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PDBsum entry 1a4f
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protein ligands Protein-protein interface(s) links
Oxygen transport PDB id
1a4f

 

 

 

 

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Contents
Protein chains
141 a.a. *
146 a.a. *
Ligands
HEM-OXY ×2
Waters ×108
* Residue conservation analysis
PDB id:
1a4f
Name: Oxygen transport
Title: Bar-headed goose hemoglobin (oxy form)
Structure: Hemoglobin (alpha chain). Chain: a. Hemoglobin (beta chain). Chain: b
Source: Anser indicus. Bar-headed goose. Organism_taxid: 8846. Organism_taxid: 8846
Biol. unit: Tetramer (from PQS)
Resolution:
2.00Å     R-factor:   0.198    
Authors: J.Zhang,X.Gu
Key ref:
J.Zhang et al. (1996). The crystal structure of a high oxygen affinity species of haemoglobin (bar-headed goose haemoglobin in the oxy form). J Mol Biol, 255, 484-493. PubMed id: 8568892 DOI: 10.1006/jmbi.1996.0040
Date:
29-Jan-98     Release date:   29-Apr-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P01990  (HBA_ANSIN) -  Hemoglobin subunit alpha-A from Anser indicus
Seq:
Struc: 		142 a.a.
141 a.a.
Protein chain
Pfam   ArchSchema ?
P02118  (HBB_ANSIN) -  Hemoglobin subunit beta from Anser indicus
Seq:
Struc: 		146 a.a.
146 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1006/jmbi.1996.0040 J Mol Biol 255:484-493 (1996)
PubMed id: 8568892  
 
 
The crystal structure of a high oxygen affinity species of haemoglobin (bar-headed goose haemoglobin in the oxy form).
J.Zhang, Z.Hua, J.R.Tame, G.Lu, R.Zhang, X.Gu.
 
  ABSTRACT  
 
We have determined the crystal structure of bar-headed goose haemoglobin in the oxy form to a resolution of 2.0 A. The R-factor of the model is 19.8%. The structure is similar to human HbA, but contacts between the subunits show slightly altered packing of the tetramer. Bar-headed goose blood shows a greatly elevated oxygen affinity compared to closely related species of geese. This is apparently due to a single proline to alanine mutation at the alpha 1 beta 1 interface which destabilises the T state of the protein. The beta chain N and C termini are well-localized, and together with other neighbouring basic groups they form a strongly positively charged groove at the entrance to the central cavity around the molecular dyad. The well-ordered conformation and the three-dimensional distribution of positive charges clearly indicate this area to be the inositol pentaphosphate binding site of bird haemoglobins.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Electron density over Ala a119 and Leu b55, contoured at 1s. The position of the ring of proline a119 of human Hb superimposed on the goose structure is shown in broken lines. 		Figure 5.
Figure 5. Ramachandran plot for bar-headed goose Hb, drawn with PROCHECK (Laskowski et al., 1993). Glycine residues are shown as triangles. Two residues have unusual fc angles, Ala b119 and Leu a2. The N-terminal region of the a chain could not be readily fitted into the density and the temperature factors of atoms in the first five residues are high, indicating some disorder. In contrast, Ala b119 is well ordered and the C b and carbonyl oxygen atoms can be clearly observed in the electron density map. This residue adopts a similar conformation to the glycine found in most vertebrate haemoglobins at this position at the GH corner.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 255, 484-493) copyright 1996.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20685719 G.R.Scott, P.M.Schulte, S.Egginton, A.L.Scott, J.G.Richards, and W.K.Milsom (2011).
Molecular evolution of cytochrome C oxidase underlies high-altitude adaptation in the bar-headed goose.
  Mol Biol Evol, 28, 351-363.  
21543841 V.S.Bhatt, S.Zaldívar-López, D.R.Harris, C.G.Couto, P.G.Wang, and A.F.Palmer (2011).
Structure of Greyhound hemoglobin: origin of high oxygen affinity.
  Acta Crystallogr D Biol Crystallogr, 67, 395-402.
PDB code: 3pel
20434566 K.G.McCracken, C.P.Barger, and M.D.Sorenson (2010).
Phylogenetic and structural analysis of the HbA (alphaA/betaA) and HbD (alphaD/betaA) hemoglobin genes in two high-altitude waterfowl from the Himalayas and the Andes: Bar-headed goose (Anser indicus) and Andean goose (Chloephaga melanoptera).
  Mol Phylogenet Evol, 56, 649-658.  
19640884 G.R.Scott, S.Egginton, J.G.Richards, and W.K.Milsom (2009).
Evolution of muscle phenotype for extreme high altitude flight in the bar-headed goose.
  Proc Biol Sci, 276, 3645-3653.  
19754505 K.G.McCracken, C.P.Barger, M.Bulgarella, K.P.Johnson, S.A.Sonsthagen, J.Trucco, T.H.Valqui, R.E.Wilson, K.Winker, and M.D.Sorenson (2009).
Parallel evolution in the major haemoglobin genes of eight species of Andean waterfowl.
  Mol Ecol, 18, 3992-4005.  
19151158 K.G.McCracken, M.Bulgarella, K.P.Johnson, M.K.Kuhner, J.Trucco, T.H.Valqui, R.E.Wilson, and J.L.Peters (2009).
Gene flow in the face of countervailing selection: adaptation to high-altitude hypoxia in the betaA hemoglobin subunit of yellow-billed pintails in the Andes.
  Mol Biol Evol, 26, 815-827.  
  19194000 P.Sathya Moorthy, K.Neelagandan, M.Balasubramanian, and M.N.Ponnuswamy (2009).
Purification, crystallization and preliminary X-ray diffraction studies on avian haemoglobin from pigeon (Columba livia).
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 120-122.  
17703238 A.M.Dean, and J.W.Thornton (2007).
Mechanistic approaches to the study of evolution: the functional synthesis.
  Nat Rev Genet, 8, 675-688.  
17516855 J.Malda, T.J.Klein, and Z.Upton (2007).
The roles of hypoxia in the in vitro engineering of tissues.
  Tissue Eng, 13, 2153-2162.  
17655497 M.T.Sanna, B.Manconi, G.Podda, A.Olianas, M.Pellegrini, M.Castagnola, I.Messana, and B.Giardina (2007).
Alkaline Bohr effect of bird hemoglobins: the case of the flamingo.
  Biol Chem, 388, 787-795.  
16845115 R.Wernersson, K.Rapacki, H.H.Staerfeldt, P.W.Sackett, and A.Mølgaard (2006).
FeatureMap3D--a tool to map protein features and sequence conservation onto homologous structures in the PDB.
  Nucleic Acids Res, 34, W84-W88.  
15117955 T.Yokoyama, K.T.Chong, G.Miyazaki, H.Morimoto, D.T.Shih, S.Unzai, J.R.Tame, and S.Y.Park (2004).
Novel mechanisms of pH sensitivity in tuna hemoglobin: a structural explanation of the root effect.
  J Biol Chem, 279, 28632-28640.
PDB codes: 1v4u 1v4w 1v4x
11566768 A.Riccio, M.Tamburrini, B.Giardina, and G.di Prisco (2001).
Molecular dynamics analysis of a second phosphate site in the hemoglobins of the seabird, south polar skua. Is there a site-site migratory mechanism along the central cavity?
  Biophys J, 81, 1938-1946.  
  11532212 D.A.Liberles, D.R.Schreiber, S.Govindarajan, S.G.Chamberlin, and S.A.Benner (2001).
The adaptive evolution database (TAED).
  Genome Biol, 2, RESEARCH0028.  
11375496 X.Z.Liu, S.L.Li, H.Jing, Y.H.Liang, Z.Q.Hua, and G.Y.Lu (2001).
Avian haemoglobins and structural basis of high affinity for oxygen: structure of bar-headed goose aquomet haemoglobin.
  Acta Crystallogr D Biol Crystallogr, 57, 775-783.
PDB code: 1c40
11717498 Y.H.Liang, X.Z.Liu, S.H.Liu, and G.Y.Lu (2001).
The structure of greylag goose oxy haemoglobin: the roles of four mutations compared with bar-headed goose haemoglobin.
  Acta Crystallogr D Biol Crystallogr, 57, 1850-1856.
PDB code: 1faw
10957640 H.C.Wang, Y.H.Liang, J.P.Zhu, and G.Y.Lu (2000).
Crystallization and preliminary crystallographic studies of bar-headed goose fluoromethaemoglobin with inositol hexaphosphate.
  Acta Crystallogr D Biol Crystallogr, 56, 1183-1184.  
10998071 M.Tamburrini, A.Riccio, M.Romano, B.Giardina, and G.di Prisco (2000).
Structural and functional analysis of the two haemoglobins of the antarctic seabird Catharacta maccormicki characterization of an additional phosphate binding site by molecular modelling.
  Eur J Biochem, 267, 6089-6098.  
10737936 R.D'Avino, and R.De Luca (2000).
Molecular modelling of Trematomus newnesi Hb 1: insights for a lowered oxygen affinity and lack of root effect.
  Proteins, 39, 155-165.  
10713517 T.H.Lu, K.Panneerselvam, Y.C.Liaw, P.Kan, and C.J.Lee (2000).
Structure determination of porcine haemoglobin.
  Acta Crystallogr D Biol Crystallogr, 56, 304-312.
PDB code: 1qpw
10037733 J.E.Knapp, M.A.Oliveira, Q.Xie, S.R.Ernst, A.F.Riggs, and M.L.Hackert (1999).
The structural and functional analysis of the hemoglobin D component from chicken.
  J Biol Chem, 274, 6411-6420.
PDB code: 1hbr
10500299 J.R.Tame (1999).
What is the true structure of liganded haemoglobin?
  Trends Biochem Sci, 24, 372-377.  
10393295 K.T.Chong, G.Miyazaki, H.Morimoto, Y.Oda, and S.Y.Park (1999).
Structures of the deoxy and CO forms of haemoglobin from Dasyatis akajei, a cartilaginous fish.
  Acta Crystallogr D Biol Crystallogr, 55, 1291-1300.
PDB codes: 1cg5 1cg8
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.

 

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