1L6G,1B54,1KNW,1RCQ,1W8G,2J66,3BTN,1TWI,2OO0,1SFT,1XFC,2DY3,3CO8,2VD9,1VFH,2RJG,2ODO,1D7K,1F3T,1QU4,1HKV,2PLJ,2TOD,2ON3,3BTN,2P3E,2YXX,3C5Q


Conserved Protein Domain Family
PLPDE_III

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cd06808: PLPDE_III 
Click on image for an interactive view with Cn3D
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes
The fold type III PLP-dependent enzyme family is predominantly composed of two-domain proteins with similarity to bacterial alanine racemases (AR) including eukaryotic ornithine decarboxylases (ODC), prokaryotic diaminopimelate decarboxylases (DapDC), biosynthetic arginine decarboxylases (ADC), carboxynorspermidine decarboxylases (CANSDC), and similar proteins. AR-like proteins contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. These proteins play important roles in the biosynthesis of amino acids and polyamine. The family also includes the single-domain YBL036c-like proteins, which contain a single PLP-binding TIM-barrel domain without any N- or C-terminal extensions. Due to the lack of a second domain, these proteins may possess only limited D- to L-alanine racemase activity or non-specific racemase activity.
Statistics
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PSSM-Id: 143484
View PSSM: cd06808
Aligned: 31 rows
Threshold Bit Score: 135.524
Threshold Setting Gi: 157830174
Created: 9-Jan-2008
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
pyridoxalcatalytic
Conserved site includes 10 residues -Click on image for an interactive view with Cn3D
Feature 1:pyridoxal 5'-phosphate (PLP) binding site [chemical binding site]
Evidence:
  • Structure:1B54_A; Saccharomyces cerevisiae Hypothetical Protein-A binds PLP; defined at 4A contacts.
    View structure with Cn3D
  • Structure:1TWI_AB; Methanocaldococcus jannaschii Diaminopimelate decarboxylase dimer binds two PLP cofactors; defined at 4A contacts.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                        # #                                             
1L6G_A        17 IYDNVENLRRllpd------------dthIMAVVKANayghgdVQVARTALeagasRLAVAFlDEALALREkgi-eaPIL 83
1B54_A        15 LIAQYESVREvvnaeaknvhvnenaskilLLVVSKLKp-----ASDIQILYdhgvrEFGENYvQELIEKAKllpddiKWH 89
1RCQ_A        13 LRHNYRLAREatg--------------arALAVIKADayghgaVRCAEALAae-adGFAVACiEEGLELREagi-rqPIL 76
1XFC_A        21 IEHNVRVLREhag-------------haqLMAVVKADgyghgaTRVAQTALgagaaELGVATvDEALALRAdgi-taPVL 86
2DY3_A        13 IAHNTRVLKQmag-------------pakLMAVVKANaynhgvEKVAPVIAahgadAFGVATlAEAMQLRDigi-sqEVL 78
1VFH_A        17 VRANVRALRArap-------------rsaLMAVVKSNayghgaVPCARAAQeagaaWLGTATpEEALELRAagi-qgRIM 82
2RJG_A        33 LRHNLQRLRElap-------------askMVAVVKANayghglLETARTLPda--dAFGVARlEEALRLRAggi-tkPVL 96
2ODO_A        13 LRHNYQLAREvtg--------------akALAVIXADayghgaVRCAQALEae-adGFAVACiEEALELRAagi-raPIL 76
gi 150390137  17 LRHNARVMTEkcne-----------ygiaIAGVTKVFgg---rPEIAQAMIdggiqYLADSRvENLKKMKDls--lpKIL 80
gi 163929821  22 ARRNAERMRErcra-----------lgvrLRPHVKTHk----tLEGGLLATggtrrGIAVSTlAEARFFADgg--fdDIL 84
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1         #                                                      #                       
1L6G_A        84 VLGAsr-paDAALAAqq-----rIALTVFrs-dWLEEASalys----gpfpIHFHLXMDtg--mGRLGVkdeeeTKRIVA 150
1B54_A        90 FIGGlq-tnKCKDLAkvp---nlYSVETIdslkKAKKLNesrakfqpdcnpILCNVQINtshedQKSGLnneaeIFEVID 165
1RCQ_A        77 LLEGffeasELELIVah-----dFWCVVHca-wQLEAIErasl-----arpLNVWLXMDsg--mHRVGFfp-edFRAAHE 142
1XFC_A        87 AWLHpp-giDFGPALla-----dVQVAVSsl-rQLDELLhavrr---tgrtATVTVKVDtg--lNRNGVgp-aqFPAMLT 153
2DY3_A        79 CWIWtp-eqDFRAAIdr-----nIDLAVIsp-aHAKALIetd------aehIRVSIKIDsg--lHRSGVde-qeWEGVFS 142
1VFH_A        83 CWLWtp-ggPWREAIet-----dIDVSVSgm-wALDEVRaaara---agrtARIQLXADtg--lGRNGCqp-adWAELVG 149
2RJG_A        97 LLEGffdarDLPTISaq-----hFHTAVHne-eQLAALEeasl-----depVTVWMXLDtg--mHRLGVrp-eqAEAFYH 162
2ODO_A        77 LLEGffeadELPLIVeh-----dFWCVVHsl-wQLDAIEqarl-----akpIHVWLXLDsg--mHRVGLhp-ndYKAAYQ 142
gi 150390137  81 LRLPmi--sRVDDVVky----cdISLNSEv--eTIIALSqaaek---qhktHKIILMVDlg--dLREGIfdsqaLKLALD 147
gi 163929821  85 LAYPvp-taRLEECAglarrldaFHVLLDrp-eALASLRqrplg---hgkrWLVWLKLDcg--nGRAGVrptdpAALELA 157
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                        # #                                                             
1L6G_A       151 LIerhp---hfvlEGLYTHFatadev--------ntdyfSYQYTRFLHMLewlp----srpPLVHCANSAaslrf----p 211
1B54_A       166 FFlseec-kyiklNGLMTIGswnvsh--------edskeNRDFATLVEWKkkida-kfgtsLKLSMGMSAdfrea----i 231
1RCQ_A       143 RLrasg---kvakIVMMSHFsradel--------dcprtEEQLAAFSAASqg-------leGEISLRNSPavlgw----p 200
1XFC_A       154 ALrqamaedavrlRGLMSHMvyadkp--------ddsinDVQAQRFTAFLaqare-qgvrfEVAHLSNSSatmar----p 220
2DY3_A       143 ALaaap---hievTGMFTHLacadep--------enpetDRQIIAFRRALalark-hglecPVNHVCNSPafltr----s 206
1VFH_A       150 AAvaaqaegtvqvTGVWSHFacadep--------ghpsiRLQLDAFRDMLayaek-egvdpEVRHIANSPatltl----p 216
2RJG_A       163 RLtqckn--vrqpVNIVSHFaradep--------kcgatEKQLAIFNTFCeg-------kpGQRSIAASGgillw----p 221
2ODO_A       143 RLqasa---nvakIVLMSHFaradel--------dctrsVEQVAVFLGARad-------ltAEISLRNSPavlgw----p 200
gi 150390137 148 EIknlk---gikvVGIGTNLtcygg----------vipdEENLGRLIAYAseieavlgtklEIISGGNSSsiymvqegrm 214
gi 163929821 158 QAiandapeevtlVGVYAHCgntygcsgadtiqaiarttTNAVLSFVAALrqag----vpcPQASIGSTPscshpi--pe 231
                        250
                 ....*....|.
Feature 1               ####
1L6G_A       212 drtfNMVRFGI 222
1B54_A       232 rqgtAEVRIGT 242
1RCQ_A       201 kvpsDWVRPGI 211
1XFC_A       221 dltfDLVRPGI 231
2DY3_A       207 dlhmEMVRPGL 217
1VFH_A       217 ethfDLVRTGL 227
2RJG_A       222 qshfDWVRPGI 232
2ODO_A       201 rvpsDWVRPGL 211
gi 150390137 215 leevNLLRLGE 225
gi 163929821 232 msqlTELHPGN 242

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