spacer
spacer
Go to PDB code: 
protein links
Intein PDB id
1am2
Jmol
Contents
Protein chain
181 a.a. *
Waters ×46
* Residue conservation analysis
PDB id:
1am2
Name: Intein
Title: Gyra intein from mycobacterium xenopi
Structure: Mxe gyra intein. Chain: a. Engineered: yes. Mutation: yes
Source: Mycobacterium xenopi. Organism_taxid: 1789. Gene: rtp. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.20Å     R-factor:   0.187     R-free:   0.252
Authors: T.Klabunde,S.Sharma,J.C.Sacchettini
Key ref: T.Klabunde et al. (1998). Crystal structure of GyrA intein from Mycobacterium xenopi reveals structural basis of protein splicing. Nat Struct Biol, 5, 31-36. PubMed id: 9437427 DOI: 10.1038/nsb0198-31
Date:
20-Jun-97     Release date:   24-Jun-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P72065  (GYRA_MYCXE) -  DNA gyrase subunit A (Fragment)
Seq:
Struc: 		327 a.a.
181 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.5.99.1.3  - Dna topoisomerase (ATP-hydrolyzing).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP-dependent breakage, passage and rejoining of double-stranded DNA.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     intein-mediated protein splicing   1 term 

 

 
DOI no: 10.1038/nsb0198-31 Nat Struct Biol 5:31-36 (1998)
PubMed id: 9437427  
 
 
Crystal structure of GyrA intein from Mycobacterium xenopi reveals structural basis of protein splicing.
T.Klabunde, S.Sharma, A.Telenti, W.R.Jacobs, J.C.Sacchettini.
 
  ABSTRACT  
 
Several genes from prokaryotes and lower eukaryotes have been found to contain an in-frame open reading frame, which encodes for an internal protein (intein). Post-translationally, the internal polypeptide auto-splices and ligates the external sequences to yield a functional external protein (extein) and an intein. Most, but not all inteins, contain, apart from a splicing domain, a separate endonucleolytic domain that enables them to maintain their presence by a homing mechanism. We report here the crystal structure of an intein found in the gyrase A subunit from Mycobacterium xenopi at 2.2 A resolution. The structure contains an unusual beta-fold with the catalytic splice junctions at the ends of two adjacent antiparallel beta-strands. The arrangement of the active site residues Ser 1, Thr 72, His 75, His 197, and Asn 198 is consistent with a four-step mechanism for the cleavage-ligation reaction. Using site-directed mutagenesis, the N-terminal cysteine, proposed as the nucleophile in the first step of the splicing reaction, was changed to a Ser 1 and Ala 0, thus capturing the intein in a pre-spliced state.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21460844 B.P.Callahan, N.I.Topilina, M.J.Stanger, P.Van Roey, and M.Belfort (2011).
Structure of catalytically competent intein caught in a redox trap with functional and evolutionary implications.
  Nat Struct Mol Biol, 18, 630-633.
PDB code: 3nzm
21539790 P.T.Shemella, N.I.Topilina, I.Soga, B.Pereira, G.Belfort, M.Belfort, and S.K.Nayak (2011).
Electronic structure of neighboring extein residue modulates intein C-terminal cleavage activity.
  Biophys J, 100, 2217-2225.  
20401371 J.Kang, and D.Macmillan (2010).
Peptide and protein thioester synthesis via N-->S acyl transfer.
  Org Biomol Chem, 8, 1993-2002.  
20521254 L.E.Brace, M.W.Southworth, K.Tori, M.L.Cushing, and F.Perler (2010).
The Deinococcus radiodurans Snf2 intein caught in the act: detection of the Class 3 intein signature Block F branched intermediate.
  Protein Sci, 19, 1525-1533.  
20449740 S.Elleuche, and S.Pöggeler (2010).
Inteins, valuable genetic elements in molecular biology and biotechnology.
  Appl Microbiol Biotechnol, 87, 479-489.  
20495572 S.Frutos, M.Goger, B.Giovani, D.Cowburn, and T.W.Muir (2010).
Branched intermediate formation stimulates peptide bond cleavage in protein splicing.
  Nat Chem Biol, 6, 527-533.  
20175182 Y.Hori, Y.Egashira, R.Kamiura, and K.Kikuchi (2010).
Noncovalent-interaction-promoted ligation for protein labeling.
  Chembiochem, 11, 646-648.  
19541659 G.Amitai, B.P.Callahan, M.J.Stanger, G.Belfort, and M.Belfort (2009).
Modulation of intein activity by its neighboring extein substrates.
  Proc Natl Acad Sci U S A, 106, 11005-11010.  
19136555 J.H.Appleby, K.Zhou, G.Volkmann, and X.Q.Liu (2009).
Novel Split Intein for trans-Splicing Synthetic Peptide onto C Terminus of Protein.
  J Biol Chem, 284, 6194-6199.  
19404746 U.Arnold (2009).
Incorporation of non-natural modules into proteins: structural features beyond the genetic code.
  Biotechnol Lett, 31, 1129-1139.  
19630416 Z.Du, P.T.Shemella, Y.Liu, S.A.McCallum, B.Pereira, S.K.Nayak, G.Belfort, M.Belfort, and C.Wang (2009).
Highly conserved histidine plays a dual catalytic role in protein splicing: a pKa shift mechanism.
  J Am Chem Soc, 131, 11581-11589.  
18334484 K.Michalska, A.Hernandez-Santoyo, and M.Jaskolski (2008).
The mechanism of autocatalytic activation of plant-type L-asparaginases.
  J Biol Chem, 283, 13388-13397.
PDB code: 3c17
18287282 Y.Sun, and H.C.Guo (2008).
Structural constraints on autoprocessing of the human nucleoporin Nup98.
  Protein Sci, 17, 494-505.
PDB codes: 2q5x 2q5y
  17389927 A.G.Senejani, and J.P.Gogarten (2007).
Structural stability and endonuclease activity of a PI-SceI GFP-fusion protein.
  Int J Biol Sci, 3, 205-211.  
17590879 J.A.Camarero, R.H.Kimura, Y.H.Woo, A.Shekhtman, and J.Cantor (2007).
Biosynthesis of a fully functional cyclotide inside living bacterial cells.
  Chembiochem, 8, 1363-1366.  
17586768 M.A.Johnson, M.W.Southworth, T.Herrmann, L.Brace, F.B.Perler, and K.Wüthrich (2007).
NMR structure of a KlbA intein precursor from Methanococcus jannaschii.
  Protein Sci, 16, 1316-1328.
PDB codes: 2jmz 2jnq
17085503 P.Shemella, B.Pereira, Y.Zhang, P.Van Roey, G.Belfort, S.Garde, and S.K.Nayak (2007).
Mechanism for intein C-terminal cleavage: a proposal from quantum mechanical calculations.
  Biophys J, 92, 847-853.  
17254599 P.Van Roey, B.Pereira, Z.Li, K.Hiraga, M.Belfort, and V.Derbyshire (2007).
Crystallographic and mutational studies of Mycobacterium tuberculosis recA mini-inteins suggest a pivotal role for a highly conserved aspartate residue.
  J Mol Biol, 367, 162-173.
PDB codes: 2imz 2in0 2in8 2in9
17325221 S.Matrat, S.Petrella, E.Cambau, W.Sougakoff, V.Jarlier, and A.Aubry (2007).
Expression and purification of an active form of the Mycobacterium leprae DNA gyrase and its inhibition by quinolones.
  Antimicrob Agents Chemother, 51, 1643-1648.  
16754679 B.Liu, C.J.Schofield, and R.C.Wilmouth (2006).
Structural analyses on intermediates in serine protease catalysis.
  J Biol Chem, 281, 24024-24035.
PDB codes: 2bb4 2bd2 2bd3 2bd4 2bd5 2bd7 2bd8 2bd9 2bda 2bdb 2bdc 2h1u
17146457 D.T.Huang, and B.A.Schulman (2006).
Breaking up with a kinky SUMO.
  Nat Struct Mol Biol, 13, 1045-1047.  
16493661 H.Matsumura, H.Takahashi, T.Inoue, T.Yamamoto, H.Hashimoto, M.Nishioka, S.Fujiwara, M.Takagi, T.Imanaka, and Y.Kai (2006).
Crystal structure of intein homing endonuclease II encoded in DNA polymerase gene from hyperthermophilic archaeon Thermococcus kodakaraensis strain KOD1.
  Proteins, 63, 711-715.
PDB codes: 2cw7 2cw8
17099698 L.Shen, M.H.Tatham, C.Dong, A.Zagórska, J.H.Naismith, and R.T.Hay (2006).
SUMO protease SENP1 induces isomerization of the scissile peptide bond.
  Nat Struct Mol Biol, 13, 1069-1077.
PDB codes: 2iy0 2iy1
15557319 K.V.Mills, D.M.Dorval, and K.T.Lewandowski (2005).
Kinetic analysis of the individual steps of protein splicing for the Pyrococcus abyssi PolII intein.
  J Biol Chem, 280, 2714-2720.  
15862101 T.C.Evans, M.Q.Xu, and S.Pradhan (2005).
Protein splicing elements and plants: from transgene containment to protein purification.
  Annu Rev Plant Biol, 56, 375-392.  
15087498 A.Romanelli, A.Shekhtman, D.Cowburn, and T.W.Muir (2004).
Semisynthesis of a segmental isotopically labeled protein splicing precursor: NMR evidence for an unusual peptide bond at the N-extein-intein junction.
  Proc Natl Acad Sci U S A, 101, 6397-6402.  
15024006 K.V.Mills, J.S.Manning, A.M.Garcia, and L.A.Wuerdeman (2004).
Protein splicing of a Pyrococcus abyssi intein with a C-terminal glutamine.
  J Biol Chem, 279, 20685-20691.  
14764082 R.David, M.P.Richter, and A.G.Beck-Sickinger (2004).
Expressed protein ligation. Method and applications.
  Eur J Biochem, 271, 663-677.  
15194682 W.Sun, J.Yang, and X.Q.Liu (2004).
Synthetic two-piece and three-piece split inteins for protein trans-splicing.
  J Biol Chem, 279, 35281-35286.  
14633979 F.Schmitzberger, M.L.Kilkenny, C.M.Lobley, M.E.Webb, M.Vinkovic, D.Matak-Vinkovic, M.Witty, D.Y.Chirgadze, A.G.Smith, C.Abell, and T.L.Blundell (2003).
Structural constraints on protein self-processing in L-aspartate-alpha-decarboxylase.
  EMBO J, 22, 6193-6204.
PDB codes: 1ppy 1pqe 1pqf 1pqh 1pt0 1pt1 1pyq 1pyu
12626339 T.W.Muir (2003).
Semisynthesis of proteins by expressed protein ligation.
  Annu Rev Biochem, 72, 249-289.  
  12906830 X.Qian, C.Guan, and H.C.Guo (2003).
A dual role for an aspartic acid in glycosylasparaginase autoproteolysis.
  Structure, 11, 997.
PDB codes: 1p4k 1p4v
12878593 Y.Ding, M.Q.Xu, I.Ghosh, X.Chen, S.Ferrandon, G.Lesage, and Z.Rao (2003).
Crystal structure of a mini-intein reveals a conserved catalytic module involved in side chain cyclization of asparagine during protein splicing.
  J Biol Chem, 278, 39133-39142.
PDB code: 1mi8
12191480 A.E.Hodel, M.R.Hodel, E.R.Griffis, K.A.Hennig, G.A.Ratner, S.Xu, and M.A.Powers (2002).
The three-dimensional structure of the autoproteolytic, nuclear pore-targeting domain of the human nucleoporin Nup98.
  Mol Cell, 10, 347-358.
PDB code: 1ko6
12219083 C.M.Moure, F.S.Gimble, and F.A.Quiocho (2002).
Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence.
  Nat Struct Biol, 9, 764-770.
PDB codes: 1lws 1lwt
12142479 J.P.Gogarten, A.G.Senejani, O.Zhaxybayeva, L.Olendzenski, and E.Hilario (2002).
Inteins: structure, function, and evolution.
  Annu Rev Microbiol, 56, 263-287.  
11600710 F.S.Gimble (2001).
Degeneration of a homing endonuclease and its target sequence in a wild yeast strain.
  Nucleic Acids Res, 29, 4215-4223.  
10828056 B.W.Poland, M.Q.Xu, and F.A.Quiocho (2000).
Structural insights into the protein splicing mechanism of PI-SceI.
  J Biol Chem, 275, 16408-16413.
PDB code: 1ef0
10592269 F.B.Perler (2000).
InBase, the Intein Database.
  Nucleic Acids Res, 28, 344-345.  
  10975457 F.B.Perler, and E.Adam (2000).
Protein splicing and its applications.
  Curr Opin Biotechnol, 11, 377-383.  
10966466 H.Paulus (2000).
Protein splicing and related forms of protein autoprocessing.
  Annu Rev Biochem, 69, 447-496.  
10990465 M.W.Southworth, J.Benner, and F.B.Perler (2000).
An alternative protein splicing mechanism for inteins lacking an N-terminal nucleophile.
  EMBO J, 19, 5019-5026.  
10861727 Q.Li, L.A.Mitscher, and L.L.Shen (2000).
The 2-pyridone antibacterial agents: bacterial topoisomerase inhibitors.
  Med Res Rev, 20, 231-293.  
11092822 X.Q.Liu (2000).
Protein-splicing intein: Genetic mobility, origin, and evolution.
  Annu Rev Genet, 34, 61-76.  
10366843 F.B.Perler (1999).
A natural example of protein trans-splicing.
  Trends Biochem Sci, 24, 209-211.  
10467135 G.J.Cotton, and T.W.Muir (1999).
Peptide ligation and its application to protein engineering.
  Chem Biol, 6, R247-R256.  
10500183 J.S.Rosenblum, and G.Blobel (1999).
Autoproteolysis in nucleoporin biogenesis.
  Proc Natl Acad Sci U S A, 96, 11370-11375.  
10490104 Q.Xu, D.Buckley, C.Guan, and H.C.Guo (1999).
Structural insights into the mechanism of intramolecular proteolysis.
  Cell, 98, 651-661.
PDB codes: 9gaa 9gac 9gaf
10231563 S.Mathys, T.C.Evans, I.C.Chute, H.Wu, S.Chong, J.Benner, X.Q.Liu, and M.Q.Xu (1999).
Characterization of a self-splicing mini-intein and its conversion into autocatalytic N- and C-terminal cleavage elements: facile production of protein building blocks for protein ligation.
  Gene, 231, 1.  
9933578 T.C.Evans, J.Benner, and M.Q.Xu (1999).
The in vitro ligation of bacterially expressed proteins using an intein from Methanobacterium thermoautotrophicum.
  J Biol Chem, 274, 3923-3926.  
9437416 B.L.Stoddard, and S.Pietrokovski (1998).
Breaking up is hard to do.
  Nat Struct Biol, 5, 3-5.  
9546209 F.B.Perler (1998).
Breaking up is easy with esters.
  Nat Struct Biol, 5, 249-252.  
9689062 H.Wu, Z.Hu, and X.Q.Liu (1998).
Protein trans-splicing by a split intein encoded in a split DnaE gene of Synechocystis sp. PCC6803.
  Proc Natl Acad Sci U S A, 95, 9226-9231.  
9737998 J.Saarela, M.Laine, R.Tikkanen, C.Oinonen, A.Jalanko, J.Rouvinen, and L.Peltonen (1998).
Activation and oligomerization of aspartylglucosaminidase.
  J Biol Chem, 273, 25320-25328.  
9739093 M.Holford, and T.W.Muir (1998).
Adding 'splice' to protein engineering.
  Structure, 6, 951-956.  
9666333 R.B.Russell, and C.P.Ponting (1998).
Protein fold irregularities that hinder sequence analysis.
  Curr Opin Struct Biol, 8, 364-371.  
9553117 S.Chong, K.S.Williams, C.Wotkowicz, and M.Q.Xu (1998).
Modulation of protein splicing of the Saccharomyces cerevisiae vacuolar membrane ATPase intein.
  J Biol Chem, 273, 10567-10577.  
9518476 W.Grindl, W.Wende, V.Pingoud, and A.Pingoud (1998).
The protein splicing domain of the homing endonuclease PI-sceI is responsible for specific DNA binding.
  Nucleic Acids Res, 26, 1857-1862.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.