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(-) Description

Title :  CRYSTAL STRUCTURE OF BETA-KETOACYL-ACP SYNTHASE III (FABH) FROM VIBRIO CHOLERAE IN COMPLEX WITH COENZYME A
 
Authors :  J. Hou, H. Zheng, K. Langner, W. F. Anderson, W. Minor, Center For Stru Genomics Of Infectious Diseases (Csgid)
Date :  04 Nov 13  (Deposition) - 25 Dec 13  (Release) - 25 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Vibrio Cholerae, Beta-Ketoacyl-(Acyl Carrier Protein) Synthase Iii, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Hou, H. Zheng, K. Langner, W. F. Anderson, W. Minor, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of Beta-Ketoacyl-Acp Synthase Iii (Fabh) From Vibrio Cholerae In Complex With Coenzyme A
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 3 PROTEIN 1
    Chains: A, B, C, D
    EC Number: 2.3.1.180
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: FABH1, VC2023, VC_2023
    Organism Scientific: VIBRIO CHOLERAE O1 BIOVAR EL TOR
    Organism Taxid: 243277
    Strain: N16961
    Synonym: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE III PROTEIN 1, BETA-KETOACYL-ACP SYNTHASE III 1, KAS III 1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 18)

Asymmetric Unit (4, 18)
No.NameCountTypeFull Name
1CA7Ligand/IonCALCIUM ION
2COA4Ligand/IonCOENZYME A
3NA3Ligand/IonSODIUM ION
4SCY4Mod. Amino AcidS-ACETYL-CYSTEINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2COA2Ligand/IonCOENZYME A
3NA-1Ligand/IonSODIUM ION
4SCY2Mod. Amino AcidS-ACETYL-CYSTEINE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2COA2Ligand/IonCOENZYME A
3NA-1Ligand/IonSODIUM ION
4SCY2Mod. Amino AcidS-ACETYL-CYSTEINE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:28 , TRP A:32 , ARG A:36 , SCY A:112 , ARG A:151 , SER A:152 , ILE A:155 , LEU A:156 , PHE A:157 , LEU A:189 , MET A:206 , GLY A:208 , ASN A:209 , VAL A:211 , PHE A:212 , HIS A:243 , ALA A:245 , ASN A:246 , ARG A:248 , ASN A:273 , HOH A:651 , HOH A:723 , HOH A:751 , HOH A:785 , LYS D:213BINDING SITE FOR RESIDUE COA A 401
02AC2SOFTWAREASN A:48 , ASP A:53 , HOH A:717 , HOH A:818 , HOH A:819 , HOH A:821 , HOH A:822BINDING SITE FOR RESIDUE CA A 402
03AC3SOFTWAREASN A:231 , HOH A:606 , HOH A:719 , HOH A:800BINDING SITE FOR RESIDUE NA A 403
04AC4SOFTWARETHR B:28 , TRP B:32 , ARG B:36 , THR B:37 , SCY B:112 , ARG B:151 , SER B:152 , ILE B:155 , PHE B:157 , LEU B:189 , MET B:206 , GLY B:208 , ASN B:209 , VAL B:211 , ASN B:246 , ARG B:248 , HOH B:611 , HOH B:612 , HOH B:635 , HOH B:705 , HOH B:711 , HOH B:740 , HOH B:784 , HOH B:832BINDING SITE FOR RESIDUE COA B 401
05AC5SOFTWAREASN B:48 , ASP B:53 , HOH B:552 , HOH B:697 , HOH B:698 , HOH B:699BINDING SITE FOR RESIDUE CA B 402
06AC6SOFTWAREASP B:72 , ASP B:74 , HOH B:822 , HOH B:823 , HOH B:824 , HOH B:835BINDING SITE FOR RESIDUE CA B 403
07AC7SOFTWARETHR C:28 , TRP C:32 , ARG C:36 , SCY C:112 , ARG C:151 , SER C:152 , ILE C:155 , LEU C:189 , MET C:206 , GLY C:208 , ASN C:209 , VAL C:211 , PHE C:212 , HIS C:243 , ALA C:245 , ASN C:246 , ARG C:248 , ILE C:249 , ASN C:273 , PHE C:303 , HOH C:678 , HOH C:716 , HOH C:721 , HOH C:756BINDING SITE FOR RESIDUE COA C 401
08AC8SOFTWAREASP C:72 , ASP C:74 , HOH C:829 , HOH C:830 , HOH C:831 , HOH C:832BINDING SITE FOR RESIDUE CA C 402
09AC9SOFTWAREASN C:48 , ASP C:53 , HOH C:707 , HOH C:835 , HOH C:837 , HOH C:838BINDING SITE FOR RESIDUE CA C 403
10BC1SOFTWARETHR D:28 , TRP D:32 , ARG D:36 , SCY D:112 , ARG D:151 , SER D:152 , ILE D:155 , LEU D:156 , GLY D:208 , ASN D:209 , HIS D:243 , ALA D:245 , ASN D:246 , ILE D:249 , ASN D:273 , PHE D:303 , HOH D:634 , HOH D:717 , HOH D:736BINDING SITE FOR RESIDUE COA D 401
11BC2SOFTWAREASN D:48 , ASP D:53 , HOH D:718 , HOH D:719 , HOH D:720 , HOH D:721BINDING SITE FOR RESIDUE CA D 402
12BC3SOFTWAREASP D:72 , ASP D:74 , HOH D:723 , HOH D:724 , HOH D:725 , HOH D:726BINDING SITE FOR RESIDUE CA D 403
13BC4SOFTWAREASN D:231 , HOH D:713 , HOH D:714 , HOH D:715 , HOH D:716BINDING SITE FOR RESIDUE NA D 404
14BC5SOFTWAREHOH A:812 , GLY D:67 , HOH D:731 , HOH D:732 , HOH D:733 , HOH D:734 , HOH D:735BINDING SITE FOR RESIDUE NA D 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NHD)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Phe A:87 -Pro A:88
2Pro A:172 -Gly A:173
3Gly A:306 -Phe A:307
4Phe B:87 -Pro B:88
5Pro B:172 -Gly B:173
6Gly B:306 -Phe B:307
7Phe C:87 -Pro C:88
8Pro C:172 -Gly C:173
9Gly C:306 -Phe C:307
10Phe D:87 -Pro D:88
11Pro D:172 -Gly D:173
12Gly D:306 -Phe D:307

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NHD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NHD)

(-) Exons   (0, 0)

(no "Exon" information available for 4NHD)

(-) 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:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4nhda1 A:0-174 automated matches                                                                                                                                              d4nhda2 A:175-316 automated matches                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee...eeeehhhhhhhh..hhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhh.hhhhh.eeeee.....eee.hhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhh....eeeeeeeee.hhhh...hhhhhh...eeeeeeeeeee....eeeeeeee...hhh.eeee............eehhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeee...hhhhhhhhhhhh..hhhhh..hhhhhh.hhhhhhhhhhhhhhhh.......eeeeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nhd A   0 AMYSKILGTGSYLPSQVRTNADLEKMVETSDEWIVARTGIRERRIAADNETVADMAFFAAQNAINMAGIDKHDIDMIIVATTSASHTFPSAACQVQGKLGIKGCPAFDLAAAcSGFMYALSIADQHVKSGMCKHVLVIGADALSKTCDPTDRSTIILFGDGAGAVVVGASNEPGILSTHIHADGEFGDLLSLEVPVRGGDSDKWLHMAGNEVFKVAVTQLSKLVVDTLKANNMHKSELDWLVPHQANYRIISATAKKLSMSLDQVVITLDRHGNTSAATVPTALDEAVRDGRIQRGQMLLLEAFGGGFTWGSALVKF 316
                                     9        19        29        39        49        59        69        79        89        99       109  |    119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       
                                                                                                                                          112-SCY                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4nhdb1 B:0-174 automated matches                                                                                                                                              d4nhdb2 B:175-316 automated matches                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee...eeeehhhhhhhh..hhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhh.hhhhh.eeeee.....eee.hhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhh....eeeeeeeee.hhhh...hhhhhh...eeeeeeeeeee....eeeeeeee...hhh.eeee............eehhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeee...hhhhhhhhhhhh..hhhhh..hhhhhh.hhhhhhhhhhhhhhhh.......eeeeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nhd B   0 AMYSKILGTGSYLPSQVRTNADLEKMVETSDEWIVARTGIRERRIAADNETVADMAFFAAQNAINMAGIDKHDIDMIIVATTSASHTFPSAACQVQGKLGIKGCPAFDLAAAcSGFMYALSIADQHVKSGMCKHVLVIGADALSKTCDPTDRSTIILFGDGAGAVVVGASNEPGILSTHIHADGEFGDLLSLEVPVRGGDSDKWLHMAGNEVFKVAVTQLSKLVVDTLKANNMHKSELDWLVPHQANYRIISATAKKLSMSLDQVVITLDRHGNTSAATVPTALDEAVRDGRIQRGQMLLLEAFGGGFTWGSALVKF 316
                                     9        19        29        39        49        59        69        79        89        99       109  |    119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       
                                                                                                                                          112-SCY                                                                                                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4nhdc1 C:0-174 automated matches                                                                                                                                              d4nhdc2 C:175-316 automated matches                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee...eeeehhhhhhhh..hhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhh.hhhhh.eeeee.....eee.hhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhh....eeeeeeeee.hhhh...hhhhhh...eeeeeeeeeee....eeeeeeee...hhh.eeee............eehhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeee...hhhhhhhhhhhh..hhhhh..hhhhhh.hhhhhhhhhhhhhhhh.......eeeeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nhd C   0 AMYSKILGTGSYLPSQVRTNADLEKMVETSDEWIVARTGIRERRIAADNETVADMAFFAAQNAINMAGIDKHDIDMIIVATTSASHTFPSAACQVQGKLGIKGCPAFDLAAAcSGFMYALSIADQHVKSGMCKHVLVIGADALSKTCDPTDRSTIILFGDGAGAVVVGASNEPGILSTHIHADGEFGDLLSLEVPVRGGDSDKWLHMAGNEVFKVAVTQLSKLVVDTLKANNMHKSELDWLVPHQANYRIISATAKKLSMSLDQVVITLDRHGNTSAATVPTALDEAVRDGRIQRGQMLLLEAFGGGFTWGSALVKF 316
                                     9        19        29        39        49        59        69        79        89        99       109  |    119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       
                                                                                                                                          112-SCY                                                                                                                                                                                                        


Chain D from PDB  Type:PROTEIN  Length:318
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4nhdd1 D:-1-174 automated matches                                                                                                                                              d4nhdd2 D:175-316 automated matches                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeeee...eeeehhhhhhhh..hhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhh.hhhhh.eeeee.....eee.hhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhh....eeeeeeeee.hhhh...hhhhhh...eeeeeeeeeee....eeeeeeee...hhh.eeee............eehhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeee...hhhhhhhhhhhh..hhhhh..hhhhhh.hhhhhhhhhhhhhhhh.......eeeeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4nhd D  -1 NAMYSKILGTGSYLPSQVRTNADLEKMVETSDEWIVARTGIRERRIAADNETVADMAFFAAQNAINMAGIDKHDIDMIIVATTSASHTFPSAACQVQGKLGIKGCPAFDLAAAcSGFMYALSIADQHVKSGMCKHVLVIGADALSKTCDPTDRSTIILFGDGAGAVVVGASNEPGILSTHIHADGEFGDLLSLEVPVRGGDSDKWLHMAGNEVFKVAVTQLSKLVVDTLKANNMHKSELDWLVPHQANYRIISATAKKLSMSLDQVVITLDRHGNTSAATVPTALDEAVRDGRIQRGQMLLLEAFGGGFTWGSALVKF 316
                                     8        18        28        38        48        58        68        78        88        98       108   |   118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308        
                                                                                                                                           112-SCY
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 8)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)
(-)
Fold: Thiolase-like (231)
(-)
Superfamily: Thiolase-like (231)
(-)
Family: automated matches (108)
(-)
Protein domain: automated matches (108)
(-)
Vibrio cholerae [TaxId: 243277] (3)
1ad4nhda1A:0-174
1bd4nhdb1B:0-174
1cd4nhdb2B:175-316
1dd4nhdc1C:0-174
1ed4nhdc2C:175-316
1fd4nhdd1D:-1-174
1gd4nhdd2D:175-316
1hd4nhda2A:175-316

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NHD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NHD)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

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