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PDBsum entry 2bo9

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
2bo9
Jmol
Contents
Protein chains
307 a.a. *
217 a.a. *
Ligands
VAL ×2
NAG ×2
MPD ×12
ACN
Metals
_ZN ×2
Waters ×1153
* Residue conservation analysis
PDB id:
2bo9
Name: Hydrolase
Title: Human carboxypeptidase a4 in complex with human latexin.
Structure: Carboxypeptidase a4. Chain: a, c. Fragment: alpha/beta-hydrolase domain, residues 114-421. Synonym: carboxypeptidase a3, unq694/pro1339. Engineered: yes. Other_details: n-glycosylation at asn148 in both copies present.. Human latexin. Chain: b, d.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: pichia pastoris. Expression_system_taxid: 4922. Other_details: cdna provided by drs.Huang and smith, mayo clinic, rochester, mn.. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Biol. unit: Dimer (from PDB file)
Resolution:
1.60Å     R-factor:   0.150     R-free:   0.176
Authors: I.Pallares,R.Bonet,R.Garcia-Castellanos,S.Ventura, F.X.Aviles,J.Vendrell,F.X.Gomis-Rueth
Key ref:
I.Pallarès et al. (2005). Structure of human carboxypeptidase A4 with its endogenous protein inhibitor, latexin. Proc Natl Acad Sci U S A, 102, 3978-3983. PubMed id: 15738388 DOI: 10.1073/pnas.0500678102
Date:
08-Apr-05     Release date:   15-Apr-05    
Supersedes: 2bk7
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9UI42  (CBPA4_HUMAN) -  Carboxypeptidase A4
Seq:
Struc:
421 a.a.
307 a.a.
Protein chains
Pfam   ArchSchema ?
Q9BS40  (LXN_HUMAN) -  Latexin
Seq:
Struc:
222 a.a.
217 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     inflammatory response   5 terms 
  Biochemical function     enzyme inhibitor activity     6 terms  

 

 
DOI no: 10.1073/pnas.0500678102 Proc Natl Acad Sci U S A 102:3978-3983 (2005)
PubMed id: 15738388  
 
 
Structure of human carboxypeptidase A4 with its endogenous protein inhibitor, latexin.
I.Pallarès, R.Bonet, R.García-Castellanos, S.Ventura, F.X.Avilés, J.Vendrell, F.X.Gomis-Rüth.
 
  ABSTRACT  
 
The only endogenous protein inhibitor known for metallocarboxypeptidases (MCPs) is latexin, a 25-kDa protein discovered in the rat brain. Latexin, alias endogenous carboxypeptidase inhibitor, inhibits human CPA4 (hCPA4), whose expression is induced in prostate cancer cells after treatment with histone deacetylase inhibitors. hCPA4 is a member of the A/B subfamily of MCPs and displays the characteristic alpha/beta-hydrolase fold. Human latexin consists of two topologically equivalent subdomains, reminiscent of cystatins, consisting of an alpha-helix enveloped by a curved beta-sheet. These subdomains are packed against each other through the helices and linked by a connecting segment encompassing a third alpha-helix. The enzyme is bound at the interface of these subdomains. The complex occludes a large contact surface but makes rather few contacts, despite a nanomolar inhibition constant. This low specificity explains the flexibility of latexin in inhibiting all vertebrate A/B MCPs tested, even across species barriers. In contrast, modeling studies reveal why the N/E subfamily of MCPs and invertebrate A/B MCPs are not inhibited. Major differences in the loop segments shaping the border of the funnel-like access to the protease active site impede complex formation with latexin. Several sequences ascribable to diverse tissues and organs have been identified in vertebrate genomes as being highly similar to latexin. They are proposed to constitute the latexin family of potential inhibitors. Because they are ubiquitous, latexins could represent for vertebrate A/B MCPs the counterparts of tissue inhibitors of metalloproteases for matrix metalloproteinases.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Sequence alignment of potential members (one per organism) of the latexin family of putative MCP inhibitors. Sequences were retrieved from Swiss-Prot/TrEMBL (www.expasy.ch), GenBank (GB; www.ncbi.nlm.nih.gov), TIGR (http://tigrblast.tigr.org/tgi), and ENSEMBL (ES; www.ensembl.org). The number of additional N-terminal protein residues is indicated in parentheses if appropriate. Some sequences are from unfinished genome projects and may be partial and still contain errors. They were compiled from EST libraries of diverse tissues and organs corresponding to different developmental stages (adult, fetal, and tailbud stages), among them from liver, kidney, gut, spleen, ovary, testis, brain, aorta, brain, cartilage, placenta, lung, thymus, and small intestine. Asterisks denote residues engaged in interactions with hCPA4. The length of each sequence, the identity to human latexin, and the number of overlapping residues are indicated. Absolutely conserved positions are shaded in black and conservatively substituted ones or those displaying two different residues are shaded in gray.
Figure 2.
Fig. 2. Structure of latexin and of its complex with hCPA4. (A) Ribbon plot of human latexin, view of the upper barrel surface. The N-terminal subdomain (cyan), the connecting segment (violet), and the C-terminal subdomain (blue) are shown. The constituting regular secondary structure elements are labeled (see also Fig. 1). (B) Ribbon plot of the inhibitor/enzyme complex showing hCPA4 in orange and latexin in cyan. Inhibitor segments contacting the protease are in magenta. The protein residues coordinating the catalytic zinc ion (yellow sphere) are violet, as is the glycosylation site (Asn148A). The catalytic solvent molecule is shown as a white sphere. (C) Superimposition of the NTS and CTS of latexin, with the same color coding as in A. (D) Stereo plot of the superimposition of human latexin (with the color coding as in A) with chicken egg-white cystatin (magenta; PDB ID code 1CEW [PDB] ) and sweet protein monellin (orange; PDB ID code 1MOL [PDB] ). The approximate position of a cysteine proteinase when inhibited by a cystatin [as inferred from the steffin/papain complex; PDB ID code 1STF [PDB] (23)] is indicated by a magenta arrow, and the localization of hCPA4 in the complex with latexin is indicated by a blue arrow. (E) Closeup view in stereo of the section around the catalytic active-site cleft and the region of main peptidase/inhibitor interactions. Latexin is in blue and hCPA4 is colored according to atom type. The catalytic zinc ion (violet) and solvent molecule (cyan) are further shown as small spheres. (F) Stereo superimposition of the C^ backbone of hCPA4 (yellow), in its complex with latexin, and dCPD2 (violet; PDB ID code 1H81 [PDB] ), as representatives of A/B- and N/E-type MCPs, respectively. The orientation corresponds to that in B rotated clockwise vertically 45° and then horizontally 90°. The regions shown comprise those shaping the rim of the funnel that leads to the active site of the enzymes, pinpointed by the catalytic zinc ion of hCPA4 (orange sphere). The five main insertions/deletions accounting for lack of interactions ( to ) or potential steric clashes ( to ) with latexin on going from hCPA4 to dCPD2 are: , Thr274A-Tyr277A; , Ser150A-Asn171A; , Ser131A-Ile139A (all of hCPA4); , Gln226-His241; , Ser124-Val133 (both of dCPD2).
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21466706 Y.Li, Z.Basang, H.Ding, Z.Lu, T.Ning, H.Wei, H.Cai, and Y.Ke (2011).
Latexin expression is downregulated in human gastric carcinomas and exhibits tumor suppressor potential.
  BMC Cancer, 11, 121.  
20525390 E.Pérez, J.L.Gallegos, L.Cortés, K.G.Calderón, J.C.Luna, F.E.Cázares, M.C.Velasquillo, J.B.Kouri, and F.C.Hernández (2010).
Identification of latexin by a proteomic analysis in rat normal articular cartilage.
  Proteome Sci, 8, 27.  
20526345 P.Van Damme, A.Staes, S.Bronsoms, K.Helsens, N.Colaert, E.Timmerman, F.X.Aviles, J.Vandekerckhove, and K.Gevaert (2010).
Complementary positional proteomics for screening substrates of endo- and exoproteases.
  Nat Methods, 7, 512-515.  
19643669 G.Pejler, S.D.Knight, F.Henningsson, and S.Wernersson (2009).
Novel insights into the biological function of mast cell carboxypeptidase A.
  Trends Immunol, 30, 401-408.  
19796245 G.Van Zant, and Y.Liang (2009).
Natural genetic diversity as a means to uncover stem cell regulatory pathways.
  Ann N Y Acad Sci, 1176, 170-177.  
19179285 L.Sanglas, F.X.Aviles, R.Huber, F.X.Gomis-Rüth, and J.L.Arolas (2009).
Mammalian metallopeptidase inhibition at the defense barrier of Ascaris parasite.
  Proc Natl Acad Sci U S A, 106, 1743-1747.
PDB code: 3fju
19245716 P.L.Ross, I.Cheng, X.Liu, M.S.Cicek, P.R.Carroll, G.Casey, and J.S.Witte (2009).
Carboxypeptidase 4 gene variants and early-onset intermediate-to-high risk prostate cancer.
  BMC Cancer, 9, 69.  
18722183 L.Sanglas, Z.Valnickova, J.L.Arolas, I.Pallarés, T.Guevara, M.Solà, T.Kristensen, J.J.Enghild, F.X.Aviles, and F.X.Gomis-Rüth (2008).
Structure of activated thrombin-activatable fibrinolysis inhibitor, a molecular link between coagulation and fibrinolysis.
  Mol Cell, 31, 598-606.
PDB code: 3d4u
17894344 N.P.Cowieson, A.J.Miles, G.Robin, J.K.Forwood, B.Kobe, J.L.Martin, and B.A.Wallace (2008).
Evaluating protein:protein complex formation using synchrotron radiation circular dichroism spectroscopy.
  Proteins, 70, 1142-1146.  
18374916 Y.Liang, and G.Van Zant (2008).
Aging stem cells, latexin, and longevity.
  Exp Cell Res, 314, 1962-1972.  
17407161 D.Fernández, J.Vendrell, F.X.Avilés, and J.Fernández-Recio (2007).
Structural and functional characterization of binding sites in metallocarboxypeptidases based on Optimal Docking Area analysis.
  Proteins, 68, 131-144.  
17996039 I.Pallarés, C.Berenguer, F.X.Avilés, J.Vendrell, and S.Ventura (2007).
Self-assembly of human latexin into amyloid-like oligomers.
  BMC Struct Biol, 7, 75.  
17401346 O.Yanes, J.Villanueva, E.Querol, and F.X.Aviles (2007).
Detection of non-covalent protein interactions by 'intensity fading' MALDI-TOF mass spectrometry: applications to proteases and protease inhibitors.
  Nat Protoc, 2, 119-130.  
17152080 R.Koike, K.Kinoshita, and A.Kidera (2007).
Probabilistic alignment detects remote homology in a pair of protein sequences without homologous sequence information.
  Proteins, 66, 655-663.  
15893421 D.Keppler (2006).
Towards novel anti-cancer strategies based on cystatin function.
  Cancer Lett, 235, 159-176.  
17112720 P.R.Mittl, and M.G.Grütter (2006).
Opportunities for structure-based design of protease-directed drugs.
  Curr Opin Struct Biol, 16, 769-775.  
16260742 A.Bayés, M.Comellas-Bigler, M.Rodríguez de la Vega, K.Maskos, W.Bode, F.X.Aviles, M.A.Jongsma, J.Beekwilder, and J.Vendrell (2005).
Structural basis of the resistance of an insect carboxypeptidase to plant protease inhibitors.
  Proc Natl Acad Sci U S A, 102, 16602-16607.
PDB code: 2c1c
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.