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PDBsum entry 1d2p

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Structural protein PDB id
1d2p
Jmol
Contents
Protein chain
373 a.a. *
Waters ×75
* Residue conservation analysis
PDB id:
1d2p
Name: Structural protein
Title: Crystal structure of two b repeat units (b1b2) of the collagen binding protein (cna) of staphylococcus aureus
Structure: Collagen adhesin. Chain: a. Fragment: b repeat regions. Synonym: cna. Engineered: yes
Source: Staphylococcus aureus. Organism_taxid: 1280. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.50Å     R-factor:   0.185     R-free:   0.245
Authors: C.C.S.Deivanayagam,R.L.Rich,M.Hook,S.V.L.Narayana
Key ref:
C.C.Deivanayagam et al. (2000). Novel fold and assembly of the repetitive B region of the Staphylococcus aureus collagen-binding surface protein. Structure, 8, 67-78. PubMed id: 10673425 DOI: 10.1016/S0969-2126(00)00081-2
Date:
25-Sep-99     Release date:   27-Sep-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q53654  (CNA_STAAU) -  Collagen adhesin
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1183 a.a.
373 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 7 residue positions (black crosses)

 

 
DOI no: 10.1016/S0969-2126(00)00081-2 Structure 8:67-78 (2000)
PubMed id: 10673425  
 
 
Novel fold and assembly of the repetitive B region of the Staphylococcus aureus collagen-binding surface protein.
C.C.Deivanayagam, R.L.Rich, M.Carson, R.T.Owens, S.Danthuluri, T.Bice, M.Höök, S.V.Narayana.
 
  ABSTRACT  
 
BACKGORUND: The Staphylococcus aureus collagen-binding protein Cna mediates bacterial adherence to collagen. The primary sequence of Cna has a non-repetitive collagen-binding A region, followed by the repetitive B region. The B region has one to four 23 kDa repeat units (B(1)-B(4)), depending on the strain of origin. The affinity of the A region for collagen is independent of the B region. However, the B repeat units have been suggested to serve as a 'stalk' that projects the A region from the bacterial surface and thus facilitate bacterial adherence to collagen. To understand the biological role of these B-region repeats we determined their three-dimensional structure. RESULTS: B(1) has two domains (D(1) and D(2)) placed side-by-side. D(1) and D(2) have similar secondary structure and exhibit a unique fold that resembles but is the inverse of the immunoglobulin-like (IgG-like) domains. Comparison with similar immunoglobulin superfamily (IgSF) structures shows novel packing arrangements between the D(1) and D(2) domains. In the B(1)B(2) crystal structure, an omission of a single glycine residue in the D(2)-D(3) linker loop, compared to the D(1)-D(2) and D(3)-D(4) linker loops, resulted in projection of the D(3) and D(4) in a spatially new orientation. We also present a model for B(1)B(2)B(3)B(4). CONCLUSIONS: The B region of the Cna collagen adhesin has a novel fold that is reminiscent of but is inverse in nature to the IgG fold. This B region assembly could effectively provide the needed flexibility and stability for presenting the ligand binding A region away from the bacterial cell surface.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. B[1]B[2] crystal structure. (a) Crystal structure of B[1]B[2] in stereo. The two individual repeat units B[1] and B[2] retain the packing arrangements observed in the B[1] structure. (b) Electron density around the KYTPGET polypeptide in the D[1]-D[2] and D[3]-D[4] linker region. (c) Electron density around the KYTPET polypeptide in the D[2]-D[3] linker region.
 
  The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 67-78) copyright 2000.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21326273 A.P.Hendrickx, J.M.Budzik, S.Y.Oh, and O.Schneewind (2011).
Architects at the bacterial surface - sortases and the assembly of pili with isopeptide bonds.
  Nat Rev Microbiol, 9, 166-176.  
21280131 E.Matsuoka, Y.Tanaka, M.Kuroda, Y.Shouji, T.Ohta, I.Tanaka, and M.Yao (2011).
Crystal structure of the functional region of Uro-adherence factor A from Staphylococcus saprophyticus reveals participation of the B domain in ligand binding.
  Protein Sci, 20, 406-416.
PDB codes: 3irp 3irz 3is1
21055949 H.J.Kang, and E.N.Baker (2011).
Intramolecular isopeptide bonds: protein crosslinks built for stress?
  Trends Biochem Sci, 36, 229-237.  
21404359 K.Vengadesan, and S.V.Narayana (2011).
Structural biology of gram-positive bacterial adhesins.
  Protein Sci, 20, 759-772.  
21333654 K.Vengadesan, X.Ma, P.Dwivedi, H.Ton-That, and S.V.Narayana (2011).
A model for group B Streptococcus pilus type 1: the structure of a 35-kDa C-terminal fragment of the major pilin GBS80.
  J Mol Biol, 407, 731-743.
PDB codes: 3pf2 3pg2
20532244 D.Lepp, B.Roxas, V.R.Parreira, P.R.Marri, E.L.Rosey, J.Gong, J.G.Songer, G.Vedantam, and J.F.Prescott (2010).
Identification of novel pathogenicity loci in Clostridium perfringens strains that cause avian necrotic enteritis.
  PLoS One, 5, e10795.  
20553501 J.Jorda, B.Xue, V.N.Uversky, and A.V.Kajava (2010).
Protein tandem repeats - the more perfect, the less structured.
  FEBS J, 277, 2673-2682.  
20497507 L.J.Brady, S.E.Maddocks, M.R.Larson, N.Forsgren, K.Persson, C.C.Deivanayagam, and H.F.Jenkinson (2010).
The changing faces of Streptococcus antigen I/II polypeptide family adhesins.
  Mol Microbiol, 77, 276-286.  
20231452 M.R.Larson, K.R.Rajashankar, M.H.Patel, R.A.Robinette, P.J.Crowley, S.Michalek, L.J.Brady, and C.Deivanayagam (2010).
Elongated fibrillar structure of a streptococcal adhesin assembled by the high-affinity association of alpha- and PPII-helices.
  Proc Natl Acad Sci U S A, 107, 5983-5988.
PDB codes: 3iox 3ipk
20152157 T.Izoré, C.Contreras-Martel, L.El Mortaji, C.Manzano, R.Terrasse, T.Vernet, A.M.Di Guilmi, and A.Dessen (2010).
Structural basis of host cell recognition by the pilus adhesin from Streptococcus pneumoniae.
  Structure, 18, 106-115.
PDB code: 2ww8
19737906 A.P.Hendrickx, M.van Luit-Asbroek, C.M.Schapendonk, W.J.van Wamel, J.C.Braat, L.M.Wijnands, M.J.Bonten, and R.J.Willems (2009).
SgrA, a nidogen-binding LPXTG surface adhesin implicated in biofilm formation, and EcbA, a collagen binding MSCRAMM, are two novel adhesins of hospital-acquired Enterococcus faecium.
  Infect Immun, 77, 5097-5106.  
19141282 C.A.McElroy, J.A.Dohm, and S.T.Walsh (2009).
Structural and biophysical studies of the human IL-7/IL-7Ralpha complex.
  Structure, 17, 54-65.
PDB codes: 3di2 3di3
19497855 H.J.Kang, and E.N.Baker (2009).
Intramolecular isopeptide bonds give thermodynamic and proteolytic stability to the major pilin protein of Streptococcus pyogenes.
  J Biol Chem, 284, 20729-20737.
PDB codes: 3gld 3gle
19226623 H.J.Kang, M.Middleditch, T.Proft, and E.N.Baker (2009).
Isopeptide bonds in bacterial pili and their characterization by X-ray crystallography and mass spectrometry.
  Biopolymers, 91, 1126-1134.  
19805181 H.J.Kang, N.G.Paterson, A.H.Gaspar, H.Ton-That, and E.N.Baker (2009).
The Corynebacterium diphtheriae shaft pilin SpaA is built of tandem Ig-like modules with stabilizing isopeptide and disulfide bonds.
  Proc Natl Acad Sci U S A, 106, 16967-16971.
PDB codes: 3hr6 3htl
  19903875 J.M.Budzik, C.B.Poor, K.F.Faull, J.P.Whitelegge, C.He, and O.Schneewind (2009).
Intramolecular amide bonds stabilize pili on the surface of bacilli.
  Proc Natl Acad Sci U S A, 106, 19992-19997.
PDB code: 3kpt
19389755 J.Sillanpää, S.R.Nallapareddy, J.Houston, V.K.Ganesh, A.Bourgogne, K.V.Singh, B.E.Murray, and M.Höök (2009).
A family of fibrinogen-binding MSCRAMMs from Enterococcus faecalis.
  Microbiology, 155, 2390-2400.  
19717590 J.Sillanpää, S.R.Nallapareddy, X.Qin, K.V.Singh, D.M.Muzny, C.L.Kovar, L.V.Nazareth, R.A.Gibbs, M.J.Ferraro, J.M.Steckelberg, G.M.Weinstock, and B.E.Murray (2009).
A collagen-binding adhesin, Acb, and ten other putative MSCRAMM and pilus family proteins of Streptococcus gallolyticus subsp. gallolyticus (Streptococcus bovis Group, biotype I).
  J Bacteriol, 191, 6643-6653.  
19424490 Y.Konto-Ghiorghi, E.Mairey, A.Mallet, G.Duménil, E.Caliot, P.Trieu-Cuot, and S.Dramsi (2009).
Dual role for pilus in adherence to epithelial cells and biofilm formation in Streptococcus agalactiae.
  PLoS Pathog, 5, e1000422.  
18808384 I.M.Frick, C.Karlsson, M.Mörgelin, A.I.Olin, R.Janjusevic, C.Hammarström, E.Holst, M.de Château, and L.Björck (2008).
Identification of a novel protein promoting the colonization and survival of Finegoldia magna, a bacterial commensal and opportunistic pathogen.
  Mol Microbiol, 70, 695-708.  
18621716 J.M.Budzik, L.A.Marraffini, P.Souda, J.P.Whitelegge, K.F.Faull, and O.Schneewind (2008).
Amide bonds assemble pili on the surface of bacilli.
  Proc Natl Acad Sci U S A, 105, 10215-10220.  
17991749 M.G.Bowden, A.P.Heuck, K.Ponnuraj, E.Kolosova, D.Choe, S.Gurusiddappa, S.V.Narayana, A.E.Johnson, and M.Höök (2008).
Evidence for the "dock, lock, and latch" ligand binding mechanism of the staphylococcal microbial surface component recognizing adhesive matrix molecules (MSCRAMM) SdrG.
  J Biol Chem, 283, 638-647.
PDB code: 2ral
17472965 C.Arrecubieta, M.H.Lee, A.Macey, T.J.Foster, and F.D.Lowy (2007).
SdrF, a Staphylococcus epidermidis surface protein, binds type I collagen.
  J Biol Chem, 282, 18767-18776.  
17554049 H.Bierne, and P.Cossart (2007).
Listeria monocytogenes surface proteins: from genome predictions to function.
  Microbiol Mol Biol Rev, 71, 377-397.  
18063798 H.J.Kang, F.Coulibaly, F.Clow, T.Proft, and E.N.Baker (2007).
Stabilizing isopeptide bonds revealed in gram-positive bacterial pilus structure.
  Science, 318, 1625-1628.
PDB code: 3b2m
17557326 K.Ponnuraj, and S.V.Narayana (2007).
Crystal structure of ACE19, the collagen binding subdomain of Enterococus faecalis surface protein ACE.
  Proteins, 69, 199-203.
PDB code: 2okm
17726530 S.B.Beres, and J.M.Musser (2007).
Contribution of exogenous genetic elements to the group A Streptococcus metagenome.
  PLoS ONE, 2, e800.  
17697995 V.Krishnan, A.H.Gaspar, N.Ye, A.Mandlik, H.Ton-That, and S.V.Narayana (2007).
An IgG-like domain in the minor pilin GBS52 of Streptococcus agalactiae mediates lung epithelial cell adhesion.
  Structure, 15, 893-903.
PDB codes: 2pz4 3phs
16040603 B.Kreikemeyer, M.Nakata, S.Oehmcke, C.Gschwendtner, J.Normann, and A.Podbielski (2005).
Streptococcus pyogenes collagen type I-binding Cpa surface protein. Expression profile, binding characteristics, biological functions, and potential clinical impact.
  J Biol Chem, 280, 33228-33239.  
15837194 S.I.Yoon, B.C.Jones, N.J.Logsdon, and M.R.Walter (2005).
Same structure, different function crystal structure of the Epstein-Barr virus IL-10 bound to the soluble IL-10R1 chain.
  Structure, 13, 551-564.
PDB codes: 1y6k 1y6m 1y6n
15093830 H.Remaut, and G.Waksman (2004).
Structural biology of bacterial pathogenesis.
  Curr Opin Struct Biol, 14, 161-170.  
15456768 Y.Xu, X.Liang, Y.Chen, T.M.Koehler, and M.Höök (2004).
Identification and biochemical characterization of two novel collagen binding MSCRAMMs of Bacillus anthracis.
  J Biol Chem, 279, 51760-51768.  
12485987 C.C.Deivanayagam, E.R.Wann, W.Chen, M.Carson, K.R.Rajashankar, M.Höök, and S.V.Narayana (2002).
A novel variant of the immunoglobulin fold in surface adhesins of Staphylococcus aureus: crystal structure of the fibrinogen-binding MSCRAMM, clumping factor A.
  EMBO J, 21, 6660-6672.
PDB code: 1n67
11207369 P.D.Carr, S.E.Gustin, A.P.Church, J.M.Murphy, S.C.Ford, D.A.Mann, D.M.Woltring, I.Walker, D.L.Ollis, and I.G.Young (2001).
Structure of the complete extracellular domain of the common beta subunit of the human GM-CSF, IL-3, and IL-5 receptors reveals a novel dimer configuration.
  Cell, 104, 291-300.
PDB code: 1gh7
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 codes are shown on the right.