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PR00815

Identifier
PIHAEM  [View Relations]  [View Alignment]  
Accession
PR00815
No. of Motifs
4
Creation Date
03-MAR-1998  (UPDATE 08-JUL-1999)
Title
Pi haemoglobin signature
Database References
PRINTS; PR00612 ALPHAHAEM
PROSITE; PS01033 GLOBIN
BLOCKS; BL01033
INTERPRO; IPR002339
PDB; 1BAB
SCOP; 1BAB
CATH; 1BAB
Literature References
1. DICKERSON, R.E. AND GEIS, I.
Hemoglobin: Structure, Function, Evolution and Pathology.
THE BENJAMIN/CUMMINGS PUBLISHING COMPANY, 1983.
 
2. KAPP, O.H., MOENS, L., VANFLETEREN, J., TROTMAN, C.N.A., SUZUKI, T.
AND VINOGRADOV, S.N.
Alignment of 700 globin sequences: Extent of amino acid substitution
and its correlation with variation in volume.
PROTEIN SCI. 4 2179-2190 (1995).
 
3. MOENS, L., VANFLETEREN, J., VAN DE PEER, Y., PEETERS, K., KAPP, O., 
CZELUZNIAK, J., GOODMAN, M., BLAXTER, M. AND VINOGRADOV, S.
Globins in nonvertebrate species: dispersal by horizontal gene transfer
and evolution of the structure-function relationships.
MOL.BIOL.EVOL. 13 324-333 (1996).
 
4. WHITAKER, T.L., BERRY, M.B., HO, E.L., HARGROVE, M.S., PHILLIPS, G.N., 
KOMIYAMA, N.H., NAGAI, K. AND OLSON, J.S.
The D-helix in myoglobin and in the beta subunit of hemoglobin is required
for the retention of heme.
BIOCHEMISTRY 34 8221-8226 (1995).
 
5. CHAPMAN, B.S., TOBIN A.J., HOOD L.E.
Complete amino acid sequence of the major early embryonic alpha-like 
globins of the chicken.
J.BIOL.CHEM. 255 9051-9059 (1980).

Documentation
Globins are haem-containing proteins involved in dioxygen binding and/or 
transport [1]. At present, more than 700 globin sequences are known [2].
It has been proposed that all globins have evolved from a family of 
ancestral, approximately 17kDa haemoproteins that displayed the globin 
fold and functioned as redox proteins [3]. The globin superfamily includes
vertebrate haemoglobins (Hb); vertebrate myoglobins (Mb); invertebrate 
globins; plant leghaemoglobins; and bacterial flavohaemoglobins. 
 
The function of haemoglobins (Hb) is transport of dioxygen in blood plasma.
Hb binds O(2) in the reduced [Fe(II)] state. The Hb molecule exists as a
tetramer, typically of two alpha- and two beta-globin chains, which form 
a well-defined quaternary structure. Each monomer binds iron protoporphyrin
IX (haem). 
 
The 3D structures of a great number of vertebrate Hbs in various states
are known. The protein is largely alpha-helical, eight conserved helices 
(A to H) providing the scaffold for a well-defined haem-binding pocket
(Hb alpha subunits lack helix D [4]). The imidazole ring of the "proximal"
His residue provides the fifth haem iron ligand; the other axial haem iron 
position remains essentially free for O(2) coordination. Conserved "distal"
His and Val residues block an unhindered access to the sixth coordination 
site so that a controlled binding of small molecules may result only as a 
consequence of side-chain dynamics of the protein [1]. O(2) binding results
in a transition from high-spin to low-spin iron, with accompanying changes 
in the Fe-N bond lengths and coordination geometry. In Hb, these subtle 
changes lead to the well-known cooperative effect. At the quaternary 
structure level, O(2) binding induces relative reorientation of the 
[alpha-1, beta-1] and [alpha-2, beta-2] dimers. 
 
It has been hypothesised that the embryonic alpha-haemoglobin family
diverged considerably earlier than the beta-haemoglobin line [5]. This
is reflected in a greater variability amongst alpha sequences, such that
two distinct sub-groups may be distinguished; these have been designated
zeta and pi.
    
PIHAEM is a 4-element fingerprint that provides a signature for the 
pi family of haemoglobins. The fingerprint was derived from an initial 
alignment of 3 sequences: the motifs were drawn from conserved regions
spanning the full alignment length, focusing on those regions that 
characterise the pi haemoglobins but distinguish them from the rest of
the globin family - motif 1 encompasses the majority of helix 1, helix 2
and the N-terminal section of helix 3; motif 2 spans the C-terminal half
of the loop between helices 4 and 5, leading into helix 5; motif 3 spans
helices 6, 7 and the N-terminus of helix 8; and motif 4 spans the C-terminal
half of helix 9 and part of the following loop region. A single iteration
on OWL30.0 was required to reach convergence, no further sequences being
identified beyond the starting set. Several partial matches were also found,
all of which are alpha-like haemoglobins.
 
An update on SPTR37_9f identified a true set of 2 sequences, and 7
partial matches.
Summary Information
   2 codes involving  4 elements
0 codes involving 3 elements
7 codes involving 2 elements
Composite Feature Index
42222
30000
27070
1234
True Positives
HBPI_CAIMO    HBPI_CHICK    
True Positive Partials
Codes involving 2 elements
HBAZ_HORSE HBAZ_HUMAN HBAZ_PANTR HBA_CHICK
HBA_COTJA HBA_MELGA HBA_PHACO
Sequence Titles
HBPI_CAIMO  HEMOGLOBIN PI' CHAIN - CAIRINA MOSCHATA (MUSCOVY DUCK). 
HBPI_CHICK HEMOGLOBIN PI AND PI' CHAINS - GALLUS GALLUS (CHICKEN).

HBAZ_HORSE HEMOGLOBIN ZETA CHAIN - EQUUS CABALLUS (HORSE).
HBAZ_HUMAN HEMOGLOBIN ZETA CHAIN - HOMO SAPIENS (HUMAN).
HBAZ_PANTR HEMOGLOBIN ZETA CHAIN - PAN TROGLODYTES (CHIMPANZEE).
HBA_CHICK HEMOGLOBIN ALPHA-A CHAIN - GALLUS GALLUS (CHICKEN).
HBA_COTJA HEMOGLOBIN ALPHA-A CHAIN - COTURNIX COTURNIX JAPONICA (JAPANESE QUAIL).
HBA_MELGA HEMOGLOBIN ALPHA-A CHAIN - MELEAGRIS GALLOPAVO (COMMON TURKEY).
HBA_PHACO HEMOGLOBIN ALPHA-A CHAIN - PHASIANUS COLCHICUS COLCHICUS (RING-NECKED PHEASANT).
Scan History
OWL30_0    3  100  NSINGLE    
SPTR37_9f 1 75 NSINGLE
Initial Motifs
Motif 1  width=26
Element Seqn Id St Int Rpt
TQAEKAAVITIWTKVATQADAIGAES HBPI_CAIMO 3 3 -
TQAEKAAVTTIWAKVATQIESIGLES HBPI_CHICK 3 3 -
TQAEKAAVTTIWAKVATQIESIGLES GGGL01 4 4 -

Motif 2 width=10
Element Seqn Id St Int Rpt
VSQGSVQLRG HBPI_CHICK 48 19 -
VSQGSVQLRG GGGL01 49 19 -
LSQGSTQLRG HBPI_CAIMO 48 19 -

Motif 3 width=11
Element Seqn Id St Int Rpt
NIDDIRGALAK GGGL01 73 14 -
NIDDIRGALAK HBPI_CHICK 72 14 -
NIDDIRGALAK HBPI_CAIMO 72 14 -

Motif 4 width=12
Element Seqn Id St Int Rpt
CILCSVAARYPS HBPI_CAIMO 104 21 -
CILCSVAARYPS HBPI_CHICK 104 21 -
CILCSVAARYPS GGGL01 105 21 -
Final Motifs
Motif 1  width=26
Element Seqn Id St Int Rpt
TQAEKAAVTTIWAKVATQIESIGLES HBPI_CHICK 3 3 -
TQAEKAAVITIWTKVATQADAIGAES HBPI_CAIMO 3 3 -

Motif 2 width=10
Element Seqn Id St Int Rpt
VSQGSVQLRG HBPI_CHICK 48 19 -
LSQGSTQLRG HBPI_CAIMO 48 19 -

Motif 3 width=11
Element Seqn Id St Int Rpt
NIDDIRGALAK HBPI_CHICK 72 14 -
NIDDIRGALAK HBPI_CAIMO 72 14 -

Motif 4 width=12
Element Seqn Id St Int Rpt
CILCSVAARYPS HBPI_CHICK 104 21 -
CILCSVAARYPS HBPI_CAIMO 104 21 -