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(-) Description

Title :  1.84 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF 3-OXOACYL-(ACYL CARRIER PROTEIN) SYNTHASE I (FABB) FROM YERSINIA PESTIS CO92
 
Authors :  A. S. Halavaty, Z. Wawrzak, O. Onopriyenko, S. Peterson, A. Savchenko, W. F. Anderson, Center For Structural Genomics Of Infectious D (Csgid)
Date :  23 Sep 10  (Deposition) - 12 Jan 11  (Release) - 12 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.84
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Condensation Reaction, Fatty Acid Synthase, Beta-Ketoacyl-Acp Synthase, Fatty Acid And Phospholipid Metabolism, 3-Oxoacyl-(Acyl Carrier Protein) Synthase I, Transferase, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. S. Halavaty, Z. Wawrzak, O. Onopriyenko, S. Peterson, A. Savchenko W. F. Anderson
1. 84 Angstrom Resolution Crystal Structure Of 3-Oxoacyl-(Acyl Carrier Protein) Synthase I (Fabb) From Yersinia Pestis Co92
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE I
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21-CODONPLUS(DE3)-RIPL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FABB, Y1591, YPO2757
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 632

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 59)

Asymmetric/Biological Unit (7, 59)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2K2Ligand/IonPOTASSIUM ION
3MSE39Mod. Amino AcidSELENOMETHIONINE
4PEG8Ligand/IonDI(HYDROXYETHYL)ETHER
5PG42Ligand/IonTETRAETHYLENE GLYCOL
6PGE1Ligand/IonTRIETHYLENE GLYCOL
7PO43Ligand/IonPHOSPHATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:297 , VAL A:298 , GLU A:343 , SER A:388 , ASN A:389BINDING SITE FOR RESIDUE K A 408
02AC2SOFTWAREPHE A:35 , LYS A:40 , HIS A:47 , ASN A:213 , ASP A:214 , HOH A:715BINDING SITE FOR RESIDUE PO4 A 409
03AC3SOFTWARELYS A:59 , ILE A:62 , ASP A:63BINDING SITE FOR RESIDUE EDO A 410
04AC4SOFTWAREARG A:45 , GLY A:206 , LYS B:128BINDING SITE FOR RESIDUE PEG A 411
05AC5SOFTWARELYS A:65 , LYS A:211 , TYR A:212 , ASP A:226BINDING SITE FOR RESIDUE PEG A 412
06AC6SOFTWAREALA A:42 , TRP A:196 , HOH A:600 , MSE B:121BINDING SITE FOR RESIDUE PEG A 413
07AC7SOFTWARETHR A:378 , GLN A:380BINDING SITE FOR RESIDUE PEG A 414
08AC8SOFTWAREALA A:287 , GLY A:288 , VAL A:289 , ARG A:315 , HOH A:594 , HOH A:597BINDING SITE FOR RESIDUE PEG A 415
09AC9SOFTWAREASP A:363 , ASN A:364 , LEU A:365 , HOH A:566BINDING SITE FOR RESIDUE PEG A 416
10BC1SOFTWAREASN B:297 , VAL B:298 , GLU B:343 , SER B:388 , ASN B:389BINDING SITE FOR RESIDUE K B 408
11BC2SOFTWAREHIS A:253 , LYS A:407 , HOH A:657 , HIS B:253 , HOH B:595BINDING SITE FOR RESIDUE PO4 B 409
12BC3SOFTWAREPHE B:35 , LYS B:40 , HIS B:47 , ASN B:213 , ASP B:214 , HOH B:455 , HOH B:570BINDING SITE FOR RESIDUE PO4 B 410
13BC4SOFTWAREGLU A:28 , ASP B:63 , PEG B:414BINDING SITE FOR RESIDUE EDO B 412
14BC5SOFTWAREASP B:294 , HOH B:584 , HOH B:648BINDING SITE FOR RESIDUE EDO B 413
15BC6SOFTWAREASP B:63 , TYR B:78 , PRO B:150 , PHE B:151 , EDO B:412 , HOH B:612BINDING SITE FOR RESIDUE PEG B 414
16BC7SOFTWARELYS B:65 , LYS B:211 , ASP B:226 , ARG B:227 , ASP B:228BINDING SITE FOR RESIDUE PEG B 415
17BC8SOFTWAREASP B:41 , ALA B:249 , ARG B:250 , PG4 B:417 , HOH B:589 , HOH B:606BINDING SITE FOR RESIDUE PGE B 416
18BC9SOFTWAREARG A:122 , ASP B:41 , GLU B:245 , LEU B:248 , PGE B:416 , HOH B:509 , HOH B:510 , HOH B:515 , HOH B:657 , HOH B:663BINDING SITE FOR RESIDUE PG4 B 417
19CC1SOFTWARELEU A:127 , LYS A:128 , ARG B:45 , ALA B:204 , GLY B:206 , THR B:210BINDING SITE FOR RESIDUE PG4 B 418

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3OYT)

(-) Sequences/Alignments

Asymmetric/Biological 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:407
 aligned with Q7CJB1_YERPE | Q7CJB1 from UniProtKB/TrEMBL  Length:407

    Alignment length:407
                                    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       
         Q7CJB1_YERPE     1 MKRAVITGLGIVSSIGNNQQEVLASLQEGRSGITFAQEFKDAGMRSHVWGDVKLQSEPKDLIDRKVLRFMSDASIYAYLAMQEAIADSGLSDSQVSNFRSGLVVGSGGGSPRNQVAGSDAMRTPRGLKGVGPYMVTKAMASGVSACLATPFKIKGVNYSISSACATSAHCIGHALELIQLGKQDIVFAGGGEELCWEMACEFDAMGALSTKYNDTPAKASRTYDQDRDGFVIAGGGGMVVVEELEHALARGAHIYAEIVGYGATSDGADMVAPSGEGAVRCMQMAMAGVDTPIDYMNVHGTSTPVGDVKELGAIREVFGNNTPAISSTKAMTGHSLGAAGVHEAIFSLLMVEHGFIAPSINIDNLDEQAQGMNIITETTQRELTTVMSNSFGFGGTNATLVMRKYQK 407
               SCOP domains d3oyta1 A:1-252 automated matches                                                                                                                                                                                                                           d3oyta2 A:253-407 automated matches                                                                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.....hhhhhhhhhhhh....eehhhhhhhh....ee.......hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhh...eeeeee....hhhhhhhhhhhhh..hhhhhhh.hhhhhhh.hhhhhhhhh.......eeeeehhhhhhhhhhhhhhhhhhh....eeeeeeee..hhhhhhhhhhh.........hhhhh...............eeeeeeeeehhhhhhhh....eeeeeeeeee.........hhhhhhhhhhhhh.......eee.....hhhhhhhhhhhhhhhhh....eee.hhhhhh.hhhhhhhhhhhhhhhhhhhhee.........hhhhh........ee....eeeeeeee...eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oyt A   1 mKRAVITGLGIVSSIGNNQQEVLASLQEGRSGITFAQEFKDAGmRSHVWGDVKLQSEPKDLIDRKVLRFmSDASIYAYLAmQEAIADSGLSDSQVSNFRSGLVVGSGGGSPRNQVAGSDAmRTPRGLKGVGPYmVTKAmASGVSACLATPFKIKGVNYSISSACATSAHCIGHALELIQLGKQDIVFAGGGEELCWEmACEFDAmGALSTKYNDTPAKASRTYDQDRDGFVIAGGGGmVVVEELEHALARGAHIYAEIVGYGATSDGADmVAPSGEGAVRCmQmAmAGVDTPIDYmNVHGTSTPVGDVKELGAIREVFGNNTPAISSTKAmTGHSLGAAGVHEAIFSLLmVEHGFIAPSINIDNLDEQAQGmNIITETTQRELTTVmSNSFGFGGTNATLVmRKYQK 407
                            |       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 |     
                            |                                         44-MSE                    70-MSE     81-MSE                                 121-MSE      134-MSE|                                                        198-MSE  |                              238-MSE                         270-MSE     282-MSE       296-MSE                            331-MSE            350-MSE               372-MSE        387-MSE        402-MSE 
                            1-MSE                                                                                                                                   139-MSE                                                           205-MSE                                                                        284-MSE                                                                                                                       
                                                                                                                                                                                                                                                                                                                       286-MSE                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:398
 aligned with Q7CJB1_YERPE | Q7CJB1 from UniProtKB/TrEMBL  Length:407

    Alignment length:406
                                    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      
         Q7CJB1_YERPE     1 MKRAVITGLGIVSSIGNNQQEVLASLQEGRSGITFAQEFKDAGMRSHVWGDVKLQSEPKDLIDRKVLRFMSDASIYAYLAMQEAIADSGLSDSQVSNFRSGLVVGSGGGSPRNQVAGSDAMRTPRGLKGVGPYMVTKAMASGVSACLATPFKIKGVNYSISSACATSAHCIGHALELIQLGKQDIVFAGGGEELCWEMACEFDAMGALSTKYNDTPAKASRTYDQDRDGFVIAGGGGMVVVEELEHALARGAHIYAEIVGYGATSDGADMVAPSGEGAVRCMQMAMAGVDTPIDYMNVHGTSTPVGDVKELGAIREVFGNNTPAISSTKAMTGHSLGAAGVHEAIFSLLMVEHGFIAPSINIDNLDEQAQGMNIITETTQRELTTVMSNSFGFGGTNATLVMRKYQ 406
               SCOP domains d3oytb1 B:1-252 automated matches                                                                                                                                                                                                                           d3oytb2 B:253-4        06 automated matches                                                                                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ketoacyl-synt-3oytB03 B:1-247                                                                                                                                                                                                                          -------Ketoacyl-synt        _C-3oytB01 B:255-363                                                                    ------------------------------------------- Pfam domains (1)
           Pfam domains (2) ketoacyl-synt-3oytB04 B:1-247                                                                                                                                                                                                                          -------Ketoacyl-synt        _C-3oytB02 B:255-363                                                                    ------------------------------------------- Pfam domains (2)
         Sec.struct. author ...eee...eee.....hhhhhhhhhhhh....eehhhhhhhh....ee.......hhhhh.hhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhh...eeeeee....hhhhhhhhhhhhh..hhhhhhh.hhhhhhh.hhhhhhhhh.......eeeeehhhhhhhhhhhhhhhhhhh....eeeeeeee..hhhhhhhhhhh.........hhhhh...............eeeeeeeeehhhhhhhh....eeeeeeeeee..--------hhhhhhhhhhhh.......eee.....hhhhhhhhhhhhhhhhh....eee.hhhhhh.hhhhhhhhhhhhhhhhhhhhee.........hhhhh........ee....eeeeeeee...eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oyt B   1 mKRAVITGLGIVSSIGNNQQEVLASLQEGRSGITFAQEFKDAGmRSHVWGDVKLQSEPKDLIDRKVLRFmSDASIYAYLAmQEAIADSGLSDSQVSNFRSGLVVGSGGGSPRNQVAGSDAmRTPRGLKGVGPYmVTKAmASGVSACLATPFKIKGVNYSISSACATSAHCIGHALELIQLGKQDIVFAGGGEELCWEmACEFDAmGALSTKYNDTPAKASRTYDQDRDGFVIAGGGGmVVVEELEHALARGAHIYAEIVGYGATSDG--------EGAVRCmQmAmAGVDTPIDYmNVHGTSTPVGDVKELGAIREVFGNNTPAISSTKAmTGHSLGAAGVHEAIFSLLmVEHGFIAPSINIDNLDEQAQGmNIITETTQRELTTVmSNSFGFGGTNATLVmRKYQ 406
                            |       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      |  -     | 280 | | | 290     | 300       310       320       330|      340       350       360       370 |     380      |390       400 |    
                            1-MSE                                     44-MSE                    70-MSE     81-MSE                                 121-MSE      134-MSE|                                                        198-MSE  |                              238-MSE                      267      276     | | |       296-MSE                            331-MSE            350-MSE               372-MSE        387-MSE        402-MSE
                                                                                                                                                                    139-MSE                                                           205-MSE                                                                      282-MSE                                                                                                                        
                                                                                                                                                                                                                                                                                                                     284-MSE                                                                                                                      
                                                                                                                                                                                                                                                                                                                       286-MSE
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Thiolase (72)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q7CJB1_YERPE | Q7CJB1)
molecular function
    GO:0004315    3-oxoacyl-[acyl-carrier-protein] synthase activity    Catalysis of the reaction: acyl-[acyl-carrier protein] + malonyl-[acyl-carrier protein] = 3-oxoacyl-[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).
biological process
    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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