Database accession: MF7000973
Name: PigE (Serratia sp. FS14)
PDB ID: 4ppm
Experimental method: X-ray (2.30 Å)
Assembly: Homodimer
Source organism: Serratia sp
Primary publication of the structure:
Lou X, Ran T, Han N, Gao Y, He J, Tang L, Xu D, Wang W
Crystal structure of the catalytic domain of PigE: a transaminase involved in the biosynthesis of 2-methyl-3-n-amyl-pyrrole (MAP) from Serratia sp. FS14.
(2014) Biochem. Biophys. Res. Commun. 447: 178-83
PMID: 24704447
Abstract:
Prodigiosin, a tripyrrole red pigment synthesized by Serratia and some other microbes through a bifurcated biosynthesis pathway, MBC (4-methoxy-2,2'-bipyrrole-5-carbaldehyde) and MAP (2-methyl-3-n-amyl-pyrrole) are synthesized separately and then condensed by PigC to form prodigiosin. MAP is synthesized sequentially by PigD, PigE and PigB. PigE catalyzes the transamination of an amino group to the aldehyde group of 3-acetyloctanal, resulting in an aminoketone, which spontaneously cyclizes to form H2MAP. Here we report the crystal structure of the catalytic domain of PigE which involved in the biosynthesis of prodigiosin precursor MAP for the first time to a resolution of 2.3Å with a homodimer in the asymmetric unit. The monomer of PigE catalytic domain is composed of three domains with PLP as cofactor: a small N-terminal domain connecting the catalytic domain with the front part of PigE, a large PLP-binding domain and a C-terminal domain. The residues from both monomers build the PLP binding site at the interface of the dimer which resembles the other PLP-dependent enzymes. Structural comparison of PigE with Thermus thermophilus AcOAT showed a higher hydrophobic and smaller active site of PigE, these differences may be the reason for substrate specificity.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
identical protein binding identical protein binding
pyridoxal binding pyridoxal binding
pyridoxal phosphate binding pyridoxal phosphate binding
transaminase activity transaminase activity
Biological process:
antibiotic biosynthetic process antibiotic biosynthetic process
Cellular component: not assigned
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, B
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: Aminotransferase PigE
Source organism: Serratia sp
Length: 853 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMKFGFIAHPTSLGLKRYVKMLDLLQRNSTEQHSGYTRELWERQNLVPFMNFARITSATGATCEGVIKYMPLVADEMLADARGIAARVVQGIEELAGDGAELVGLGGFTSIVGRRGEATAEKSPVPVTSGNSLTTYAGYKALMQIQSWLEIRPEEEPVAIVGYPGSICLALSRLLLAHGFSLHLLHRAGNHDRSELLSHLPEEYHSRVTLTSDPEDLYPRCKLFAAATSAGGVIDPARLQPGSIFIDVALPRDIASETRPARDDILIIDGGCVTATDAVKLGGESLNVTIKQQLNGCMAETIVLALENRRENFSLGRYLAPEKVLEIGEIAERHGFFAYPLASYGERIDRQSVTNLKRYYHHDIYAGESADAALPASRLAFIDAVIAQTPAREDTLDRYHQYINPMMVDFLKLQRCDNVFRSAAGTQLYDDAGEAFLDMVAGYGCLNLGHNPQPVVNALKNYLDAQGPNFIQYISIPEQTAKLAEVLCRLAPGNMGRVFFSNSGTEAVEAAMKIAKASTGKPGIAYLRNSYHGKTLGALSITGRDKHRRYFTPLLDAMVEVPFGDLAALREALNREDVGALMIEPIQGEGGVHIPPAGYLQAVQQLCRETGVLLMVDEVQTGLGRTGKLFACEWDGIEPDVLMLSKSLSGGLIPIGATLCRADLWQKAYGTADRFLVHSSTYGGGNLASVVALSALREILAQDLVGHAERMGAYFKQALSEIAARYPFVSEVRGRGLMLGIQFDQAFTGAVNASAREFATRLPGDWHTTWKFLPDPVQAHLRAAMDRMEQALGEMFCMKFVTKLCQDHKILTFITANSSTVIRIQPPLIISKAEIDRFVGAFATVCEELSTFLD
UniProtKB AC: A0A0J9X1Q5 (positions: 372-853)
Coverage: 56%
Name: Aminotransferase PigE
Source organism: Serratia sp
Length: 853 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMKFGFIAHPTSLGLKRYVKMLDLLQRNSTEQHSGYTRELWERQNLVPFMNFARITSATGATCEGVIKYMPLVADEMLADARGIAARVVQGIEELAGDGAELVGLGGFTSIVGRRGEATAEKSPVPVTSGNSLTTYAGYKALMQIQSWLEIRPEEEPVAIVGYPGSICLALSRLLLAHGFSLHLLHRAGNHDRSELLSHLPEEYHSRVTLTSDPEDLYPRCKLFAAATSAGGVIDPARLQPGSIFIDVALPRDIASETRPARDDILIIDGGCVTATDAVKLGGESLNVTIKQQLNGCMAETIVLALENRRENFSLGRYLAPEKVLEIGEIAERHGFFAYPLASYGERIDRQSVTNLKRYYHHDIYAGESADAALPASRLAFIDAVIAQTPAREDTLDRYHQYINPMMVDFLKLQRCDNVFRSAAGTQLYDDAGEAFLDMVAGYGCLNLGHNPQPVVNALKNYLDAQGPNFIQYISIPEQTAKLAEVLCRLAPGNMGRVFFSNSGTEAVEAAMKIAKASTGKPGIAYLRNSYHGKTLGALSITGRDKHRRYFTPLLDAMVEVPFGDLAALREALNREDVGALMIEPIQGEGGVHIPPAGYLQAVQQLCRETGVLLMVDEVQTGLGRTGKLFACEWDGIEPDVLMLSKSLSGGLIPIGATLCRADLWQKAYGTADRFLVHSSTYGGGNLASVVALSALREILAQDLVGHAERMGAYFKQALSEIAARYPFVSEVRGRGLMLGIQFDQAFTGAVNASAREFATRLPGDWHTTWKFLPDPVQAHLRAAMDRMEQALGEMFCMKFVTKLCQDHKILTFITANSSTVIRIQPPLIISKAEIDRFVGAFATVCEELSTFLD
UniProtKB AC: A0A0J9X1Q5 (positions: 372-853)
Coverage: 56%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: Aminotransferase class-III
Evidence level: Direct evidence
Evidence coverage: The full structure participates in mutual synergistic folding.
Complex Evidence:
The equilibrium unfolding of pig liver 4-aminobutyrate aminotransferase by urea was found to be a cooperative process. The kinetic results indicated that the aminotransferase unfolds in a single kinetic phase (PMID:8075151).
Chain A:
N/A
Chain B:
N/A
Surface and contacts features:
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). Download the CIF file (.cif)
Download this entry's XML file (.xml)
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