1VL6,2A9F


Conserved Protein Domain Family
NAD_bind_2_malic_enz

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cd05311: NAD_bind_2_malic_enz 
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NAD(P) binding domain of malic enzyme (ME), subgroup 2
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 primarily of archaeal 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: 133453
View PSSM: cd05311
Aligned: 22 rows
Threshold Bit Score: 236.395
Threshold Setting Gi: 19554200
Created: 30-Aug-2005
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
putative NAD(P)
Conserved site includes 15 residues -Click on image for an interactive view with Cn3D
Feature 1:putative NAD(P) binding site [chemical binding site]
Evidence:

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                     ####                     ##                     
1VL6_D    168 QQGTAVVVSAAFLNALKLTEKKIEEVKVVVNGIGAAGYNIVKFLLDLGVk--NVVAVDRKGILNEndpetclneyHLEIA 245 Thermotoga maritim...
BAA19451  176 QHGTAIITVAGLLNSFKLTGKNPDDVKVVICGAGAAGIAIAELIQHIGIkkeQIFLVDTKGVIHHnr------ndLNDSK 249 Leptospira interro...
AAQ65499  163 QHGTAIISSAGLINALMIAGKKIEDVRIVVNGAGASAFSCTKLYESFGArreNILMLDSKGVITAdr------tdLTEQK 236 Porphyromonas ging...
NP_623869 160 QHGTAIVTFAALVNALKIVKKSLYEIVAVVNGAGAAGVAISKFLVNAGVk--DVIVCDRSGIIYEgrkd--ldssKQKIA 235 Thermoanaerobacter...
NP_273713 163 QHGTAIITAAAVLNALRFTGRKIEEATLVCSGAGAAAIACLNQLLDLGLkreNVTVCDSKGVIYQtred---kdrMDESK 239 Neisseria meningit...
NP_863831 237 QHGTAIVVLAGLKNSLLRVGKALPNIRIVVNGAGAAGTAIVKLLLISGAk--DIVVCDRDGAIHAgepsq-pdasKQWIA 313 Pirellula sp. 1
NP_616662 151 QHGAAIVVFAGLLNALKIVKKELGELKILITGLGAAGVAIFRFLVRAGAdpaKILTCDSQGIVYEgrekd-mnpiKAEIA 229 Methanosarcina ace...
AAG19885  161 QHGTAIISGAALLNAAEIAGKDLSDLDVVFSGAGASAIATAKFYVSLGVdreHITMCDSSGVITEdr-------dVNEFK 233 Halobacterium sp. ...
Q9ZDF6    166 QHGTAIITAAGLINAAYLTNRTLKDLKIVINGAGAAAIACIDLLIALGVdksKIILCDTKGVIYKgrt-----sgMNKWK 240 Rickettsia prowazekii
P76558    163 QHGTAIISTAAILNGLRVVEKNISDVRMVVSGAGAAAIACMNLLVALGLqkhNIVVCDSKGVIYQgre-----pnMAETK 237 Escherichia coli
Feature 1                                 ##   #                 ###                      #   
1VL6_D    246 RITn--pERLSg--dLETALEGADFFIGVSrGNILKPEWIKKXSRKPVIFALANPVPEIDPELAREAGAf--IVATGRSD 319 Thermotoga maritim...
BAA19451  250 KKYi---QKTDst-tLRDVMKGSDIFIGVSvENMVDEDMVRSMSKNPVIFALANPDPEIPYRVAKAVRSd-lIMGTGRSD 324 Leptospira interro...
AAQ65499  237 RYFa--tERTDvh-tLAEAIAGADVFVGLSrPNVLTQDMVRTMAPNPIVFALANPNPEITYEQATAAREd-iIMATGRSD 312 Porphyromonas ging...
NP_623869 236 KITn--kKKIKg--tLKEALEGADVFIGVSgPNLLTKEMVKKMAKKPIVFALANPVPEIHPEEAKEAGAy--VVGTGRSD 309 Thermoanaerobacter...
NP_273713 240 QFYa--iEDNGqr-vLADAVKGKDIFLGLSgANLLTPEILNTMNEKPIVFAMANPNPEILPPLAKETRPd-vVIGTGRSD 315 Neisseria meningit...
NP_863831 314 DNTn--pRGASg--kLSEVIQGADVFIGVSaPNVLQTEDVAAMAADPIVFALANPDPEILPANAAPHVR---IMATGRSD 386 Pirellula sp. 1
NP_616662 230 TLTnpgkLKGG----LKEAFPGTDLFIGVSvGGIVTEEMISSMANDAIVMAMANPTPEIMPDAAKRAGAr--IVATGRSD 303 Methanosarcina ace...
AAG19885  234 AAFa---QPADsggdLADAMAGADVFVGLSvGGIVNQAMVRSMADDPIVFAMANPDPEIDYESAKAAREdtvIMATGRSD 310 Halobacterium sp. ...
Q9ZDF6    241 ERYa---SDTKir-tLTESLNNADVFIGLSvKGAVTKDMISKMAHKPIIFAMANPDPEITPEDIKFVRDd-aIIATGRSD 315 Rickettsia prowazekii
P76558    238 AAYa--vVDDGkr-tLDDVIEGADIFLGCSgPKVLTQEMVKKMARAPMILALANPEPEILPPLAKEVRPd-aIICTGRSD 313 Escherichia coli
Feature 1         # #                                                                         
1VL6_D    320 HPNQVNNLLAFPGIXKGAVEKR-SKITKNXLLSAVEAIARSCEPe-----------------pERIIPEAfdxkVHLNVY 381 Thermotoga maritim...
BAA19451  325 NPNQVNNVLGFPFIFRGALDVRaRHITLEMKLAAARSLAELARLevpevvskayggekftfgpEYLIPKPfdkrVLFHVA 404 Leptospira interro...
AAQ65499  313 YPNQINNVIGFPYIFRGALDVSaKAINEEMKRAATMAIADLAREtvpdevlraygntqlhfgkDYFIPKPvdprLIVRVS 392 Porphyromonas ging...
NP_623869 310 FPNQVNNVLAFPGVFKGALRVRaTTINERMKLAAAYAIANTISEeel--------------ssEYILPKPfdkrVAENVA 375 Thermoanaerobacter...
NP_273713 316 FPNQVNNVLCFPFIFRGALDVGaTTINEEMKRACVYALADLAMEevteevvaa-ygkkfefgaEYLIPTPfdsrLLPRVA 394 Neisseria meningit...
NP_863831 387 FPNQINNVLCFPGLFRGVLDVRaTTINNEMKLAAAEAIAATIPEsdl--------------ldDYVIPSVfdrrVAKVVA 452 Pirellula sp. 1
NP_616662 304 FPNQLNNCLSFPGVFKGALGTCaRKITPEMEMAAAHALANVVSVgel--------------seDYIIPEPldkhVVPAVA 369 Methanosarcina ace...
AAG19885  311 YPNQVNNVLGFPFIFRGALDVRaTDINEEMKVAAATALADLAKQdvpdevvkaygdqplqfgsEYIIPKPldprVLFEVA 390 Halobacterium sp. ...
Q9ZDF6    316 YNNQVNNVMGFPYIFRGALDVRaSTINTEMKIAAARAIADLARRpvpeevykaysgrkmvfgnEYIIPVPfdprLITVVA 395 Rickettsia prowazekii
P76558    314 YPNQVNNVLCFPFIFRGALDVGaTAINEEMKLAAVRAIAELAHAeqsevvasaygdqdlsfgpEYIIPKPfdprLIVKIA 393 Escherichia coli
Feature 1            
1VL6_D    382 TAVKGSA 388 Thermotoga maritima MSB8
BAA19451  405 PAVAEAA 411 Leptospira interrogans
AAQ65499  393 TAVARAA 399 Porphyromonas gingivalis W83
NP_623869 376 YAVAKEA 382 Thermoanaerobacter tengcongensis MB4
NP_273713 395 TAAAKAA 401 Neisseria meningitidis MC58
NP_863831 453 QAVAKAA 459 Pirellula sp. 1
NP_616662 370 KAVANAS 376 Methanosarcina acetivorans C2A
AAG19885  391 PAVADAA 397 Halobacterium sp. NRC-1
Q9ZDF6    396 TAVAVAA 402 Rickettsia prowazekii
P76558    394 PAVAKAA 400 Escherichia coli

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