1VL6,2A9F


Conserved Protein Domain Family
NAD_bind_2_malic_enz

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cd05311: NAD_bind_2_malic_enz 
Click on image for an interactive view with Cn3D
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: 17-Jan-2013
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:
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                       ####                     ##                     
1VL6_D      168 QQGTAVVVSAAFLNALKLTEKKIEEVKVVVNGIGAAGYNIVKFLLDLGVk--NVVAVDRKGILNEndpetclneyHLEIA 245
gi 1902828  176 QHGTAIITVAGLLNSFKLTGKNPDDVKVVICGAGAAGIAIAELIQHIGIkkeQIFLVDTKGVIHHnr------ndLNDSK 249
gi 34396433 163 QHGTAIISSAGLINALMIAGKKIEDVRIVVNGAGASAFSCTKLYESFGArreNILMLDSKGVITAdr------tdLTEQK 236
gi 20808698 160 QHGTAIVTFAALVNALKIVKKSLYEIVAVVNGAGAAGVAISKFLVNAGVk--DVIVCDRSGIIYEgrkd--ldssKQKIA 235
gi 15676569 163 QHGTAIITAAAVLNALRFTGRKIEEATLVCSGAGAAAIACLNQLLDLGLkreNVTVCDSKGVIYQtred---kdrMDESK 239
gi 32470838 237 QHGTAIVVLAGLKNSLLRVGKALPNIRIVVNGAGAAGTAIVKLLLISGAk--DIVVCDRDGAIHAgepsq-pdasKQWIA 313
gi 20090587 151 QHGAAIVVFAGLLNALKIVKKELGELKILITGLGAAGVAIFRFLVRAGAdpaKILTCDSQGIVYEgrekd-mnpiKAEIA 229
gi 10581097 161 QHGTAIISGAALLNAAEIAGKDLSDLDVVFSGAGASAIATAKFYVSLGVdreHITMCDSSGVITEdr-------dVNEFK 233
gi 6685636  166 QHGTAIITAAGLINAAYLTNRTLKDLKIVINGAGAAAIACIDLLIALGVdksKIILCDTKGVIYKgrt-----sgMNKWK 240
gi 6685630  163 QHGTAIISTAAILNGLRVVEKNISDVRMVVSGAGAAAIACMNLLVALGLqkhNIVVCDSKGVIYQgre-----pnMAETK 237
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                   ##   #                 ###                      #   
1VL6_D      246 RITn--pERLSg--dLETALEGADFFIGVSrGNILKPEWIKKXSRKPVIFALANPVPEIDPELAREAGAf--IVATGRSD 319
gi 1902828  250 KKYi---QKTDst-tLRDVMKGSDIFIGVSvENMVDEDMVRSMSKNPVIFALANPDPEIPYRVAKAVRSd-lIMGTGRSD 324
gi 34396433 237 RYFa--tERTDvh-tLAEAIAGADVFVGLSrPNVLTQDMVRTMAPNPIVFALANPNPEITYEQATAAREd-iIMATGRSD 312
gi 20808698 236 KITn--kKKIKg--tLKEALEGADVFIGVSgPNLLTKEMVKKMAKKPIVFALANPVPEIHPEEAKEAGAy--VVGTGRSD 309
gi 15676569 240 QFYa--iEDNGqr-vLADAVKGKDIFLGLSgANLLTPEILNTMNEKPIVFAMANPNPEILPPLAKETRPd-vVIGTGRSD 315
gi 32470838 314 DNTn--pRGASg--kLSEVIQGADVFIGVSaPNVLQTEDVAAMAADPIVFALANPDPEILPANAAPHVR---IMATGRSD 386
gi 20090587 230 TLTnpgkLKGG----LKEAFPGTDLFIGVSvGGIVTEEMISSMANDAIVMAMANPTPEIMPDAAKRAGAr--IVATGRSD 303
gi 10581097 234 AAFa---QPADsggdLADAMAGADVFVGLSvGGIVNQAMVRSMADDPIVFAMANPDPEIDYESAKAAREdtvIMATGRSD 310
gi 6685636  241 ERYa---SDTKir-tLTESLNNADVFIGLSvKGAVTKDMISKMAHKPIIFAMANPDPEITPEDIKFVRDd-aIIATGRSD 315
gi 6685630  238 AAYa--vVDDGkr-tLDDVIEGADIFLGCSgPKVLTQEMVKKMARAPMILALANPEPEILPPLAKEVRPd-aIICTGRSD 313
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1           # #                                                                         
1VL6_D      320 HPNQVNNLLAFPGIXKGAVEKR-SKITKNXLLSAVEAIARSCEPe-----------------pERIIPEAfdxkVHLNVY 381
gi 1902828  325 NPNQVNNVLGFPFIFRGALDVRaRHITLEMKLAAARSLAELARLevpevvskayggekftfgpEYLIPKPfdkrVLFHVA 404
gi 34396433 313 YPNQINNVIGFPYIFRGALDVSaKAINEEMKRAATMAIADLAREtvpdevlraygntqlhfgkDYFIPKPvdprLIVRVS 392
gi 20808698 310 FPNQVNNVLAFPGVFKGALRVRaTTINERMKLAAAYAIANTISEeel--------------ssEYILPKPfdkrVAENVA 375
gi 15676569 316 FPNQVNNVLCFPFIFRGALDVGaTTINEEMKRACVYALADLAMEevteevvaa-ygkkfefgaEYLIPTPfdsrLLPRVA 394
gi 32470838 387 FPNQINNVLCFPGLFRGVLDVRaTTINNEMKLAAAEAIAATIPEsdl--------------ldDYVIPSVfdrrVAKVVA 452
gi 20090587 304 FPNQLNNCLSFPGVFKGALGTCaRKITPEMEMAAAHALANVVSVgel--------------seDYIIPEPldkhVVPAVA 369
gi 10581097 311 YPNQVNNVLGFPFIFRGALDVRaTDINEEMKVAAATALADLAKQdvpdevvkaygdqplqfgsEYIIPKPldprVLFEVA 390
gi 6685636  316 YNNQVNNVMGFPYIFRGALDVRaSTINTEMKIAAARAIADLARRpvpeevykaysgrkmvfgnEYIIPVPfdprLITVVA 395
gi 6685630  314 YPNQVNNVLCFPFIFRGALDVGaTAINEEMKLAAVRAIAELAHAeqsevvasaygdqdlsfgpEYIIPKPfdprLIVKIA 393

                ....*..
Feature 1              
1VL6_D      382 TAVKGSA 388
gi 1902828  405 PAVAEAA 411
gi 34396433 393 TAVARAA 399
gi 20808698 376 YAVAKEA 382
gi 15676569 395 TAAAKAA 401
gi 32470838 453 QAVAKAA 459
gi 20090587 370 KAVANAS 376
gi 10581097 391 PAVADAA 397
gi 6685636  396 TAVAVAA 402
gi 6685630  394 PAVAKAA 400

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