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PR00816

Identifier
ZETAHAEM  [View Relations]  [View Alignment]  
Accession
PR00816
No. of Motifs
4
Creation Date
03-MAR-1998  (UPDATE 07-JUN-1999)
Title
Zeta haemoglobin signature
Database References
PRINTS; PR00612 ALPHAHAEM
PROSITE; PS01033 GLOBIN
BLOCKS; BL01033
INTERPRO; IPR002340
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. WERNKE S.M. AND LINGREL J.B.
Nucleotide sequence of the goat embryonic alpha globin gene (zeta) and
linkage and evolutionary analysis of the complete alpha globin cluster. 
J.MOL.BIOL. 192 457-471 (1986). 

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
pi and zeta.
 
ZETAHAEM is a 4-element fingerprint that provides a signature for the 
zeta family of haemoglobins. The fingerprint was derived from an initial 
alignment of 7 sequences: the motifs were drawn from conserved sections
spanning the full alignment length, focusing on those regions that 
characterise the zeta-haemoglobins but distinguish them from the rest of
the globin family - motif 1 includes the N-terminus of helix 1; motif 2 
spans the C-terminal half of the loop between helices 4 and 5, leading 
into helix 5; motif 3 encompasses helices 6 and 7; and motif 4 spans the 
C-terminal portion of helix 10. A single iteration on OWL30.0 was required
to reach convergence, no further sequence being identified beyond the
starting set. A single partial match was found, HBAD_BRACA, a Canada goose
alpha-D haemoglobin that fails to match motifs 1 and 4.
 
An update on SPTR37_9f identified a true set of 6 sequences.
Summary Information
6 codes involving  4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
46666
30000
20000
1234
True Positives
HBAZ_CAPHI    HBAZ_HORSE    HBAZ_HUMAN    HBAZ_MOUSE    
HBAZ_PANTR HBAZ_PIG
Sequence Titles
HBAZ_CAPHI  HEMOGLOBIN ZETA CHAIN - CAPRA HIRCUS (GOAT).  
HBAZ_HORSE HEMOGLOBIN ZETA CHAIN - EQUUS CABALLUS (HORSE).
HBAZ_HUMAN HEMOGLOBIN ZETA CHAIN - HOMO SAPIENS (HUMAN).
HBAZ_MOUSE HEMOGLOBIN ZETA CHAIN - MUS MUSCULUS (MOUSE).
HBAZ_PANTR HEMOGLOBIN ZETA CHAIN - PAN TROGLODYTES (CHIMPANZEE).
HBAZ_PIG HEMOGLOBIN ZETA CHAIN - SUS SCROFA (PIG).
Scan History
OWL30_0    1  100  NSINGLE    
SPTR37_9f 2 12 NSINGLE
Initial Motifs
Motif 1  width=13
Element Seqn Id St Int Rpt
SLTKAERTMVVSI HBAZ_HORSE 1 1 -
SLTKAERTIIGSM HBAZ_PIG 1 1 -
SLMKNERAIIMSM MUSGLOBZ 2 2 -
SLMKNERAIIMSM HBAZ_MOUSE 1 1 -
SLTKTEGTIIVSM HBAZ_PANTR 1 1 -
SLTKTERTIIVSM HBAZ_HUMAN 1 1 -
SLTRTERTIILSL HBAZ_CAPHI 1 1 -

Motif 2 width=10
Element Seqn Id St Int Rpt
LNPGSAQLRA HBAZ_PIG 48 34 -
LHHGSQQLRA MUSGLOBZ 49 34 -
LHPGSAQLRA HBAZ_PANTR 48 34 -
LHPGSAQLRA HBAZ_HUMAN 48 34 -
LHSGSAQLRA HBAZ_CAPHI 48 34 -
LHEGSPQLRA HBAZ_HORSE 48 34 -
LHHGSQQLRA HBAZ_MOUSE 48 34 -

Motif 3 width=7
Element Seqn Id St Int Rpt
SIDNLSS MUSGLOBZ 73 14 -
SIDNIGG HBAZ_PANTR 72 14 -
SIDDIGG HBAZ_HUMAN 72 14 -
SIDNVTS HBAZ_CAPHI 72 14 -
SIDNVAG HBAZ_HORSE 72 14 -
SIDNVSA HBAZ_PIG 72 14 -
SIDNLSS HBAZ_MOUSE 72 14 -

Motif 4 width=9
Element Seqn Id St Int Rpt
TIVSGVLTE HBAZ_PIG 130 51 -
SILSSILTE HBAZ_MOUSE 130 51 -
SVVSSVLTE HBAZ_PANTR 130 51 -
SILSSILTE MUSGLOBZ 131 51 -
SVVSSVLTE HBAZ_HUMAN 130 51 -
SIVSGVLTE HBAZ_CAPHI 130 51 -
SIVSSVLTE HBAZ_HORSE 130 51 -
Final Motifs
Motif 1  width=13
Element Seqn Id St Int Rpt
SLTKTEGTIIVSM HBAZ_PANTR 1 1 -
SLTKTERTIIVSM HBAZ_HUMAN 1 1 -
SLTRTERTIILSL HBAZ_CAPHI 1 1 -
SLTKAERTMVVSI HBAZ_HORSE 1 1 -
SLTKAERTIIGSM HBAZ_PIG 1 1 -
SLMKNERAIIMSM HBAZ_MOUSE 1 1 -

Motif 2 width=10
Element Seqn Id St Int Rpt
LHPGSAQLRA HBAZ_PANTR 48 34 -
LHPGSAQLRA HBAZ_HUMAN 48 34 -
LHSGSAQLRA HBAZ_CAPHI 48 34 -
LHEGSPQLRA HBAZ_HORSE 48 34 -
LNPGSAQLRA HBAZ_PIG 48 34 -
LHHGSQQLRA HBAZ_MOUSE 48 34 -

Motif 3 width=7
Element Seqn Id St Int Rpt
SIDNIGG HBAZ_PANTR 72 14 -
SIDDIGG HBAZ_HUMAN 72 14 -
SIDNVTS HBAZ_CAPHI 72 14 -
SIDNVAG HBAZ_HORSE 72 14 -
SIDNVSA HBAZ_PIG 72 14 -
SIDNLSS HBAZ_MOUSE 72 14 -

Motif 4 width=9
Element Seqn Id St Int Rpt
SVVSSVLTE HBAZ_PANTR 130 51 -
SVVSSVLTE HBAZ_HUMAN 130 51 -
SIVSGVLTE HBAZ_CAPHI 130 51 -
SIVSSVLTE HBAZ_HORSE 130 51 -
TIVSGVLTE HBAZ_PIG 130 51 -
SILSSILTE HBAZ_MOUSE 130 51 -