Structure of the γ-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-γ-d-Glu

Insights into substrate recognition by NlpC/P60 cysteine peptidases

Qingping Xu, Polat Abdubek, Tamara Astakhova, Herbert L. Axelrod, Constantina Bakolitsa, Xiaohui Cai, Dennis Carlton, Connie Chen, Hsiu Ju Chiu, Michelle Chiu, Thomas Clayton, Debanu Das, Marc C. Deller, Lian Duan, Kyle Ellrott, Carol L. Farr, Julie Feuerhelm, Joanna C. Grant, Anna Grzechnik, Gye Won Han & 29 others Lukasz Jaroszewski, Kevin K. Jin, Heath E. Klock, Mark W. Knuth, Piotr Kozbial, S. Sri Krishna, Abhinav Kumar, Winnie W. Lam, David Marciano, Mitchell D. Miller, Andrew T. Morse, Edward Nigoghossian, Amanda Nopakun, Linda Okach, Christina Puckett, Ron Reyes, Henry J. Tien, Christine B. Trame, Henry Van Den Bedem, Dana Weekes, Tiffany Wooten, Andrew Yeh, Keith O. Hodgson, John Wooley, Marc André Elsliger, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, Ian A. Wilson

Research output: Contribution to journalArticle

40 Citations (Scopus)

Abstract

Dipeptidyl-peptidase VI from Bacillus sphaericus and YkfC from Bacillus subtilis have both previously been characterized as highly specific γ-D-glutamyl-L-diamino acid endopeptidases. The crystal structure of a YkfC ortholog from Bacillus cereus (BcYkfC) at 1.8 Å resolution revealed that it contains two N-terminal bacterial SH3 (SH3b) domains in addition to the C-terminal catalytic NlpC/P60 domain that is ubiquitous in the very large family of cell-wall-related cysteine peptidases. A bound reaction product (L-Ala-γ-D-Glu) enabled the identification of conserved sequence and structural signatures for recognition of L-Ala and γ-D-Glu and, therefore, provides a clear framework for understanding the substrate specificity observed in dipeptidyl-peptidase VI, YkfC and other NlpC/P60 domains in general. The first SH3b domain plays an important role in defining substrate specificity by contributing to the formation of the active site, such that only murein peptides with a free N-terminal alanine are allowed. A conserved tyrosine in the SH3b domain of the YkfC subfamily is correlated with the presence of a conserved acidic residue in the NlpC/P60 domain and both residues interact with the free amine group of the alanine. This structural feature allows the definition of a subfamily of NlpC/P60 enzymes with the same N-terminal substrate requirements, including a previously characterized cyanobacterial L-alanine-γ-D- glutamate endopeptidase that contains the two key components (an NlpC/P60 domain attached to an SH3b domain) for assembly of a YkfC-like active site.

Original languageEnglish (US)
Pages (from-to)1354-1364
Number of pages11
JournalActa Crystallographica Section F: Structural Biology and Crystallization Communications
Volume66
Issue number10
DOIs
StatePublished - Oct 2010
Externally publishedYes

Fingerprint

Bacillus cereus
Endopeptidases
Bacillus
cysteine
Dipeptidyl-Peptidases and Tripeptidyl-Peptidases
Alanine
Cysteine
Peptide Hydrolases
Bacilli
Substrate Specificity
acids
Acids
Catalytic Domain
Substrates
alanine
src Homology Domains
Peptidoglycan
Conserved Sequence
Bacillus subtilis
Reaction products

Keywords

  • γ-D-glutamyl-l-diamino acid endopeptidase
  • cell-wall recycling
  • cysteine peptidases
  • enzyme specificity
  • NlpC/P60
  • SH3b

ASJC Scopus subject areas

  • Biochemistry
  • Biophysics
  • Structural Biology
  • Genetics
  • Condensed Matter Physics

Cite this

Structure of the γ-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-γ-d-Glu : Insights into substrate recognition by NlpC/P60 cysteine peptidases. / Xu, Qingping; Abdubek, Polat; Astakhova, Tamara; Axelrod, Herbert L.; Bakolitsa, Constantina; Cai, Xiaohui; Carlton, Dennis; Chen, Connie; Chiu, Hsiu Ju; Chiu, Michelle; Clayton, Thomas; Das, Debanu; Deller, Marc C.; Duan, Lian; Ellrott, Kyle; Farr, Carol L.; Feuerhelm, Julie; Grant, Joanna C.; Grzechnik, Anna; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K.; Klock, Heath E.; Knuth, Mark W.; Kozbial, Piotr; Krishna, S. Sri; Kumar, Abhinav; Lam, Winnie W.; Marciano, David; Miller, Mitchell D.; Morse, Andrew T.; Nigoghossian, Edward; Nopakun, Amanda; Okach, Linda; Puckett, Christina; Reyes, Ron; Tien, Henry J.; Trame, Christine B.; Van Den Bedem, Henry; Weekes, Dana; Wooten, Tiffany; Yeh, Andrew; Hodgson, Keith O.; Wooley, John; Elsliger, Marc André; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A.

In: Acta Crystallographica Section F: Structural Biology and Crystallization Communications, Vol. 66, No. 10, 10.2010, p. 1354-1364.

Research output: Contribution to journalArticle

Xu, Q, Abdubek, P, Astakhova, T, Axelrod, HL, Bakolitsa, C, Cai, X, Carlton, D, Chen, C, Chiu, HJ, Chiu, M, Clayton, T, Das, D, Deller, MC, Duan, L, Ellrott, K, Farr, CL, Feuerhelm, J, Grant, JC, Grzechnik, A, Han, GW, Jaroszewski, L, Jin, KK, Klock, HE, Knuth, MW, Kozbial, P, Krishna, SS, Kumar, A, Lam, WW, Marciano, D, Miller, MD, Morse, AT, Nigoghossian, E, Nopakun, A, Okach, L, Puckett, C, Reyes, R, Tien, HJ, Trame, CB, Van Den Bedem, H, Weekes, D, Wooten, T, Yeh, A, Hodgson, KO, Wooley, J, Elsliger, MA, Deacon, AM, Godzik, A, Lesley, SA & Wilson, IA 2010, 'Structure of the γ-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-γ-d-Glu: Insights into substrate recognition by NlpC/P60 cysteine peptidases', Acta Crystallographica Section F: Structural Biology and Crystallization Communications, vol. 66, no. 10, pp. 1354-1364. https://doi.org/10.1107/S1744309110021214
Xu, Qingping ; Abdubek, Polat ; Astakhova, Tamara ; Axelrod, Herbert L. ; Bakolitsa, Constantina ; Cai, Xiaohui ; Carlton, Dennis ; Chen, Connie ; Chiu, Hsiu Ju ; Chiu, Michelle ; Clayton, Thomas ; Das, Debanu ; Deller, Marc C. ; Duan, Lian ; Ellrott, Kyle ; Farr, Carol L. ; Feuerhelm, Julie ; Grant, Joanna C. ; Grzechnik, Anna ; Han, Gye Won ; Jaroszewski, Lukasz ; Jin, Kevin K. ; Klock, Heath E. ; Knuth, Mark W. ; Kozbial, Piotr ; Krishna, S. Sri ; Kumar, Abhinav ; Lam, Winnie W. ; Marciano, David ; Miller, Mitchell D. ; Morse, Andrew T. ; Nigoghossian, Edward ; Nopakun, Amanda ; Okach, Linda ; Puckett, Christina ; Reyes, Ron ; Tien, Henry J. ; Trame, Christine B. ; Van Den Bedem, Henry ; Weekes, Dana ; Wooten, Tiffany ; Yeh, Andrew ; Hodgson, Keith O. ; Wooley, John ; Elsliger, Marc André ; Deacon, Ashley M. ; Godzik, Adam ; Lesley, Scott A. ; Wilson, Ian A. / Structure of the γ-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-γ-d-Glu : Insights into substrate recognition by NlpC/P60 cysteine peptidases. In: Acta Crystallographica Section F: Structural Biology and Crystallization Communications. 2010 ; Vol. 66, No. 10. pp. 1354-1364.
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abstract = "Dipeptidyl-peptidase VI from Bacillus sphaericus and YkfC from Bacillus subtilis have both previously been characterized as highly specific γ-D-glutamyl-L-diamino acid endopeptidases. The crystal structure of a YkfC ortholog from Bacillus cereus (BcYkfC) at 1.8 {\AA} resolution revealed that it contains two N-terminal bacterial SH3 (SH3b) domains in addition to the C-terminal catalytic NlpC/P60 domain that is ubiquitous in the very large family of cell-wall-related cysteine peptidases. A bound reaction product (L-Ala-γ-D-Glu) enabled the identification of conserved sequence and structural signatures for recognition of L-Ala and γ-D-Glu and, therefore, provides a clear framework for understanding the substrate specificity observed in dipeptidyl-peptidase VI, YkfC and other NlpC/P60 domains in general. The first SH3b domain plays an important role in defining substrate specificity by contributing to the formation of the active site, such that only murein peptides with a free N-terminal alanine are allowed. A conserved tyrosine in the SH3b domain of the YkfC subfamily is correlated with the presence of a conserved acidic residue in the NlpC/P60 domain and both residues interact with the free amine group of the alanine. This structural feature allows the definition of a subfamily of NlpC/P60 enzymes with the same N-terminal substrate requirements, including a previously characterized cyanobacterial L-alanine-γ-D- glutamate endopeptidase that contains the two key components (an NlpC/P60 domain attached to an SH3b domain) for assembly of a YkfC-like active site.",
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T1 - Structure of the γ-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-γ-d-Glu

T2 - Insights into substrate recognition by NlpC/P60 cysteine peptidases

AU - Xu, Qingping

AU - Abdubek, Polat

AU - Astakhova, Tamara

AU - Axelrod, Herbert L.

AU - Bakolitsa, Constantina

AU - Cai, Xiaohui

AU - Carlton, Dennis

AU - Chen, Connie

AU - Chiu, Hsiu Ju

AU - Chiu, Michelle

AU - Clayton, Thomas

AU - Das, Debanu

AU - Deller, Marc C.

AU - Duan, Lian

AU - Ellrott, Kyle

AU - Farr, Carol L.

AU - Feuerhelm, Julie

AU - Grant, Joanna C.

AU - Grzechnik, Anna

AU - Han, Gye Won

AU - Jaroszewski, Lukasz

AU - Jin, Kevin K.

AU - Klock, Heath E.

AU - Knuth, Mark W.

AU - Kozbial, Piotr

AU - Krishna, S. Sri

AU - Kumar, Abhinav

AU - Lam, Winnie W.

AU - Marciano, David

AU - Miller, Mitchell D.

AU - Morse, Andrew T.

AU - Nigoghossian, Edward

AU - Nopakun, Amanda

AU - Okach, Linda

AU - Puckett, Christina

AU - Reyes, Ron

AU - Tien, Henry J.

AU - Trame, Christine B.

AU - Van Den Bedem, Henry

AU - Weekes, Dana

AU - Wooten, Tiffany

AU - Yeh, Andrew

AU - Hodgson, Keith O.

AU - Wooley, John

AU - Elsliger, Marc André

AU - Deacon, Ashley M.

AU - Godzik, Adam

AU - Lesley, Scott A.

AU - Wilson, Ian A.

PY - 2010/10

Y1 - 2010/10

N2 - Dipeptidyl-peptidase VI from Bacillus sphaericus and YkfC from Bacillus subtilis have both previously been characterized as highly specific γ-D-glutamyl-L-diamino acid endopeptidases. The crystal structure of a YkfC ortholog from Bacillus cereus (BcYkfC) at 1.8 Å resolution revealed that it contains two N-terminal bacterial SH3 (SH3b) domains in addition to the C-terminal catalytic NlpC/P60 domain that is ubiquitous in the very large family of cell-wall-related cysteine peptidases. A bound reaction product (L-Ala-γ-D-Glu) enabled the identification of conserved sequence and structural signatures for recognition of L-Ala and γ-D-Glu and, therefore, provides a clear framework for understanding the substrate specificity observed in dipeptidyl-peptidase VI, YkfC and other NlpC/P60 domains in general. The first SH3b domain plays an important role in defining substrate specificity by contributing to the formation of the active site, such that only murein peptides with a free N-terminal alanine are allowed. A conserved tyrosine in the SH3b domain of the YkfC subfamily is correlated with the presence of a conserved acidic residue in the NlpC/P60 domain and both residues interact with the free amine group of the alanine. This structural feature allows the definition of a subfamily of NlpC/P60 enzymes with the same N-terminal substrate requirements, including a previously characterized cyanobacterial L-alanine-γ-D- glutamate endopeptidase that contains the two key components (an NlpC/P60 domain attached to an SH3b domain) for assembly of a YkfC-like active site.

AB - Dipeptidyl-peptidase VI from Bacillus sphaericus and YkfC from Bacillus subtilis have both previously been characterized as highly specific γ-D-glutamyl-L-diamino acid endopeptidases. The crystal structure of a YkfC ortholog from Bacillus cereus (BcYkfC) at 1.8 Å resolution revealed that it contains two N-terminal bacterial SH3 (SH3b) domains in addition to the C-terminal catalytic NlpC/P60 domain that is ubiquitous in the very large family of cell-wall-related cysteine peptidases. A bound reaction product (L-Ala-γ-D-Glu) enabled the identification of conserved sequence and structural signatures for recognition of L-Ala and γ-D-Glu and, therefore, provides a clear framework for understanding the substrate specificity observed in dipeptidyl-peptidase VI, YkfC and other NlpC/P60 domains in general. The first SH3b domain plays an important role in defining substrate specificity by contributing to the formation of the active site, such that only murein peptides with a free N-terminal alanine are allowed. A conserved tyrosine in the SH3b domain of the YkfC subfamily is correlated with the presence of a conserved acidic residue in the NlpC/P60 domain and both residues interact with the free amine group of the alanine. This structural feature allows the definition of a subfamily of NlpC/P60 enzymes with the same N-terminal substrate requirements, including a previously characterized cyanobacterial L-alanine-γ-D- glutamate endopeptidase that contains the two key components (an NlpC/P60 domain attached to an SH3b domain) for assembly of a YkfC-like active site.

KW - γ-D-glutamyl-l-diamino acid endopeptidase

KW - cell-wall recycling

KW - cysteine peptidases

KW - enzyme specificity

KW - NlpC/P60

KW - SH3b

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