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(-) Description

Title :  CRYSTAL STRUCTURE OF MYCOLIC ACID CYCLOPROPANE SYNTHASE CMAA2 COMPLEXED WITH SAH AND DDDMAB
 
Authors :  C. -C. Huang, C. V. Smith, W. R. Jacobs Jr. , M. S. Glickman, J. C. Sacchet Structural Genomics Consortium (Tbsgc)
Date :  30 Dec 01  (Deposition) - 11 Jan 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Mixed Alpha Beta Fold, Structural Genomics, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc, Transferase (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

(-) Compounds

Molecule 1 - CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE 2
    Chains: A
    EC Number: 2.1.1.79
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET30B(CMAA1)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PET
    Gene: CMAA2
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Synonym: CYCLOPROPANE FATTY ACID SYNTHASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
110A1Ligand/IonDIDECYL-DIMETHYL-AMMONIUM
2CO31Ligand/IonCARBONATE ION
3SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
4SO44Ligand/IonSULFATE ION
Biological Unit 1 (4, 7)
No.NameCountTypeFull Name
110A1Ligand/IonDIDECYL-DIMETHYL-AMMONIUM
2CO31Ligand/IonCARBONATE ION
3SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
4SO44Ligand/IonSULFATE ION
Biological Unit 2 (4, 14)
No.NameCountTypeFull Name
110A2Ligand/IonDIDECYL-DIMETHYL-AMMONIUM
2CO32Ligand/IonCARBONATE ION
3SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
4SO48Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:42 , CYS A:43 , GLY A:145 , GLU A:148 , HIS A:182 , THR A:183 , ILE A:184 , TYR A:247 , 10A A:901BINDING SITE FOR RESIDUE CO3 A 902
2AC2SOFTWAREASN A:28 , LYS A:32 , HIS A:110BINDING SITE FOR RESIDUE SO4 A 903
3AC3SOFTWARETYR A:58 , LYS A:62 , HOH A:1014BINDING SITE FOR RESIDUE SO4 A 904
4AC4SOFTWAREARG A:205 , LEU A:211 , GLY A:217 , HOH A:1028 , HOH A:1045 , HOH A:1059BINDING SITE FOR RESIDUE SO4 A 905
5AC5SOFTWARELYS A:26 , LYS A:269BINDING SITE FOR RESIDUE SO4 A 906
6AC6SOFTWAREPRO A:16 , VAL A:20 , TYR A:24 , THR A:40 , TYR A:41 , SER A:42 , GLY A:80 , GLY A:82 , THR A:102 , LEU A:103 , GLN A:107 , GLY A:130 , TRP A:131 , GLU A:132 , LEU A:144 , GLY A:145 , ALA A:146 , HIS A:149 , 10A A:901 , HOH A:1005 , HOH A:1025BINDING SITE FOR RESIDUE SAH A 900
7AC7SOFTWARETYR A:24 , TYR A:41 , GLY A:145 , GLU A:148 , ILE A:184 , MET A:201 , LEU A:211 , PHE A:215 , TYR A:247 , TYR A:280 , CYS A:284 , LEU A:287 , SAH A:900 , CO3 A:902BINDING SITE FOR RESIDUE 10A A 901

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1KPI)

(-) Sequences/Alignments

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:291
 aligned with CMAS2_MYCTO | P9WPB4 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:291
                                    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 
          CMAS2_MYCTO    12 QLKPPVEAVRSHYDKSNEFFKLWLDPSMTYSCAYFERPDMTLEEAQYAKRKLALDKLNLEPGMTLLDIGCGWGSTMRHAVAEYDVNVIGLTLSENQYAHDKAMFDEVDSPRRKEVRIQGWEEFDEPVDRIVSLGAFEHFADGAGDAGFERYDTFFKKFYNLTPDDGRMLLHTITIPDKEEAQELGLTSPMSLLRFIKFILTEIFPGGRLPRISQVDYYSSNAGWKVERYHRIGANYVPTLNAWADALQAHKDEAIALKGQETYDIYMHYLRGCSDLFRDKYTDVCQFTLVK 302
               SCOP domains d1kpia_ A: CmaA2                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1kpiA00 A:12-302 Vaccinia Virus protein VP39                                                                                                                                                                                                                                                        CATH domains
               Pfam domains CMAS-1kpiA01 A:12-298                                                                                                                                                                                                                                                                          ---- Pfam domains
         Sec.struct. author ....hhhhhhhhhh.hhhhhhhhh................hhhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhh.....eeeee.hhhhh.....eeeee.hhhhh.........hhhhhhhhhhhhh.....eeeeeeee..hhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kpi A  12 QLKPPVEAVRSHYDKSNEFFKLWLDPSMTYSCAYFERPDMTLEEAQYAKRKLALDKLNLEPGMTLLDIGCGWGSTMRHAVAEYDVNVIGLTLSENQYAHDKAMFDEVDSPRRKEVRIQGWEEFDEPVDRIVSLGAFEHFADGAGDAGFERYDTFFKKFYNLTPDDGRMLLHTITIPDKEEAQELGLTSPMSLLRFIKFILTEIFPGGRLPRISQVDYYSSNAGWKVERYHRIGANYVPTLNAWADALQAHKDEAIALKGQETCDIYMHYLRGCSDLFRDKYTDVCQFTLVK 302
                                    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 


Chain A from PDB  Type:PROTEIN  Length:291
 aligned with CMAS2_MYCTU | P9WPB5 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:291
                                    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 
          CMAS2_MYCTU    12 QLKPPVEAVRSHYDKSNEFFKLWLDPSMTYSCAYFERPDMTLEEAQYAKRKLALDKLNLEPGMTLLDIGCGWGSTMRHAVAEYDVNVIGLTLSENQYAHDKAMFDEVDSPRRKEVRIQGWEEFDEPVDRIVSLGAFEHFADGAGDAGFERYDTFFKKFYNLTPDDGRMLLHTITIPDKEEAQELGLTSPMSLLRFIKFILTEIFPGGRLPRISQVDYYSSNAGWKVERYHRIGANYVPTLNAWADALQAHKDEAIALKGQETYDIYMHYLRGCSDLFRDKYTDVCQFTLVK 302
               SCOP domains d1kpia_ A: CmaA2                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1kpiA00 A:12-302 Vaccinia Virus protein VP39                                                                                                                                                                                                                                                        CATH domains
               Pfam domains CMAS-1kpiA01 A:12-298                                                                                                                                                                                                                                                                          ---- Pfam domains
         Sec.struct. author ....hhhhhhhhhh.hhhhhhhhh................hhhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhh.....eeeee.hhhhh.....eeeee.hhhhh.........hhhhhhhhhhhhh.....eeeeeeee..hhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kpi A  12 QLKPPVEAVRSHYDKSNEFFKLWLDPSMTYSCAYFERPDMTLEEAQYAKRKLALDKLNLEPGMTLLDIGCGWGSTMRHAVAEYDVNVIGLTLSENQYAHDKAMFDEVDSPRRKEVRIQGWEEFDEPVDRIVSLGAFEHFADGAGDAGFERYDTFFKKFYNLTPDDGRMLLHTITIPDKEEAQELGLTSPMSLLRFIKFILTEIFPGGRLPRISQVDYYSSNAGWKVERYHRIGANYVPTLNAWADALQAHKDEAIALKGQETCDIYMHYLRGCSDLFRDKYTDVCQFTLVK 302
                                    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
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (15, 22)

Asymmetric Unit(hide GO term definitions)
Chain A   (CMAS2_MYCTO | P9WPB4)
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   (CMAS2_MYCTU | P9WPB5)
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:0071766    Actinobacterium-type cell wall biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cell wall of the type found in Actinobacteria. The cell wall is the rigid or semi-rigid envelope lying outside the cell membrane. Actinobacterial cell walls contain characteristic mycolic acids, of which some are covalently linked to the cell wall peptidoglycan and others accumulate at the cell surface.
    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: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:0071769    mycolate cell wall layer assembly    The aggregation, arrangement and bonding together of a set of components, including arabinogalactan mycolate and trehalose dimycolate, to form the mycolate layer of the Actinobacterium-type cell wall. The mycolate layer is physically attached to the peptidoglycan layer.
    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:0001666    response to hypoxia    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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(-) Related Entries Specified in the PDB File

1kp9
1kpg
1kph RELATED ID: RV0503C RELATED DB: TARGETDB