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(-) Description

Title :  HOLO-(ACYL CARRIER PROTEIN) SYNTHASE AT 1.8A
 
Authors :  K. D. Parris, L. Lin, A. Tam, R. Mathew, J. Hixon, M. Stahl, C. C. Fritz, J. W. S. Somers
Date :  27 Jun 00  (Deposition) - 27 Jun 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Biol. Unit 3:  A (1x),B (1x),C (1x),D (1x),E (1x),F (1x)
Keywords :  9-Strand Pseudo Beta Barrel, Lipid Synthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. D. Parris, L. Lin, A. Tam, R. Mathew, J. Hixon, M. Stahl, C. C. Fritz, J. Seehra, W. S. Somers
Crystal Structures Of Substrate Binding To Bacillus Subtili Holo-(Acyl Carrier Protein) Synthase Reveal A Novel Trimeri Arrangement Of Molecules Resulting In Three Active Sites.
Structure Fold. Des. V. 8 883 2000
PubMed-ID: 10997907  |  Reference-DOI: 10.1016/S0969-2126(00)00178-7

(-) Compounds

Molecule 1 - HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
    Chains: A, B, C, D, E, F
    EC Number: 2.7.8.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD-HIS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF
Biological Unit 3 (1x): A (1x)B (1x)C (1x)D (1x)E (1x)F (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 34)

Asymmetric Unit (4, 34)
No.NameCountTypeFull Name
1CL19Ligand/IonCHLORIDE ION
2DTT5Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
3GOL2Ligand/IonGLYCEROL
4NA8Ligand/IonSODIUM ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2DTT2Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
3GOL1Ligand/IonGLYCEROL
4NA-1Ligand/IonSODIUM ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2DTT3Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
3GOL1Ligand/IonGLYCEROL
4NA-1Ligand/IonSODIUM ION
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2DTT2Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
3GOL1Ligand/IonGLYCEROL
4NA-1Ligand/IonSODIUM ION

(-) Sites  (34, 34)

Asymmetric Unit (34, 34)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:105 , HOH A:536 , ILE B:9 , CL B:490 , HOH B:528BINDING SITE FOR RESIDUE NA A 472
02AC2SOFTWAREVAL B:101 , CL B:484 , HOH B:529 , CL C:491 , HOH C:543BINDING SITE FOR RESIDUE NA B 473
03AC3SOFTWAREILE A:9 , CL A:494 , HOH A:526 , HIS C:105 , HOH C:564BINDING SITE FOR RESIDUE NA C 474
04AC4SOFTWAREHIS D:105 , HOH D:547 , ILE E:9 , CL E:482 , HOH E:528BINDING SITE FOR RESIDUE NA D 475
05AC5SOFTWAREHIS E:105 , HOH E:543 , ILE F:9 , CL F:485 , HOH F:539BINDING SITE FOR RESIDUE NA E 476
06AC6SOFTWAREILE D:9 , CL D:492 , HOH D:544 , HIS F:105 , HOH F:546BINDING SITE FOR RESIDUE NA D 478
07AC7SOFTWAREHIS B:105 , HOH B:544 , ILE C:9 , CL C:483 , HOH C:551BINDING SITE FOR RESIDUE NA B 479
08AC8SOFTWAREGLU A:27 , GLN A:75 , HOH A:520 , HOH A:557 , HOH A:565BINDING SITE FOR RESIDUE NA A 480
09AC9SOFTWAREARG A:80 , LYS A:81BINDING SITE FOR RESIDUE CL A 481
10BC1SOFTWARENA D:475 , GLU E:11 , ARG E:14 , HOH E:515BINDING SITE FOR RESIDUE CL E 482
11BC2SOFTWARENA B:479 , GLU C:11 , ARG C:14BINDING SITE FOR RESIDUE CL C 483
12BC3SOFTWAREVAL B:101 , NA B:473 , HOH B:519 , CL C:491 , ARG D:24BINDING SITE FOR RESIDUE CL B 484
13BC4SOFTWARENA E:476 , THR F:10 , GLU F:11 , ARG F:14 , HOH F:534BINDING SITE FOR RESIDUE CL F 485
14BC5SOFTWARELYS F:86 , PRO F:87 , SER F:102 , ILE F:103BINDING SITE FOR RESIDUE CL F 486
15BC6SOFTWARELYS A:86 , PRO A:87 , SER A:102 , ILE A:103 , HOH A:576BINDING SITE FOR RESIDUE CL A 487
16BC7SOFTWARELYS C:86 , PRO C:87 , SER C:102 , ILE C:103 , DTT C:502 , HOH C:519BINDING SITE FOR RESIDUE CL C 489
17BC8SOFTWARENA A:472 , THR B:10 , GLU B:11 , ARG B:14BINDING SITE FOR RESIDUE CL B 490
18BC9SOFTWARENA B:473 , CL B:484 , HOH B:510 , GLY C:4 , ILE C:5 , LYS D:23BINDING SITE FOR RESIDUE CL C 491
19CC1SOFTWAREGLU D:11 , ARG D:14 , NA D:478BINDING SITE FOR RESIDUE CL D 492
20CC2SOFTWARETHR A:106 , LYS A:107 , GLU A:108 , TYR B:109 , HOH B:540BINDING SITE FOR RESIDUE CL A 493
21CC3SOFTWAREGLU A:11 , ARG A:14 , HOH A:525 , NA C:474BINDING SITE FOR RESIDUE CL A 494
22CC4SOFTWARETHR D:106 , LYS D:107 , GLU D:108 , TYR E:109 , HOH E:491BINDING SITE FOR RESIDUE CL D 495
23CC5SOFTWAREGLY D:4 , ILE D:5 , GOL D:506 , LYS F:86 , HIS F:100 , VAL F:101 , HOH F:508BINDING SITE FOR RESIDUE CL F 496
24CC6SOFTWARELYS D:86 , SER D:102 , ILE D:103 , DTT D:505BINDING SITE FOR RESIDUE CL D 497
25CC7SOFTWAREARG C:32 , HOH F:530BINDING SITE FOR RESIDUE CL C 498
26CC8SOFTWARETYR A:109 , THR C:106 , LYS C:107 , GLU C:108BINDING SITE FOR RESIDUE CL C 499
27CC9SOFTWARELYS D:86 , HIS D:100 , VAL D:101 , HOH D:517 , GLY E:4 , ILE E:5BINDING SITE FOR RESIDUE CL D 500
28DC1SOFTWAREASN A:84 , GLY A:85 , LYS A:86 , HOH A:576 , THR B:66BINDING SITE FOR RESIDUE DTT A 501
29DC2SOFTWAREGLY A:65 , THR A:66 , ASN C:84 , LYS C:86 , CL C:489 , HOH C:519BINDING SITE FOR RESIDUE DTT C 502
30DC3SOFTWAREASP D:76 , GLU D:78 , CYS D:91 , HOH D:560BINDING SITE FOR RESIDUE DTT D 503
31DC4SOFTWAREGLY D:65 , THR D:66 , ASN F:84 , LYS F:86 , HOH F:509BINDING SITE FOR RESIDUE DTT F 504
32DC5SOFTWAREASN D:84 , GLY D:85 , LYS D:86 , CL D:497 , GLY E:65 , THR E:66BINDING SITE FOR RESIDUE DTT D 505
33DC6SOFTWAREARG C:24 , TYR D:3 , LYS D:62 , ALA D:63 , PHE D:64 , GLY D:65 , LYS F:86 , CL F:496BINDING SITE FOR RESIDUE GOL D 506
34DC7SOFTWAREGLN B:75 , ASP B:76 , GLU B:78 , ILE B:90 , CYS B:91 , THR B:92 , HOH B:556 , HOH B:570BINDING SITE FOR RESIDUE GOL B 507

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1F7T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1F7T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1F7T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1F7T)

(-) Exons   (0, 0)

(no "Exon" information available for 1F7T)

(-) 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:119
 aligned with ACPS_BACSU | P96618 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:119
                                    10        20        30        40        50        60        70        80        90       100       110         
           ACPS_BACSU     1 MIYGIGLDITELKRIASMAGRQKRFAERILTRSELDQYYELSEKRKNEFLAGRFAAKEAFSKAFGTGIGRQLSFQDIEIRKDQNGKPYIICTKLSQAAVHVSITHTKEYAAAQVVIERL 119
               SCOP domains d1f7ta_ A: Holo-(acyl carrier protein) synthase ACPS                                                                    SCOP domains
               CATH domains 1f7tA00 A:1-119 4'-phosphopantetheinyl transferase                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeehhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh........hhh.eeeee.....eeeee...hhh.eeeeeee...eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1f7t A   1 GIYGIGLDITELKRIASMAGRQKRFAERILTRSELDQYYELSEKRKNEFLAGRFAAKEAFSKAFGTGIGRQLSFQDIEIRKDQNGKPYIICTKLSPAAVHVSITHTKEYAAAQVVIERL 119
                                    10        20        30        40        50        60        70        80        90       100       110         


Chain B from PDB  Type:PROTEIN  Length:119
 aligned with ACPS_BACSU | P96618 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:119
                             1                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109         
           ACPS_BACSU     - -MIYGIGLDITELKRIASMAGRQKRFAERILTRSELDQYYELSEKRKNEFLAGRFAAKEAFSKAFGTGIGRQLSFQDIEIRKDQNGKPYIICTKLSQAAVHVSITHTKEYAAAQVVIER 118
               SCOP domains d1f7tb_ B: Holo-(acyl carrier protein) synthase ACPS                                                                    SCOP domains
               CATH domains 1f7tB00 B:0-118 4'-phosphopantetheinyl transferase                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeehhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh........hhhhheeee.....eeee.......eeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1f7t B   0 GGIYGIGLDITELKRIASMAGRQKRFAERILTRSELDQYYELSEKRKNEFLAGRFAAKEAFSKAFGTGIGRQLSFQDIEIRKDQNGKPYIICTKLSPAAVHVSITHTKEYAAAQVVIER 118
                                     9        19        29        39        49        59        69        79        89        99       109         


Chain C from PDB  Type:PROTEIN  Length:119
 aligned with ACPS_BACSU | P96618 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:119
                                    10        20        30        40        50        60        70        80        90       100       110         
           ACPS_BACSU     1 MIYGIGLDITELKRIASMAGRQKRFAERILTRSELDQYYELSEKRKNEFLAGRFAAKEAFSKAFGTGIGRQLSFQDIEIRKDQNGKPYIICTKLSQAAVHVSITHTKEYAAAQVVIERL 119
               SCOP domains d1f7tc_ C: Holo-(acyl carrier protein) synthase ACPS                                                                    SCOP domains
               CATH domains 1f7tC00 C:1-119 4'-phosphopantetheinyl transferase                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeehhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhheeee.....eeee....hhh.eeeeeee...eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1f7t C   1 GIYGIGLDITELKRIASMAGRQKRFAERILTRSELDQYYELSEKRKNEFLAGRFAAKEAFSKAFGTGIGRQLSFQDIEIRKDQNGKPYIICTKLSPAAVHVSITHTKEYAAAQVVIERL 119
                                    10        20        30        40        50        60        70        80        90       100       110         


Chain D from PDB  Type:PROTEIN  Length:119
 aligned with ACPS_BACSU | P96618 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:119
                             1                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109         
           ACPS_BACSU     - -MIYGIGLDITELKRIASMAGRQKRFAERILTRSELDQYYELSEKRKNEFLAGRFAAKEAFSKAFGTGIGRQLSFQDIEIRKDQNGKPYIICTKLSQAAVHVSITHTKEYAAAQVVIER 118
               SCOP domains d1f7td_ D: Holo-(acyl carrier protein) synthase ACPS                                                                    SCOP domains
               CATH domains 1f7tD00 D:0-118 4'-phosphopantetheinyl transferase                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeehhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh........hhh.eeeee.....eeeee...hhh.eeeeeee...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1f7t D   0 GGIYGIGLDITELKRIASMAGRQKRFAERILTRSELDQYYELSEKRKNEFLAGRFAAKEAFSKAFGTGIGRQLSFQDIEIRKDQNGKPYIICTKLSPAAVHVSITHTKEYAAAQVVIER 118
                                     9        19        29        39        49        59        69        79        89        99       109         


Chain E from PDB  Type:PROTEIN  Length:118
 aligned with ACPS_BACSU | P96618 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:118
                                    10        20        30        40        50        60        70        80        90       100       110        
           ACPS_BACSU     1 MIYGIGLDITELKRIASMAGRQKRFAERILTRSELDQYYELSEKRKNEFLAGRFAAKEAFSKAFGTGIGRQLSFQDIEIRKDQNGKPYIICTKLSQAAVHVSITHTKEYAAAQVVIER 118
               SCOP domains d1f7te_ E: Holo-(acyl carrier protein) synthase ACPS                                                                   SCOP domains
               CATH domains 1f7tE00 E:1-118 4'-phosphopantetheinyl transferase                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeehhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh........hhhhheeee.....eeee.......eeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1f7t E   1 GIYGIGLDITELKRIASMAGRQKRFAERILTRSELDQYYELSEKRKNEFLAGRFAAKEAFSKAFGTGIGRQLSFQDIEIRKDQNGKPYIICTKLSPAAVHVSITHTKEYAAAQVVIER 118
                                    10        20        30        40        50        60        70        80        90       100       110        


Chain F from PDB  Type:PROTEIN  Length:119
 aligned with ACPS_BACSU | P96618 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:119
                                    10        20        30        40        50        60        70        80        90       100       110         
           ACPS_BACSU     1 MIYGIGLDITELKRIASMAGRQKRFAERILTRSELDQYYELSEKRKNEFLAGRFAAKEAFSKAFGTGIGRQLSFQDIEIRKDQNGKPYIICTKLSQAAVHVSITHTKEYAAAQVVIERL 119
               SCOP domains d1f7tf_ F: Holo-(acyl carrier protein) synthase ACPS                                                                    SCOP domains
               CATH domains 1f7tF00 F:1-119 4'-phosphopantetheinyl transferase                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeehhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh........hhhhheeee.....eeee....hhh.eeeeeee...eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1f7t F   1 GIYGIGLDITELKRIASMAGRQKRFAERILTRSELDQYYELSEKRKNEFLAGRFAAKEAFSKAFGTGIGRQLSFQDIEIRKDQNGKPYIICTKLSPAAVHVSITHTKEYAAAQVVIERL 119
                                    10        20        30        40        50        60        70        80        90       100       110
   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, 6)

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

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1F7T)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (ACPS_BACSU | P96618)
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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  1f7t
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    Orientation in Membranes: OPM
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  ACPS_BACSU | P96618
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  2.7.8.7
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    Interatomic Contacts of Structural Units: CSU
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  ACPS_BACSU | P96618
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 Related Entries

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

UniProtKB/Swiss-Prot
        ACPS_BACSU | P96618: 1f7l 1f80

(-) Related Entries Specified in the PDB File

1f7l 1F7L CONTAINS THE SAME PROTEIN IN COMPLEX WITH COENZYME A.