1QR6,1GQ2,1LLQ,2AW5


Conserved Protein Domain Family
NAD_bind_1_malic_enz

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cd05312: NAD_bind_1_malic_enz 
Click on image for an interactive view with Cn3D
NAD(P) binding domain of malic enzyme (ME), subgroup 1
Malic enzyme (ME), a member of the amino acid dehydrogenase (DH)-like domain family, catalyzes the oxidative decarboxylation of L-malate to pyruvate in the presence of cations (typically Mg++ or Mn++) with the concomitant reduction of cofactor NAD+ or NADP+. ME has been found in all organisms, and plays important roles in diverse metabolic pathways such as photosynthesis and lipogenesis. This enzyme generally forms homotetramers. The conversion of malate to pyruvate by ME typically involves oxidation of malate to produce oxaloacetate, followed by decarboxylation of oxaloacetate to produce pyruvate and CO2. This subfamily consists of eukaryotic and bacterial ME. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts.
Statistics
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PSSM-Id: 133454
View PSSM: cd05312
Aligned: 32 rows
Threshold Bit Score: 348.769
Threshold Setting Gi: 50257587
Created: 30-Aug-2005
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
NAD(P) binding
Conserved site includes 14 residues -Click on image for an interactive view with Cn3D
Feature 1:NAD(P) binding site [chemical binding site]
Evidence:
  • Structure:1QR6_A: human Mt malic enzyme binds NAD, contacts determined at 3.5A
    View structure with Cn3D
  • Comment:2nd NAD binding site away from active site may be the binding site for ATP, an allosteric inhibitor of the enzyme
  • Structure:1GQ2_A: pigeon liver malic enzyme binds NAD, contacts determined at 3.5A
    View structure with Cn3D
  • Structure:1LLQ_A: Acsaris suum malic enzyme binds NAD, contacts determined at 3.5A
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                           ####                              ##      
1QR6_A    280 IQGTAAVALAGLLAAQKVISKPIS------EHKILFLGAGEAALGIANLIVXSXVe-nGLSEQEAQKKIWXFDKYGLLVK 352 human
P40375    273 IQGTGAVALAAIIGALHVTKSPLT------EQRIMIFGAGTAGVGIANQIVAGMVt-dGLSLDKARGNLFMIDRCGLLLE 345 fission yeast
P78715    301 IQSTGAITLASVLATMRARGGTFAdi---kKETFLCLGAGSSGVGVCETIVDCIVa-eGATREEAYAQFYMFDHKGLLGK 376 Neocallimastix fro...
AAF12481  291 IQGTGAVVLAGVLNACRIKGEALK------DQVVVVHGAGAGGAGVAAAIREGMHr-eGLSPDEIARRVFVLDSRGLLTD 363 Deinococcus radiod...
YP_065939 279 VQGTGAITFSAILSAMKVKRAKLT------DQVFLIHGAGAGGVGIGEQIQVALMa-eGLSEEEARDKVFTIDSRGVVTV 351 Desulfotalea psych...
CAG22269  286 IQGTGAVVLAGILGAVKIKEEKLA------DQTYVVYGAGAGGVGVADQIYAGLLk-eGCSHSAAREKIFVLDSQGLVFD 358 Photobacterium pro...
P36013    355 IQGTGAVVMASLIAALKHTNRDLK------DTRVLIYGAGSAGLGIADQIVNHMVt-hGVDKEEARKKIFLMDRRGLILQ 427 baker's yeast
EAL20292  321 IQGTGAVALAALLSAIKVAGSRLS------DQRIVIYGAGSAGMGIADQIKDGLMileGLNKDEAARRFWCVDRNGLLVE 394 Cryptococcus neofo...
AAA92715  280 IEGTAAVAAATLASATHMEGVPDLk-----NQKIIFIGAGSAATGIANLIVDMAVsrgGITKEQAYKNIIMFDHKGMVHS 354 Trichomonas vaginalis
AAC47396  259 IQGTGCIAAATIAAGLRAISLKMNrtakasEQVYVMFGAGAGGIGVADNIASLSVs-eGYTLEQARKQFYVIDSQGLLTA 337 Giardia intestinalis
Feature 1                                                           ##                        
1QR6_A    353 GRka----kiDSYQEPFthsape----------sipdtFEDAVnilKPSTIIGVAGAGRLFTPDVIRAXASIN---ERPV 415 human
P40375    346 RHak----iaTDGQKPFlkkdsdfk-----evpsgdinLESAIalvKPTILLGCSGQPGKFTEKAIREMSKHV---ERPI 413 fission yeast
P78715    377 GRdd-----lLPSQQVFmrkei-----------eggktPAELLkkiKPTCLLGLSTCPKLFNKEMLSYVASYC---EKPG 437 Neocallimastix fro...
AAF12481  364 DRs------mEAYKQALatpralv-------sgwsgtdLLGVVreaKATVLLGLSGVPGTFDEDIVKAALANT---PRPL 427 Deinococcus radiod...
YP_065939 352 DRk------iEAYKKKFakdgaklsw----ladpenhkLENVIkqaGVTVLIGTSGQGGCFTETVVKNMLGNT---ERPV 418 Desulfotalea psych...
CAG22269  359 DReg-----lDEYKKRYakprelannw--qtkelgkvsLTELIdnhRVTVLLGTSGIGGAFKAEHVQKMMEYT---KRPM 428 Photobacterium pro...
P36013    428 SYea----nsTPAQHVYaksdaew-------agintrsLHDVVenvKPTCLVGCSTQAGAFTQDVVEEMHKHN---PRPI 493 baker's yeast
EAL20292  395 SMgn----glRHSQMPYarpdaevehwnkededrngiwLMDVIknvKPTVLIGTSTHSRAFSEELVREMGKHV---ERPI 467 Cryptococcus neofo...
AAA92715  355 GRtd-----lYDFNIPYmhdme------------hygsVLEAVkkfKATCVIGVSGVPGLITKEIVQATLENA---EHPV 414 Trichomonas vaginalis
AAC47396  338 DRddfvngtmPGHKLPYvrhdls---------ikghttLLSVIkavKPTCLLGLSTVGKSFTREILETMCEGLptgQPPI 408 Giardia intestinalis
Feature 1        ###                        #                  # #                            
1QR6_A    416 IFALSNPTAQAECTAEEAYTLTEGRCLFASGSPFGPvkltdGRVFTPGQGNNVYIFPGVALAVILCNTRHISDSVFLEAA 495 human
P40375    414 IFPISNPTTLMEAKPDQIDKWSDGKALIATGSPLPPln-rnGKKYVISQCNNALLYPALGVACVLSRCKLLSDGMLKAAS 492 fission yeast
P78715    438 IFPLSNPTSRSECTAEEAVEFTDGNLIFASGSPFDPve-wkGKTIQTNQCNNSYSFPGIGLGLVSSRATRVPFETFQVCA 516 Neocallimastix fro...
AAF12481  428 VFPLSNPTAHSEALPEDILRWTDGAAIVATGSPFAPve-hgGQTHEIGQGNNAFIFPGLGFGAILARVREITDEMVTEAA 506 Deinococcus radiod...
YP_065939 419 IFPLSNPTHMAEAQPKDIYAWTNGQALVATGSPFAPve-hdGKTSRIGQCNNVFVFPGVGLGVLASGAREVLPEFFTAAA 497 Desulfotalea psych...
CAG22269  429 VFPLSNPTANCEALPEDVYQWSDGQVIVATGSPFSDvn-ynGREYRIGQGNNVFIFPGVGLASIVSGTPKITLDMFTMAS 507 Photobacterium pro...
P36013    494 IFPLSNPTRLHEAVPADLMKWTNNNALVATGSPFPP-----VDGYRISENNNCYSFPGIGLGAVLSRATTITDKMISAAV 568 baker's yeast
EAL20292  468 IFPMSNPTALCEVDPADALAWTENRALVATGSPFPPvqlgnGQEYIVAQTNNALIYPALGLGAILARSKTISNSMLMAGV 547 Cryptococcus neofo...
AAA92715  415 IMPLSNPTPKAEATPHDVYLWSNGKALCATGSPFPAeq-vnGRKIITAQANNSWIFPAVGYALVTTQARHCPPKVFEIAA 493 Trichomonas vaginalis
AAC47396  409 VLALSNPTEKCECTFAECMEYTNNTAYYASGSLMPSltlpnGTTIQPAQCNNFYVFPGIGLGAYVCRAKKITDEMITGVS 488 Giardia intestinalis
Feature 1                                                                                  
1QR6_A    496 KALTSQLTdee-laqGRLYPPLANIQEVSINIAIKVTEYLYa-NKXAFrypep----------edkaKYVKERTWRS 560 human
P40375    493 DALATVPRslf-aadEALLPDLNNAREISRHIVFAVLKQAVs-EGMSTvdlpkd--------daklkEWIIEREWNP 559 fission yeast
P78715    517 RVIASLGTpem-latGKIFPDLDNLRAVSLEVGIEVAKMAEr-MNIATqfppk---------gmdwrEWLKHNMWQP 582 Neocallimastix frontalis
AAF12481  507 YALADYTQah---hpGRTYPPVNELSQASVQVAVAVIKQAIk-DGVATefsvrrl------sdgelrAFVERKFWEP 573 Deinococcus radiodura...
YP_065939 498 YAVSNSLSqea-ldrGCLVPEVSEISKVSEKVALAVATCAIe-HGVSRpcvysdfsh--nndparmkVLISKMRWSP 570 Desulfotalea psychrop...
CAG22269  508 YALADCISddd-laaGCVFPRISKLKEVSMVVATRILENMQttEPNSPlrgk------------niqQELAMHMWEP 571 Photobacterium profun...
P36013    569 DQLAELSPlregdsrPGLLPGLDTITNTSARLATAVILQALe-EGTARieqeqvpggapgetvkvprDFDECLQWVK 644 baker's yeast
EAL20292  548 NSLASLSPals-nseASLLPDLADVRKVSVDVAAAVVRQAVe-DGNAYdentikyvk--gkgdvsleEYIRSRMWDA 620 Cryptococcus neoforma...
AAA92715  494 ESLASLVKked-hdqGNLLPPLNKIREYSFGIAYDVSKYLId-NVLATavppk---------gtslkDWLKAQLFEP 559 Trichomonas vaginalis
AAC47396  489 GALAQMVPeek-lrrGELLPDLDEIREISCQCALGLIRIAEk-QGQSRrilpss--------dtellAQLRDTQWSP 555 Giardia intestinalis

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