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(-) Description

Title :  CHRONOBACTERIUM AMMOINIAGENES APO-ACPS STRUCUTRE
 
Authors :  K. Gokulan, Mycobacterium Tuberculosis Structural Proteomics P (Xmtb)
Date :  08 Jun 10  (Deposition) - 25 Aug 10  (Release) - 25 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Acyl Carrier Protein Synthase, Acyl Carrier Protein, Fatty Acid Synthase, Acps, Mycobacterium Tuberculosis Structural Proteomics Project, Transferase, Xmtb, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Gokulan, A. Aggarwal, L. Shipman, G. S. Besra, J. C. Sacchettini
Mycobacterium Tuberculosis Acyl Carrier Protein Synthase Adopts Two Different Ph-Dependent Structural Conformations.
Acta Crystallogr. , Sect. D V. 67 657 2011
PubMed-ID: 21697604  |  Reference-DOI: 10.1107/S0907444911020221

(-) Compounds

Molecule 1 - PHOSPHOPANTETHEINE PROTEIN TRANSFERASE, PPT1P
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PET28A
    Gene: ACPS, PPT1
    Organism Common: BREVIBACTERIUM AMMONIAGENES
    Organism Scientific: CORYNEBACTERIUM AMMONIAGENES
    Organism Taxid: 1697

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE
2SO4-1Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:13 , LYS A:78 , SER C:137 , HIS C:138BINDING SITE FOR RESIDUE SO4 A 231
2AC2SOFTWAREARG A:46 , HIS A:65 , HIS A:138BINDING SITE FOR RESIDUE SO4 A 232
3AC3SOFTWARESER B:137 , HIS B:138 , ASP C:13 , LYS C:78BINDING SITE FOR RESIDUE SO4 B 233
4AC4SOFTWAREARG B:46 , HIS B:65 , HIS B:138BINDING SITE FOR RESIDUE SO4 B 234

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NE9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NE9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NE9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NE9)

(-) Exons   (0, 0)

(no "Exon" information available for 3NE9)

(-) 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:138
 aligned with O31302_CORAM | O31302 from UniProtKB/TrEMBL  Length:153

    Alignment length:149
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144         
         O31302_CORAM     5 REAMTVGVDLVHIPGFAEQLSRPGSTFEQVFSPLERRHAQTRRDAAADATNSSLAGSRTEHLAGRWAAKEAFIKAWSQAIYGKPPVIEPDLVNFAEIEVLPDRWGRVALQLKGEVAAKLQESIGDVELALSISHDGDYATAQCLLRYQR 153
               SCOP domains d3ne9a_ A: automated matches                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeehhhhhhhhhh..hhhhh..hhhhhhhhh...-----------.hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh.eeeee.....eeeeehhhhhhhhhhhh..eeeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ne9 A   5 REAmTVGVDLVHIPGFAEQLSRPGSTFEQVFSPLERRHAQTRR-----------AGSRTEHLAGRWAAKEAFIKAWSQAIYGKPPVIEPDLVNFAEIEVLPDRWGRVALQLKGEVAAKLQESIGDVELALSISHDGDYATALCLLRYQR 153
                               |    14        24        34        44  |      -    |   64        74        84        94       104       114       124       134       144         
                               |                                     47          59                                                                                              
                               8-MSE                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:138
 aligned with O31302_CORAM | O31302 from UniProtKB/TrEMBL  Length:153

    Alignment length:149
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144         
         O31302_CORAM     5 REAMTVGVDLVHIPGFAEQLSRPGSTFEQVFSPLERRHAQTRRDAAADATNSSLAGSRTEHLAGRWAAKEAFIKAWSQAIYGKPPVIEPDLVNFAEIEVLPDRWGRVALQLKGEVAAKLQESIGDVELALSISHDGDYATAQCLLRYQR 153
               SCOP domains d3ne9b_ B: automated matches                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeehhhhhhhhhh.........hhhhhhhh.....-----------.hhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhh.eeeee.....eeeeehhhhhhhhhhhhh..eeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ne9 B   5 REAmTVGVDLVHIPGFAEQLSRPGSTFEQVFSPLERRHAQTRRS-----------GSRTEHLAGRWAAKEAFIKAWSQAIYGKPPVIEPDLVNFAEIEVLPDRWGRVALQLKGEVAAKLQESIGDVELALSISHDGDYATALCLLRYQR 153
                               |    14        24        34        44   |     -     |  64        74        84        94       104       114       124       134       144         
                               8-MSE                                  48          60                                                                                             


Chain C from PDB  Type:PROTEIN  Length:133
 aligned with O31302_CORAM | O31302 from UniProtKB/TrEMBL  Length:153

    Alignment length:149
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144         
         O31302_CORAM     5 REAMTVGVDLVHIPGFAEQLSRPGSTFEQVFSPLERRHAQTRRDAAADATNSSLAGSRTEHLAGRWAAKEAFIKAWSQAIYGKPPVIEPDLVNFAEIEVLPDRWGRVALQLKGEVAAKLQESIGDVELALSISHDGDYATAQCLLRYQR 153
               SCOP domains d3ne9c_ C: automated matches                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----ACPS-3ne9C01 C:9-147                                                                                                                       ------ Pfam domains (1)
           Pfam domains (2) ----ACPS-3ne9C02 C:9-147                                                                                                                       ------ Pfam domains (2)
           Pfam domains (3) ----ACPS-3ne9C03 C:9-147                                                                                                                       ------ Pfam domains (3)
         Sec.struct. author .eeeeeeeeeeehhhhhhhhhh...hhhhhhhhhhhhh...----------------hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh.eeeee.....eeeeehhhhhhhhhhhh..eeeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ne9 C   5 REAmTVGVDLVHIPGFAEQLSRPGSTFEQVFSPLERRHAQT----------------RTEHLAGRWAAKEAFIKAWSQAIYGKPPVIEPDLVNFAEIEVLPDRWGRVALQLKGEVAAKLQESIGDVELALSISHDGDYATALCLLRYQR 153
                               |    14        24        34        44|        -       |64        74        84        94       104       114       124       134       144         
                               8-MSE                               45               62
   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, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NE9)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: ACPS] (13)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (O31302_CORAM | O31302)
molecular function
    GO:0008897    holo-[acyl-carrier-protein] synthase activity    Catalysis of the reaction: CoA + substrate-serine = adenosine 3',5'-bisphosphate + substrate-serine-4'-phosphopantetheine. The transfer of the 4'-phosphopantetheine (Ppant) co-factor from coenzyme A to the hydroxyl side chain of the serine residue of acyl- or peptidyl-carrier protein (ACP or PCP) to convert them from the apo to the holo form.
    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: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:0006633    fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
    GO:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    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.
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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 Related Entries

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

UniProtKB/TrEMBL
        O31302_CORAM | O31302: 3nfd

(-) Related Entries Specified in the PDB File

3ne1 3ne3