1NVM


Conserved Protein Domain Family
DRE_TIM_HOA

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cd07943: DRE_TIM_HOA 
Click on image for an interactive view with Cn3D
4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain
4-hydroxy 2-ketovalerate aldolase (Also known as 4-hydroxy-2-ketovalerate aldolase and 4-hydroxy-2-oxopentanoate aldolase (HOA)) converts 4-hydroxy-2-oxopentanoate to acetaldehyde and pyruvate, the penultimate step in the meta-cleavage pathway for the degradation of phenols, cresols and catechol. This family includes the Escherichia coli MhpE aldolase, the Pseudomonas DmpG aldolase, and the Burkholderia xenovorans BphI pyruvate aldolase. In Pseudomonas, the DmpG aldolase tightly associates with a dehydrogenase (DmpF ) and is inactive without it. HOA has a canonical TIM-barrel fold with a C-terminal extension that forms a funnel leading to the active site. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name "DRE-TIM".
Statistics
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PSSM-Id: 163681
View PSSM: cd07943
Aligned: 100 rows
Threshold Bit Score: 310.585
Threshold Setting Gi: 225178512
Created: 14-Sep-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 9 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                ##  #                          #                                        
1NVM_A         9 LYISDVTLRDGSHAIRHQYTLDDVRAIARALDKAKVDSIEVAHGDGLQGSSFNYGFGRHTDLEYIEAVAGei-----shA 83  Pseudomonas sp.
AAL85691      15 VQIHDPTLRDGQHAVRHSLGAEQFRAYLKAADAAAVPVVEVGHGNGLAASSLQVGRARLSDDEMMSIAREtl-----ttS 89  Streptomyces an...
ZP_04608973   14 ILIHDPTLRDGHHAVRHQLGREQLRAYAKAADAAGIPVVEVGHGNGLGASSLQAGRALLSDEAMLSVVREal-----ttS 88  Micromonospora ...
YP_001581478   5 VQILDTTLRDGSYSVNFSFTSSDTSIICSKLEKSGIKLIEVGHGLGFNASNSGYGKSTQSDEEYMIAAKEsl-----skS 79  Nitrosopumilus ...
ZP_01756738    7 PKVLDCTLRDGSYVIDFQFTSADTESIGGALDQAGFPYIEVGHGVGMGASETGNNVAAASDADYMAAAAKsv-----tsG 81  Roseobacter sp....
YP_001030423   1 MEILDTTIRDGGYAVDFNFSCSDVRNISSKLEGMGIGLIEIGHGMGLNASSPKNGIAAQTDEEYMRAAGEvl-----tkS 75  Methanocorpuscu...
ZP_05068161    1 MKILDTTLRDGSYVNNFSFTLDETRFFTRELSRLGLELIEVGHGIGLGATEKGISPAVETDQDYMKAAALaveesgsqkA 80  Octadecabacter ...
ZP_01385454    8 VDILDTTLRDGSYTIGYQFTADETALIAHGLELSGINYIEVGHGLGLGADRAGKGAQAVTDLVYMRACSNai-----rrA 82  Chlorobium ferr...
YP_001822076   4 VVIHDPTLRDGQHAVHHRLGLTELRRYAEAADAARVPVVEVGHGNGLGASSLQVGLAAATDDAMLSTVREal-----rhS 78  Streptomyces gr...
YP_002457738   4 VKIFDLTLRDGSHAKSHQFTPEQMAVLAEQIDSTGVAAIEFGHGNGLGGSALQYGFAAATDREYMEAVAPvv-----knA 78  Desulfitobacter...
Feature 1                                                               # #                      
1NVM_A        84 QIATLLLPGIGSvHDLKNAYQAGARVVRVATHCTEADVSKQHIEYARNLGmDTVGFLMMSHMIPAEKLAEQGKLMESYGA 163 Pseudomonas sp.
AAL85691      90 KLGVLMFPGWATtQDIKNALAYEVDLVRIATHCTEASVAERHLGFLRDEGvEAHGILLMTHMASPDQLAEECARLVGYGA 169 Streptomyces an...
ZP_04608973   89 KLGVFMLPGWGTtENIRQAISYDVDLVRIGTHCTEGNLAERHLGLLRDAGvDAHGVLLMSHMANPERLAEECARLVGFGA 168 Micromonospora ...
YP_001581478  80 MYGMFCIPGIAKlSDLELAKKHGMGFIRVGTDVTKVHQSEKFIKKAKNLGfFVASNFMKSYVMPPDKFASIVKQSEEFGT 159 Nitrosopumilus ...
ZP_01756738   82 KWGMFCIPGVANlDHVRLAADHGIGFIRVGTDVAQADSAIPFIELARKLGiEVFANFMKSYVLEPEAFGALAARSYDYGA 161 Roseobacter sp....
YP_001030423  76 KFGMFCIPGIARlEDLQLAVDCGASFIRVGINADQIPLTEPYIREAKDLGlTVMTNYMKSYVLTPDEFAQNVMLSEKYGA 155 Methanocorpuscu...
ZP_05068161   81 KWGMFCIPGIAElNHIDLAHDHNMGFIRIGVTVEDINLARSFVEKSKKLGlYVCVNFMKSYTSSPQEFSAAVAQAASFGA 160 Octadecabacter ...
ZP_01385454   83 RFGFFYIPGIGElSDLKLLADEGGAFVRVGVSLDAIDQACHAIREAKRLGlEVWANIMKIYAYSLKESREGSLRFVEAGA 162 Chlorobium ferr...
YP_001822076  79 RLGTFMLPGWGTsDDLRRAISHGVDVFRVGVHATEASLAEHHLGFLRDAGaEAHCVLMMSHMASPGELAEQAARAVGYGA 158 Streptomyces gr...
YP_002457738  79 DLSIIILPGVGTrHELHLAKEFGAKYARMCTQITEVDIAEQHIKMAKQLGmIPIAVLPCAGIIPVKDTVRYTQMAESYGA 158 Desulfitobacter...
Feature 1               #                               # #                                      
1NVM_A       164 TCIYMADSGGAMSMNDIRDRMRAFKAVLkpe---tqVGMHAHHNLSLGVANSIVAVEEGCDRVDASLAGMGAGAGNAPLE 240 Pseudomonas sp.
AAL85691     170 TGVGILDSSGHFLPSDVTARIGAIRAAVdv-----pVMFHGHNNLGMAVANSVAAAHAGAGILDACARGFGAGAGNTQLE 244 Streptomyces an...
ZP_04608973  169 TGVGILDSSGYYLPADVTTRIAAIRSAVdv-----pVMFHGHNNLGMAVANSIAAAEAGATILDACARGFGAGAGNTQLE 243 Micromonospora ...
YP_001581478 160 DMVYIVDSAGGMFSSDLLEYYNSIRNVSei-----pLGFHGHDNLGMAISNSLYAADLGMEYIDSSLQGIGRSSGNACTE 234 Nitrosopumilus ...
ZP_01756738  162 EMVYLVDSAGGMLPHEVRAYLQAAKSAApe----lpLGFHGHDNLGLAVANSLVSLEEGAAMVDTSLQGFGRSSGNTATE 237 Roseobacter sp....
YP_001030423 156 DCVYIVDSAGGMFPGEIQEYYDTIREYSsi-----qLGFHGHNNLGLAVANSVYCAKLGFDFIDCSLQGLGRSSGNACTE 230 Methanocorpuscu...
ZP_05068161  161 DIAYLVDSAGTMVPADVEDYFRTVRRNSil-----pLGFHGHNNLGLANINAYTAYNEGAGIVDVSMQGMGRCTGNTSTE 235 Octadecabacter ...
ZP_01385454  163 DGVYVVDSAGGMLPSEVAEYVSEIRKEFtlagvsarIGFHGHDNLSLSTACSLSAVGAGCDIVDGSLLGIGRSIGNAATE 242 Chlorobium ferr...
YP_001822076 159 QAVGIMDSAGHFLPPDVTARIGAIVEAVgt----vpVIFHGHNNLGMAVANSVAAAEAGARIIDGCARGFGAGAGNTQLE 234 Streptomyces gr...
YP_002457738 159 EVIYLLDGGGYQLPEQTYERIAAMKKAVdv-----pIGFHGHNNLQLAVANSKAAVEAGAEYIDCCLKGFGAGAGNCPTE 233 Desulfitobacter...
Feature 1                                        
1NVM_A       241 VFIAVAERLGWNHGTDLYTLMDAADDIVRPLQ 272 Pseudomonas sp.
AAL85691     245 VLVPVLERLGFRTGIDLYRLLDAADIAGRELM 276 Streptomyces ansochromogenes
ZP_04608973  244 VLVPVLERLGYDTGIDLYRLLDAADIAERELM 275 Micromonospora sp. ATCC 39149
YP_001581478 235 VLVMALKKKGFKIDVDFHSLFEAGQECVYPLI 266 Nitrosopumilus maritimus SCM1
ZP_01756738  238 LFLGATIRSGYEAFAEPIEVMDLGETLVRPLI 269 Roseobacter sp. SK209-2-6
YP_001030423 231 MFLAILEKNGYRTDVDLVELFSAGYDLLRPIT 262 Methanocorpusculum labreanum Z
ZP_05068161  236 HFLALLGKQGIAHNLDPIGLMDLSEKYVRPKL 267 Octadecabacter antarcticus 238
ZP_01385454  243 VLAMVLCRAGYETGVNAWNAGDLAEKTIRPFL 274 Chlorobium ferrooxidans DSM 13031
YP_001822076 235 VLVPVLERSGFATGIDLYALLDAADLAERELM 266 Streptomyces griseus subsp. griseus NBRC 13350
YP_002457738 234 IFAAVMDRMEIDCGIDLYKTMDIAEQYLRPLM 265 Desulfitobacterium hafniense DCB-2

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