTLQEAQIAKIDLALGKLNLEPGMTLLDIGCGWGATMRRAIEKYDVNVVGLTLSENQAGHVQKMFDQMDTPRSRRVLLEGWEKFDEPVDRIVSIGAFEHFGHQRYHHFFEVTHRTLPADGKMLLHTIVRPTFKEGREKGLTLTHELVHFTKFILAEIFPGGWLPSIPTVHEYAEKVGFRVTAVQSLQLHYARTLDMWATALEANKDQAIAIQSQTVYDRYMKYLTGCAKLFRQGYTDVDQFTLEK 287
               SCOP domains d1l1eb_ B: PccA                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1l1eB00 B:16-287 Vaccinia Virus protein VP39                                                                                                                                                                                                                                     CATH domains
           Pfam domains (1) CMAS-1l1eB01 B:16-283                                                                                                                                                                                                                                                       ---- Pfam domains (1)
           Pfam domains (2) CMAS-1l1eB02 B:16-283                                                                                                                                                                                                                                                       ---- Pfam domains (2)
         Sec.struct. author ...hhhhhh...................hhhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhhh.eeeee..hhhhhhhhhhhhh.......eeee..hhhhh.....eeeee.hhhhhh..hhhhhhhhhh.......eeeeeeee.....------------...hhhhhhhhh.......hhhhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l1e B  16 YDLSDDFFRLFLDPTQTYSCAYFERDDMTLQEAQIAKIDLALGKLNLEPGMTLLDIGCGWGATMRRAIEKYDVNVVGLTLSENQAGHVQKMFDQMDTPRSRRVLLEGWEKFDEPVDRIVSIGAFEHFGHQRYHHFFEVTHRTLPADGKMLLHTIVRPTFK------------LVHFTKFILAEIFPGGWLPSIPTVHEYAEKVGFRVTAVQSLQLHYARTLDMWATALEANKDQAIAIQSQTVYDRYMKYLTGCAKLFRQGYTDVDQFTLEK 287
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175         -  |    195       205       215       225       235       245       255       265       275       285  
                                                                                                                                                                                         175          188

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: S-adenosyl-L-methionine-dependent methyltransferases (533)

Superfamily: S-adenosyl-L-methionine-dependent methyltransferases (533)

Family: Mycolic acid cyclopropane synthase (13)

Protein domain: PccA (1)

Mycobacterium tuberculosis [TaxId: 1773] (1)

1a	d1l1ea_	A:
1b	d1l1eb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: Vaccinia Virus protein VP39 (378)

Mycobacterium tuberculosis. Organism_taxid: 1773. (7)

1a	1l1eB00	B:16-287
1b	1l1eA00	A:16-287

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: CMAS (6)

Mycobacterium tuberculosis (6)

1a	CMAS-1l1eB01	B:16-283
1b	CMAS-1l1eB02	B:16-283

Asymmetric Unit(hide GO term definitions)

Chain A,B (CMAS3_MYCTO | P9WPB2)

molecular function
	GO:0008825	cyclopropane-fatty-acyl-phospholipid synthase activity	Catalysis of the reaction: S-adenosyl-L-methionine + phospholipid olefinic fatty acid = S-adenosyl-L-homocysteine + phospholipid cyclopropane fatty acid.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	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:0008610	lipid biosynthetic process	The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
	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:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A,B (CMAS3_MYCTU | P9WPB3)

molecular function
	GO:0008825	cyclopropane-fatty-acyl-phospholipid synthase activity	Catalysis of the reaction: S-adenosyl-L-methionine + phospholipid olefinic fatty acid = S-adenosyl-L-homocysteine + phospholipid cyclopropane fatty acid.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	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:0046500	S-adenosylmethionine metabolic process	The chemical reactions and pathways involving S-adenosylmethionine, S-(5'-adenosyl)-L-methionine, an important intermediate in one-carbon metabolism.
	GO:0042783	active evasion of host immune response	Any mechanism of immune avoidance that directly affects the host immune system, e.g. blocking any stage in host MHC class I and II presentation. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0008610	lipid biosynthetic process	The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
	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:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0052167	modulation by symbiont of host innate immune response	Any process in which an organism modulates the frequency, rate or extent of the innate immune response of the host organism; the innate immune response is the host's first line of defense against infection. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0071768	mycolic acid biosynthetic process	The chemical reactions and pathways resulting in the formation of mycolic acids, beta-hydroxy fatty acids with a long alpha-alkyl side chain.
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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