1LUA,1LU9


Conserved Protein Domain Family
NAD_bind_H4MPT_DH

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cd01078: NAD_bind_H4MPT_DH 
Click on image for an interactive view with Cn3D
NADP binding domain of methylene tetrahydromethanopterin dehydrogenase
Methylene Tetrahydromethanopterin Dehydrogenase (H4MPT DH) NADP binding domain. NADP-dependent H4MPT DH catalyzes the dehydrogenation of methylene- H4MPT and methylene-tetrahydrofolate (H4F) with NADP+ as cofactor. H4F and H4MPT are both cofactors that carry the one-carbon units between the formyl and methyl oxidation level. H4F and H4MPT are structurally analogous to each other with respect to the pterin moiety, but each has distinct side chain. H4MPT is present only in anaerobic methanogenic archaea and aerobic methylotrophic proteobacteria. H4MPT seems to have evolved independently from H4F and functions as a distinct carrier in C1 metabolism. 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: 133446
View PSSM: cd01078
Aligned: 11 rows
Threshold Bit Score: 164.874
Threshold Setting Gi: 53802885
Created: 30-Apr-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
NADP binding
Conserved site includes 15 residues -Click on image for an interactive view with Cn3D
Feature 1:NADP binding site [chemical binding site]
Evidence:

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1         #    #                                ####                    #    #           
1LUA_A        95 SNGSNTTAAAGVALVVKAAg------gSVKGKKAVVLAGTGPVGMRSAALLAGE-GAEVVLCGRKL-DKAQAAADSVn-k 165 Methylobacteriu...
1LU9_A        95 SNGSNTTAAAGVALVVKAAg------gSVKGKKAVVLAGTGPVGMRSAALLAGE-GAEVVLCGRKL-DKAQAAADSVn-k 165 Methylobacteriu...
O85012        96 PAGSFTTGAAMVAEVNRALkar--fstDLKGKRIVIFGGAGVVAYVAAVIGALE-GAQTVLVGHDGeERVSKIAFTMk-w 171 Methylobacteriu...
NP_869351    110 ASGCNTTAAAAVASASKHV--------SLNGCTAVVLGGTGPVGRRVAQMLARQ-NADVLLTSRSL-NRAEIACKEIgeh 179 Pirellula sp. 1
YP_001022447  95 SNGSNTTAAAGVAWLAHGR--------SLAGKRAVVLAGTGPVGQRAAVMLAKE-GARVAITSRTL-ERAQAAARAIa-e 163 Methylibium pet...
YP_113027     95 SNGSNTTAAAGVAKLASSG--------TLAGKKAVVLAGTGPVGQRAAVMLAKEgCSEVVITSRQM-ARAEHACAEMk-a 164 Methylococcus c...
AAS87052     100 SNGSNTTAAAAVRAAGRHL--------DLSRANSLVLGGTGPVGQRVARLLARA-GGNVRLGSRQK-ERAEAVCAVIrah 169 Gemmata sp. Wa1-1
ZP_01088550   97 PNGANTTAAAAVLAAGRHL--------QLAGSETLVLAGTGPVGQRAARLLAQQ-GAHVRVASRRL-EKATKVCESLqae 166 Blastopirellula...
YP_115406     89 PSGAFTTAAAMVAMAEGELrkh--yqtGLEGKSVLALGGTGPVGQIAAVLAARA-GAQVKIIGRQL-EKAQKVATLCn-a 163 Methylococcus c...
AAM25513     124 TTGNSYTVATAIEGAIKAAelm---gkDVRDSHVVVIGATGSIGKVCAEILSRD-AKYMTLVARNK-EKLQNFRDYL--- 195 Thermoanaerobac...
YP_004162    336 TNGGAYTAGTVRAAIPKILahfaqsgkDLKGATAAVVGANGVVAFGIARQIAPL-VGRLILVGRDL-ERLKRAAESLr-- 411 Thermus thermop...
Feature 1                                     #### #                     #                       
1LUA_A       166 RFKVNVTAAETADDASRAEAVkgAHFVFTAGAIGLe--lLPQAAWQNEssIEIVADYNAQPPLGIGGIDATDKGkeyg-- 241 Methylobacteriu...
1LU9_A       166 RFKVNVTAAETADDASRAEAVkgAHFVFTAGAIGLe--lLPQAAWQNEssIEIVADYNAQPPLGIGGIDATDKGkeyg-- 241 Methylobacteriu...
O85012       172 RFGIDVGAVDGTLPEARRAAItdADVILSAGPAGVsiltAEDLESAPK--LLVASDVNAVPPAGIAGIDVNAVDvplpt- 248 Methylobacteriu...
NP_869351    180 VNSGNLEAAAPETPDDFRALLerADVIIASGAAGVel-aSKELIDSLSk-LRVAIDLNAVPPAGLGGVEAFDKAkllheg 257 Pirellula sp. 1
YP_001022447 164 RFKIEVDAIEADDNAARARAIegANLVFATGAAGVa--lLDEAAWKDHpqLELLSDANATPTLGIEGIDMMDKGaqrh-- 239 Methylibium pet...
YP_113027    165 RFGVDLVPVEAFDDDARAAAIadAQIVFATGAAGVr--lLEECHWRDRpdLELLADANATPPLGLGGTDMMDRGtdrh-- 240 Methylococcus c...
AAS87052     170 VPGADIQAVSVASSSDAPTALdgRNLVVAAGAAGAvl-lPKKLRLACKs-LKVAIDLNGVPPAGIEGVELPDKAadrd-- 245 Gemmata sp. Wa1-1
ZP_01088550  167 VADGAFRPFAVSDDDSLKAALngVAVVIAAGAANVrlagQENLRQAAD--LQVLIDLNAAPPVGLEGVDPMDKAqdrd-- 242 Blastopirellula...
YP_115406    164 EFGEGQTAIEGDADANKGELLktADVVFATAAAGIqvlsAELLAASPR--LKVAADVNAVPPSGIAGLDPHHKGtpie-- 239 Methylococcus c...
AAM25513     196 MQKTGMSAHITSDVKEALEDA--DIIITVTSAVDT----VIKPEYLKP--GAVVCDVARPRDVSKEVADKRDDVlviegg 267 Thermoanaerobac...
YP_004162    412 KNLERKGEVPEILATTEIAAIreADLVFTATSDPN----PVIYPEHVKp-GAWIYDEGVPPDVHPSVREVPGVRvi---- 482 Thermus thermop...
Feature 1                        #                                            
1LUA_A       242 ---gkraFGALGIGGLKLKLHRACIAKLFEs--sEGVFD-----------AEEIYKLAKEM 286 Methylobacterium extorquens
1LU9_A       242 ---gkraFGALGIGGLKLKLHRACIAKLFEs--sEGVFD-----------AEEIYKLAKEM 286 Methylobacterium extorquens
O85012       249 --gkgvgIGALAVGNVKYQTQCRMFRKMLEaq-ePLCLD-----------FRDAYKLAVEI 295 Methylobacterium extorquens
NP_869351    258 dedgpvaYGPIGVGGLKMRTHKAAIAKLFTs--nSLVLD-----------ADEIYDLTIEQ 305 Pirellula sp. 1
YP_001022447 240 ---gktvFGAIGFGALKIALHRACIARMFEq--qDLVLD-----------GEEIYAIAKTM 284 Methylibium petroleiphilum PM1
YP_113027    241 ---gkivWGAIGFGTLKLAVHRACIAKLFEr--nDQVFD-----------AEEIFALAKTM 285 Methylococcus capsulatus str. Bath
AAS87052     246 ---ghvcYGALGVGGTKMKVHRAAINKLFEs--nNAVLD-----------IEEVYSLALQL 290 Gemmata sp. Wa1-1
ZP_01088550  243 ---gricYGAIGVGGTKMKIHKRALARLFEq--nDLVLN-----------AEEVYAIGRTL 287 Blastopirellula marina DSM 3645
YP_115406    240 ----gspSGAIGIGALAIGNVKYQAQHRLL----LRMRS-----------TDKPVYLAFNE 281 Methylococcus capsulatus str. Bath
AAM25513     268 vvevpgdVDFHFNFGFPPKTSYACMAETMIlameGRIENyslgrdltveqVDEIARLAKKH 328 Thermoanaerobacter tengcongensis MB4
YP_004162    483 ------pGGVVRLPGEARATLDLHFGAPDQv---PACLAetm-----ilaAEEAFDRKSLG 529 Thermus thermophilus HB27

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