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(-) Description

Title :  CRYSTAL STRUCTURE OF 3-OXOACYL-(ACYL-CARRIER PROTEIN) SYNTHASE II FROM THERMUS THERMOPHILUS HB8
 
Authors :  B. Bagautdinov, M. Miyano, T. H. Tahirov, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  10 Feb 03  (Deposition) - 11 Mar 03  (Release) - 20 May 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Condensing Enzymes, Fatty Acid Elongation, Acyl-Carrier Protein (Acp), Beta-Keto-Acp Synthase (Kas), Homodimer, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Bagautdinov, Y. Ukita, M. Miyano, N. Kunishima
Structure Of 3-Oxoacyl-(Acyl-Carrier Protein) Synthase Ii From Thermus Thermophilus Hb8.
Acta Crystallogr. , Sect. F V. 64 358 2008
PubMed-ID: 18453702  |  Reference-DOI: 10.1107/S1744309108010336
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 3-OXOACYL-(ACYL-CARRIER PROTEIN) SYNTHASE II
    Chains: A, B
    EC Number: 2.3.1.41
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 11A
    Expression System Strain: DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FABF
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:718 , THR B:208 , ARG B:209 , HOH B:721 , HOH B:723 , HOH B:726BINDING SITE FOR RESIDUE MG B 501
2AC2SOFTWAREVAL A:118 , ARG A:122 , ARG A:126 , HOH A:548 , HOH A:565 , ARG B:204BINDING SITE FOR RESIDUE CIT A 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J3N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1J3N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J3N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1J3N)

(-) Exons   (0, 0)

(no "Exon" information available for 1J3N)

(-) 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:408
 aligned with Q5SL80_THET8 | Q5SL80 from UniProtKB/TrEMBL  Length:408

    Alignment length:408
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400        
         Q5SL80_THET8     1 MRRVVVTGLGALTPIGVGQEAFHKAQLAGKSGVRPITRFDASALPVRIAAEVDVDPGAYLDRKELRRLDRFVQYALIAAQLALEDAGLKPEDLDPERVGTLVGTGIGGMETWEAQSRVFLERGPNRISPFFIPMMIANMASAHIAMRYGFTGPSSTVVTACATGADALGSALRMIQLGEADLVLAGGTEAAITPMAIGAFAVMRALSTRNEEPEKASRPFTLSRDGFVMGEGAGVLVLEAYEHAKKRGARIYAELVGFGRSADAHHITEPHPEGKGAALAMARALKDAGIAPEQVGYINAHGTSTPVGDRAEVLAIKRVFGDHAKRLMVSSTKSMIGHLLGAAGAVEAIATVQALYHGVIPPTINLEDPDPELDLDFVPEPREAKVDYALSNSFAFGGHNAVLAFKRV 408
               SCOP domains d1j3na1 A:1-249 Beta-ketoacyl-ACP synthase II                                                                                                                                                                                                            d1j3na2 A:250-408 Beta-ketoacyl-ACP synthase II                                                                                                                 SCOP domains
               CATH domains -----1j3nA01 A:6-259  [code=3.40.47.10, no name defined]                                                                                                                                                                                                           1j3nA02 A:260-404  [code=3.40.47.10, no name defined]                                                                                            ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeeee..eehhhhhhhhhhhh...eee............eee....hhhhh.hhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhh.eeeeee....hhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh....eeeeeeee...hhhhhhhhhhh........hhhhhh..............eeeeeeeeehhhhhhh.....eeeeeeeeee...........hhhhhhhhhhhhhhhh.hhhhh.eee.....hhhhhhhhhhhhhhhhhhhhh..eee.hhhhhh.hhhhhhhhhhhhhhhhhhhhee.....................ee....eeeeeee....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1j3n A   1 MRRVVVTGLGALTPIGVGQEAFHKAQLAGKSGVRPITRFDASALPVRIAAEVDVDPGAYLDRKELRRLDRFVQYALIAAQLALEDAGLKPEDLDPERVGTLVGTGIGGMETWEAQSRVFLERGPNRISPFFIPMMIANMASAHIAMRYGFTGPSSTVVTACATGADALGSALRMIQLGEADLVLAGGTEAAITPMAIGAFAVMRALSTRNEEPEKASRPFTLSRDGFVMGEGAGVLVLEAYEHAKKRGARIYAELVGFGRSADAHHITEPHPEGKGAALAMARALKDAGIAPEQVGYINAHGTSTPVGDRAEVLAIKRVFGDHAKRLMVSSTKSMIGHLLGAAGAVEAIATVQALYHGVIPPTINLEDPDPELDLDFVPEPREAKVDYALSNSFAFGGHNAVLAFKRV 408
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400        


Chain B from PDB  Type:PROTEIN  Length:408
 aligned with Q5SL80_THET8 | Q5SL80 from UniProtKB/TrEMBL  Length:408

    Alignment length:408
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400        
         Q5SL80_THET8     1 MRRVVVTGLGALTPIGVGQEAFHKAQLAGKSGVRPITRFDASALPVRIAAEVDVDPGAYLDRKELRRLDRFVQYALIAAQLALEDAGLKPEDLDPERVGTLVGTGIGGMETWEAQSRVFLERGPNRISPFFIPMMIANMASAHIAMRYGFTGPSSTVVTACATGADALGSALRMIQLGEADLVLAGGTEAAITPMAIGAFAVMRALSTRNEEPEKASRPFTLSRDGFVMGEGAGVLVLEAYEHAKKRGARIYAELVGFGRSADAHHITEPHPEGKGAALAMARALKDAGIAPEQVGYINAHGTSTPVGDRAEVLAIKRVFGDHAKRLMVSSTKSMIGHLLGAAGAVEAIATVQALYHGVIPPTINLEDPDPELDLDFVPEPREAKVDYALSNSFAFGGHNAVLAFKRV 408
               SCOP domains d1j3nb1 B:1-249 Beta-ketoacyl-ACP synthase II                                                                                                                                                                                                            d1j3nb2 B:250-408 Beta-ketoacyl-ACP synthase II                                                                                                                 SCOP domains
               CATH domains -----1j3nB01 B:6-259  [code=3.40.47.10, no name defined]                                                                                                                                                                                                           1j3nB02 B:260-404  [code=3.40.47.10, no name defined]                                                                                            ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeeee..eehhhhhhhhhhh....eee............eee....hhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh.eeeeee....hhhhhhhhhhhhhhhh......hhhhhhh.hhhhhhhhhhhh....ee...hhhhhhhhhhhhhhhhhhh....eeeeeeee...hhhhhhhhhhh........hhhhh...............eeeeeeeeehhhhhhhh....eeeeeeeeee...........hhhhhhhhhhhhhhhh.hhhhh.eee.....hhhhhhhhhhhhhhhhhhhhhh.eee.hhhhhh.hhhhhhhhhhhhhhhhhhhhee.....................ee....eeeeeee....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1j3n B   1 MRRVVVTGLGALTPIGVGQEAFHKAQLAGKSGVRPITRFDASALPVRIAAEVDVDPGAYLDRKELRRLDRFVQYALIAAQLALEDAGLKPEDLDPERVGTLVGTGIGGMETWEAQSRVFLERGPNRISPFFIPMMIANMASAHIAMRYGFTGPSSTVVTACATGADALGSALRMIQLGEADLVLAGGTEAAITPMAIGAFAVMRALSTRNEEPEKASRPFTLSRDGFVMGEGAGVLVLEAYEHAKKRGARIYAELVGFGRSADAHHITEPHPEGKGAALAMARALKDAGIAPEQVGYINAHGTSTPVGDRAEVLAIKRVFGDHAKRLMVSSTKSMIGHLLGAAGAVEAIATVQALYHGVIPPTINLEDPDPELDLDFVPEPREAKVDYALSNSFAFGGHNAVLAFKRV 408
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J3N)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q5SL80_THET8 | Q5SL80)
molecular function
    GO:0033817    beta-ketoacyl-acyl-carrier-protein synthase II activity    Catalysis of the reaction: (Z)-hexadec-11-enoyl-[acyl-carrier protein] + malonyl-[acyl-carrier protein] = (Z)-3-oxooctadec-13-enoyl-[acyl-carrier protein] + CO2 + [acyl-carrier protein].
    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: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.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
    GO:0016747    transferase activity, transferring acyl groups other than amino-acyl groups    Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor).
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: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.

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