Functional Diversification of Tripeptidyl Peptidase and Endopeptidase Sedolisins in Fungi

AbstractSedolisins are acid proteases that are related to the basic subtilisins. They have been identified in all three superkingdoms but are not ubiquitous, although fungi that secrete acids as part of their lifestyle can have up to six paralogs. Both tripeptidyl peptidase (TPP) and endopeptidase activity have been identified and it has been suggested that these correspond to separate subfamilies.We studied eukaryotic sedolisins by computational analysis. A maximum likelihood tree shows three major clades of which two contain only fungal sequences. One fungal clade contains all known TPPs whereas the other contains the endosedolisins. We identified four cluster specific inserts (CSIs) in endosedolisins, of which CSIs 1, 3 and 4 appear as solvent exposed according to structure modeling. Part of CSI2 is exposed but a short stretch forms a novel and partially buried α-helix that induces a conformational change near the binding pocket. We also identified a total of 12 specificity determining positions (SDPs) divided over three SDP sub-networks. The major SDP network contains eight directly connected SDPs and modeling of virtual mutants suggests a key role for the W307A or F307A substitution. This substitution is accompanied by a group of four SDPs that physically interact at the interface of the catalytic domain and the enzyme’s prosegment. Modeling of virtual mutants suggests these SDPs are indeed required to compensate the conformational change induced by CSI2 and the A307. The additional major network SDPs as well as the two small SDP networks appear to be linked to this major substitution, all together explaining the hypothesized functional diversification of fungal sedolisins.HighlightsThere are two sedolisin subfamilies in fungi: tripeptidyl peptidases and endopeptidasesFunctional Diversification of fungal sedolisins led to a conformational change in the pocketFunctional Diversification centers around buried SDP307SDP307 is aromatic in TPPs and Alanine in endosedolisinsAdditional SDPs affect the interaction between core and chaperone-like prosegment

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Kinetic and structural analysis of human ALDH9A1

Bioscience Reports ◽

10.1042/bsr20190558 ◽

2019 ◽

Vol 39 (4) ◽

Cited By ~ 3

Author(s):

Radka Končitíková ◽

Armelle Vigouroux ◽

Martina Kopečná ◽

Marek Šebela ◽

Solange Moréra ◽

...

Keyword(s):

Metabolic Pathways ◽

Catalytic Domain ◽

Aromatic Aldehydes ◽

Binding Pocket ◽

Kinetic Properties ◽

Crystal Forms ◽

Dimer Interface ◽

Aldehyde Dehydrogenases ◽

Α Helix ◽

Oligomerization Domain

Abstract Aldehyde dehydrogenases (ALDHs) constitute a superfamily of NAD(P)+-dependent enzymes, which detoxify aldehydes produced in various metabolic pathways to the corresponding carboxylic acids. Among the 19 human ALDHs, the cytosolic ALDH9A1 has so far never been fully enzymatically characterized and its structure is still unknown. Here, we report complete molecular and kinetic properties of human ALDH9A1 as well as three crystal forms at 2.3, 2.9, and 2.5 Å resolution. We show that ALDH9A1 exhibits wide substrate specificity to aminoaldehydes, aliphatic and aromatic aldehydes with a clear preference for γ-trimethylaminobutyraldehyde (TMABAL). The structure of ALDH9A1 reveals that the enzyme assembles as a tetramer. Each ALDH monomer displays a typical ALDHs fold composed of an oligomerization domain, a coenzyme domain, a catalytic domain, and an inter-domain linker highly conserved in amino-acid sequence and folding. Nonetheless, structural comparison reveals a position and a fold of the inter-domain linker of ALDH9A1 never observed in any other ALDH so far. This unique difference is not compatible with the presence of a bound substrate and a large conformational rearrangement of the linker up to 30 Å has to occur to allow the access of the substrate channel. Moreover, the αβE region consisting of an α-helix and a β-strand of the coenzyme domain at the dimer interface are disordered, likely due to the loss of interactions with the inter-domain linker, which leads to incomplete β-nicotinamide adenine dinucleotide (NAD+) binding pocket.

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pH-Dependent Changes in Photoaffinity Labeling Patterns of the H1 Influenza Virus Hemagglutinin by Using an Inhibitor of Viral Fusion

Journal of Virology ◽

10.1128/jvi.73.3.1785-1794.1999 ◽

1999 ◽

Vol 73 (3) ◽

pp. 1785-1794 ◽

Cited By ~ 28

Author(s):

Christopher Cianci ◽

Kuo-Long Yu ◽

Douglas D. Dischino ◽

William Harte ◽

Milind Deshpande ◽

...

Keyword(s):

Conformational Change ◽

Binding Pocket ◽

Low Ph ◽

Cross Linking ◽

Viral Fusion ◽

Binding Characteristics ◽

Influenza Virus Hemagglutinin ◽

Attachment Sites ◽

Α Helix ◽

Ha Protein

ABSTRACT The hemagglutinin (HA) protein undergoes a low-pH-induced conformational change in the acidic milieu of the endosome, resulting in fusion of viral and cellular membranes. A class of compounds that specifically interact with the HA protein of H1 and H2 subtype viruses and inhibit this conformational change was recently described (G. X. Luo et al., Virology 226:66–76, 1996, and J. Virol. 71:4062–4070, 1997). In this study, purified HA trimers (bromelain-cleaved HA [BHA]) are used to examine the properties and binding characteristics of these inhibitors. Compounds were able to inhibit the low-pH-induced change of isolated trimers, as detected by resistance to digestion with trypsin. Protection from digestion was extremely stable, as BHA-inhibitor complexes could be incubated for 24 h in low pH with almost no change in BHA structure. One inhibitor was prepared as a radiolabeled photoaffinity analog and used to probe for specific drug interactions with the HA protein. Analysis of BHA after photoaffinity analog binding and UV cross-linking revealed that the HA2 subunit of the HA was specifically radiolabeled. Cross-linking of the photoaffinity analog to BHA under neutral (native) pH conditions identified a stretch of amino acids within the α-helix of HA2 that interact with the inhibitor. Interestingly, cross-linking of the analog under acidic conditions identified a different region within the HA2 N terminus which interacts with the photoaffinity compound. These attachment sites help to delineate a potential binding pocket and suggest a model whereby the BHA is able to undergo a partial, reversible structural change in the presence of inhibitor compound.

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Characterization of Recombinant Human Coagulation Factor XFriuli

Thrombosis and Haemostasis ◽

10.1055/s-0038-1650267 ◽

1996 ◽

Vol 75 (02) ◽

pp. 313-317 ◽

Cited By ~ 8

Author(s):

D J Kim ◽

A Girolami ◽

H L James

Keyword(s):

Catalytic Domain ◽

Coagulation Factor ◽

Molecular Size ◽

Binding Pocket ◽

Site Directed Mutagenesis ◽

Bleeding Tendency ◽

Factor X ◽

Amino Terminal ◽

Normal Plasma ◽

Plasma Factor

SummaryNaturally occurring plasma factor XFriuli (pFXFr) is marginally activated by both the extrinsic and intrinsic coagulation pathways and has impaired catalytic potential. These studies were initiated to obtain confirmation that this molecule is multi-functionally defective due to the substitution of Ser for Pro at position 343 in the catalytic domain. By the Nelson-Long site-directed mutagenesis procedure a construct of cDNA in pRc/CMV was derived for recombinant factor XFriuli (rFXFr) produced in human embryonic (293) kidney cells. The rFXFr was purified and shown to have a molecular size identical to that of normal plasma factor X (pFX) by gel electrophoretic, and amino-terminal sequencing revealed normal processing cleavages. Using recombinant normal plasma factor X (rFXN) as a reference, the post-translational y-carboxy-glutamic acid (Gla) and (β-hydroxy aspartic acid (β-OH-Asp) content of rFXFr was over 85% and close to 100%, respectively, of expected levels. The specific activities of rFXFr in activation and catalytic assays were the same as those of pFXFr. Molecular modeling suggested the involvement of a new H-bond between the side-chains of Ser-343 and Thr-318 as they occur in anti-parallel (3-pleated sheets near the substrate-binding pocket of pFXFr. These results support the conclusion that the observed mutation in pFXFr is responsible for its dysfunctional activation and catalytic potentials, and that it accounts for the moderate bleeding tendency in the homozygous individuals who possess this variant procoagulant.

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The insert within the catalytic domain of tripeptidyl-peptidase II is important for the formation of the active complex

European Journal of Biochemistry ◽

10.1046/j.1432-1033.2002.02783.x ◽

2002 ◽

Vol 269 (5) ◽

pp. 1438-1443 ◽

Cited By ~ 16

Author(s):

Birgitta Tomkinson ◽

Bairbre Ní Laoi ◽

Kimberly Wellington

Keyword(s):

Catalytic Domain ◽

Active Complex ◽

Tripeptidyl Peptidase ◽

Tripeptidyl Peptidase Ii

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The Crystal Structure of Shikimate Dehydrogenase (AroE) Reveals a Unique NADPH Binding Mode

Journal of Bacteriology ◽

10.1128/jb.185.14.4144-4151.2003 ◽

2003 ◽

Vol 185 (14) ◽

pp. 4144-4151 ◽

Cited By ~ 32

Author(s):

Sheng Ye ◽

Frank von Delft ◽

Alexei Brooun ◽

Mark W. Knuth ◽

Ronald V. Swanson ◽

...

Keyword(s):

Catalytic Domain ◽

Binding Pocket ◽

Binding Mode ◽

Sequence Motif ◽

Binary Complex ◽

Shikimate Dehydrogenase ◽

Conserved Residues ◽

Conserved Sequence ◽

Nicotinamide Mononucleotide ◽

Reversible Reduction

ABSTRACT Shikimate dehydrogenase catalyzes the NADPH-dependent reversible reduction of 3-dehydroshikimate to shikimate. We report the first X-ray structure of shikimate dehydrogenase from Haemophilus influenzae to 2.4-Å resolution and its complex with NADPH to 1.95-Å resolution. The molecule contains two domains, a catalytic domain with a novel open twisted α/β motif and an NADPH binding domain with a typical Rossmann fold. The enzyme contains a unique glycine-rich P-loop with a conserved sequence motif, GAGGXX, that results in NADPH adopting a nonstandard binding mode with the nicotinamide and ribose moieties disordered in the binary complex. A deep pocket with a narrow entrance between the two domains, containing strictly conserved residues primarily contributed by the catalytic domain, is identified as a potential 3-dehydroshikimate binding pocket. The flexibility of the nicotinamide mononucleotide portion of NADPH may be necessary for the substrate 3-dehydroshikimate to enter the pocket and for the release of the product shikimate.

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Structure–function analysis of water-soluble inhibitors of the catalytic domain of exotoxin A from Pseudomonas aeruginosa

Biochemical Journal ◽

10.1042/bj20041480 ◽

2005 ◽

Vol 385 (3) ◽

pp. 667-675 ◽

Cited By ~ 33

Author(s):

Susan P. YATES ◽

Patricia L. TAYLOR ◽

René JØRGENSEN ◽

Dana FERRARIS ◽

Jie ZHANG ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Diphtheria Toxin ◽

Catalytic Domain ◽

Competitive Inhibition ◽

Function Analysis ◽

Binding Pocket ◽

Ring Structure ◽

Water Soluble ◽

Exotoxin A ◽

Ic50 Values

The mono-ADPRT (mono-ADP-ribosyltransferase), Pseudomonas aeruginosa ETA (exotoxin A), catalyses the transfer of ADP-ribose from NAD+ to its protein substrate. A series of water-soluble compounds that structurally mimic the nicotinamide moiety of NAD+ was investigated for their inhibition of the catalytic domain of ETA. The importance of an amide locked into a hetero-ring structure and a core hetero-ring system that is planar was a trend evident by the IC50 values. Also, the weaker inhibitors have core ring structures that are less planar and thus more flexible. One of the most potent inhibitors, PJ34, was further characterized and shown to exhibit competitive inhibition with an inhibition constant Ki of 140 nM. We also report the crystal structure of the catalytic domain of ETA in complex with PJ34, the first example of a mono-ADPRT in complex with an inhibitor. The 2.1 Å (1 Å=0.1 nm) resolution structure revealed that PJ34 is bound within the nicotinamide-binding pocket and forms stabilizing hydrogen bonds with the main chain of Gly-441 and to the side-chain oxygen of Gln-485, a member of a proposed catalytic loop. Structural comparison of this inhibitor complex with diphtheria toxin (a mono-ADPRT) and with PARPs [poly(ADP-ribose) polymerases] shows similarity of the catalytic residues; however, a loop similar to that found in ETA is present in diphtheria toxin but not in PARP. The present study provides insight into the important features required for inhibitors that mimic NAD+ and their binding to the mono-ADPRT family of toxins.

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Effect of salts on conformational change of basic amphipathic peptides from β-structure to α-helix in the presence of phospholipid liposomes and their channel-forming ability

Biochimica et Biophysica Acta (BBA) - Biomembranes ◽

10.1016/0005-2736(93)90073-9 ◽

1993 ◽

Vol 1151 (1) ◽

pp. 76-82 ◽

Cited By ~ 29

Author(s):

Sannamu Lee ◽

Toshihide Iwata ◽

Hatsuyo Oyagi ◽

Haruhiko Aoyagi ◽

Motonori Ohno ◽

...

Keyword(s):

Conformational Change ◽

Amphipathic Peptides ◽

Phospholipid Liposomes ◽

Α Helix

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Crystal structure of microtubule affinity-regulating kinase 4 catalytic domain in complex with a pyrazolopyrimidine inhibitor

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x15024747 ◽

2016 ◽

Vol 72 (2) ◽

pp. 129-134 ◽

Cited By ~ 22

Author(s):

John S. Sack ◽

Mian Gao ◽

Susan E. Kiefer ◽

Joseph E. Myers ◽

John A. Newitt ◽

...

Keyword(s):

Crystal Structure ◽

Catalytic Domain ◽

Neurofibrillary Tangle ◽

Binding Pocket ◽

Atp Binding ◽

Activation Loop ◽

Serine Threonine Kinase ◽

Atp Binding Site ◽

Threonine Kinase ◽

Catalytic Loop

Microtubule-associated protein/microtubule affinity-regulating kinase 4 (MARK4) is a serine/threonine kinase involved in the phosphorylation of MAP proteins that regulate microtubule dynamics. Abnormal activity of MARK4 has been proposed to contribute to neurofibrillary tangle formation in Alzheimer's disease. The crystal structure of the catalytic and ubiquitin-associated domains of MARK4 with a potent pyrazolopyrimidine inhibitor has been determined to 2.8 Å resolution with anRworkof 22.8%. The overall structure of MARK4 is similar to those of the other known MARK isoforms. The inhibitor is located in the ATP-binding site, with the pyrazolopyrimidine group interacting with the inter-lobe hinge region while the aminocyclohexane moiety interacts with the catalytic loop and the DFG motif, forcing the activation loop out of the ATP-binding pocket.

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Chemical Footprinting Reveals Conformational Changes Following Activation of Factor XI

Thrombosis and Haemostasis ◽

10.1160/th17-09-0676 ◽

2018 ◽

Vol 118 (02) ◽

pp. 340-350 ◽

Cited By ~ 3

Author(s):

Ingrid Stroo ◽

J. Marquart ◽

Kamran Bakhtiari ◽

Tom Plug ◽

Alexander Meijer ◽

...

Keyword(s):

Conformational Change ◽

Conformational Changes ◽

Catalytic Domain ◽

Active Form ◽

Coagulation Factor ◽

Lysine Residue ◽

Factor Ix ◽

Factor Xi ◽

Lysine Residues ◽

Factor Xia

AbstractCoagulation factor XI is activated by thrombin or factor XIIa resulting in a conformational change that converts the catalytic domain into its active form and exposing exosites for factor IX on the apple domains. Although crystal structures of the zymogen factor XI and the catalytic domain of the protease are available, the structure of the apple domains and hence the interactions with the catalytic domain in factor XIa are unknown. We now used chemical footprinting to identify lysine residue containing regions that undergo a conformational change following activation of factor XI. To this end, we employed tandem mass tag in conjunction with mass spectrometry. Fifty-two unique peptides were identified, covering 37 of the 41 lysine residues present in factor XI. Two identified lysine residues that showed altered flexibility upon activation were mutated to study their contribution in factor XI stability or enzymatic activity. Lys357, part of the connecting loop between A4 and the catalytic domain, was more reactive in factor XIa but mutation of this lysine residue did not impact on factor XIa activity. Lys516 and its possible interactor Glu380 are located in the catalytic domain and are covered by the activation loop of factor XIa. Mutating Glu380 enhanced Arg369 cleavage and thrombin generation in plasma. In conclusion, we have identified novel regions that undergo a conformational change following activation. This information improves knowledge about factor XI and will contribute to development of novel inhibitors or activators for this coagulation protein.

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