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PR00624

Identifier
HISTONEH5  [View Relations]  [View Alignment]  
Accession
PR00624
No. of Motifs
7
Creation Date
07-DEC-1996  (UPDATE 10-JUN-1999)
Title
Histone H5 signature
Database References

INTERPRO; IPR001386
PDB; 1HST
SCOP; 1HST
CATH; 1HST
Literature References
1. RAMAKRISHNAN, V., FINCH, J.T., GRAZIANO, V., LEE, P.L. AND SWEET, R.M.
Crystal structure of globular domain of histone H5 and its implications
for nucleosome binding.
NATURE 362 219-23 (1993).
 
2. ZARBOCK, J., CLORE, G.M. AND GRONENBORN, A.M.
Nuclear magnetic resonance study of the globular domain of chicken
histone H5: resonance assignment and secondary structure.
PROC.NATL.ACAD.SCI.U.S.A. 83 7628-7632 (1986).

Documentation
Histone H5 is a nuclear protein involved in the condensation of nucleosome
chains into higher order structures. In this respect, it performs the same
function as histone H1, and replaces H1 in certain cells.
 
The structure of GH5, the globular domain (residues 22-100) of the linker
histone H5, has been solved [1,2]. The fold is similar to the DNA-binding
domain of the catabolite gene activator protein, CAP, thus providing a
possible model for the binding of GH5 to DNA. The structure comprises 3
alpha-helices and 2 short beta-strands.
 
HISTONEH5 is a 7-element fingerprint that provides a signature for the
H5 histones. The fingerprint was derived from an initial alignment of
5 sequences: the motifs were drawn from short conserved regions spanning
the full alignment length - motifs 1-3 encode most of helices 1-3 res.; 
motif 4 spans the 2 beta-strands; and motifs 5-7 span a lysine-rich region
in the C-terminal section beyond the globular domain. Two iterations on
OWL29.0 were required to reach convergence, at which point a true set
comprising 9 sequences was identified. Several partial matches were also
found, all of which are closely related H1 histones.
 
An update on SPTR37_9f identified a true set of 9 sequences, and 84
partial matches.
Summary Information
   9 codes involving  7 elements
0 codes involving 6 elements
5 codes involving 5 elements
14 codes involving 4 elements
28 codes involving 3 elements
37 codes involving 2 elements
Composite Feature Index
79999999
60000000
55505505
4139112885
341902615128
231122711128
1234567
True Positives
H10_HUMAN     H10_MOUSE     H10_RAT       H5A_XENLA     
H5B_XENLA H5_ANSAN H5_CAIMO H5_CHICK
Q91759
True Positive Partials
Codes involving 5 elements
O46140 O46141 O46142 O46143
O46362
Codes involving 4 elements
H11_MOUSE H13_MOUSE H13_RABIT H1B_HUMAN
H1D_STRPU H1G_STRPU H1_CHITH H1_LYTPI
H1_TIGCA Q02539 Q19743 Q23785
Q23791 Q39576
Codes involving 3 elements
H11R_CHICK H12_CAEEL H12_GLYBA H12_MOUSE
H12_RAT H13_GLYBA H14_MOUSE H1A_CHITE
H1B_STRPU H1C2_XENLA H1C_CHITE H1C_HUMAN
H1E_STRPU H1_DROHY H1_DROVI H1_PARAN
O16277 O18317 O18319 O18642
O18649 O65794 O65795 Q23792
Q91369 Q91760 Q94555 Q94972
Codes involving 2 elements
H101_CHICK H103_CHICK H110_CHICK H11L_CHICK
H11_CAEEL H12_VOLCA H15_MOUSE H162_TRYCR
H1A_HUMAN H1A_PLADU H1A_XENLA H1B_CHITE
H1B_XENLA H1C1_XENLA H1D_HUMAN H1E_CHIPA
H1E_CHITE H1L_MYTCA H1L_MYTTR H1O_CHITH
H1T_MOUSE H1T_RAT H1_ANAPL H1_CHICK
H1_DROME H1_LYCES H1_ONCMY H1_SALTR
H1_WHEAT O01833 O18316 O22672
Q14529 Q18336 Q26072 Q40225
Q93901
Sequence Titles
H10_HUMAN   HISTONE H1' (H1.0) (H1(0)) - HOMO SAPIENS (HUMAN). 
H10_MOUSE HISTONE H1' (H1.0) (H1(0)) - MUS MUSCULUS (MOUSE).
H10_RAT HISTONE H1' (H1.0) (H1(0)) - RATTUS NORVEGICUS (RAT).
H5A_XENLA HISTONE H5A (XLH5A) (H1D) (H1-SA) - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
H5B_XENLA HISTONE H5B (XLH5B) (H1E) (H1-SB) - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
H5_ANSAN HISTONE H5 - ANSER ANSER ANSER (WESTERN GRAYLAG GOOSE).
H5_CAIMO HISTONE H5 - CAIRINA MOSCHATA (MUSCOVY DUCK).
H5_CHICK HISTONE H5 - GALLUS GALLUS (CHICKEN).
Q91759 HISTONE H1(0)-1 - XENOPUS LAEVIS (AFRICAN CLAWED FROG).

O46140 HISTONE 1 - MYTILUS EDULIS (BLUE MUSSEL).
O46141 HISTONE 1 - MYTILUS EDULIS (BLUE MUSSEL).
O46142 HISTONE 1 - MYTILUS EDULIS (BLUE MUSSEL).
O46143 HISTONE 1 - MYTILUS EDULIS (BLUE MUSSEL).
O46362 HISTONE 1 - MYTILUS EDULIS (BLUE MUSSEL).

H11_MOUSE HISTONE H1.1 (H1 VAR.3) (H1A) - MUS MUSCULUS (MOUSE).
H13_MOUSE HISTONE H1.3 (H1 VAR.4) (H1D) - MUS MUSCULUS (MOUSE).
H13_RABIT HISTONE H1.3 - ORYCTOLAGUS CUNICULUS (RABBIT).
H1B_HUMAN HISTONE H1B (H1.4) - HOMO SAPIENS (HUMAN).
H1D_STRPU HISTONE H1-DELTA - STRONGYLOCENTROTUS PURPURATUS (PURPLE SEA URCHIN).
H1G_STRPU HISTONE H1-GAMMA, LATE - STRONGYLOCENTROTUS PURPURATUS (PURPLE SEA URCHIN).
H1_CHITH HISTONE H1 - CHIRONOMUS THUMMI THUMMI (MIDGE).
H1_LYTPI LATE HISTONE H1 - LYTECHINUS PICTUS (PAINTED SEA URCHIN).
H1_TIGCA HISTONE H1 - TIGRIOPUS CALIFORNICUS.
Q02539 HISTONE H1.1 - HOMO SAPIENS (HUMAN).
Q19743 SIMILAR TO HISTONE H1. NCBI GI: 1118043 - CAENORHABDITIS ELEGANS.
Q23785 HISTONE H1-III - CHIRONOMUS THUMMI PIGER (MIDGE).
Q23791 HISTONE H1-II - CHIRONOMUS THUMMI THUMMI (MIDGE).
Q39576 HISTONE H1 - CHLAMYDOMONAS REINHARDTII.

H11R_CHICK HISTONE H1.11R - GALLUS GALLUS (CHICKEN).
H12_CAEEL HISTONE H1.2 - CAENORHABDITIS ELEGANS.
H12_GLYBA HISTONE H1-II - GLYPTOTENDIPES BARBIPES.
H12_MOUSE HISTONE H1.2 (H1 VAR.1) (H1C) - MUS MUSCULUS (MOUSE).
H12_RAT HISTONE H1.2 (H1D) - RATTUS NORVEGICUS (RAT).
H13_GLYBA HISTONE H1-III - GLYPTOTENDIPES BARBIPES.
H14_MOUSE HISTONE H1.4 (H1 VAR.2) (H1E) - MUS MUSCULUS (MOUSE).
H1A_CHITE HISTONE H1A - CHIRONOMUS TENTANS (MIDGE).
H1B_STRPU HISTONE H1-BETA, LATE EMBRYONIC - STRONGYLOCENTROTUS PURPURATUS (PURPLE SEA URCHIN).
H1C2_XENLA HISTONE H1C (CLONE XLHW8) - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
H1C_CHITE HISTONE H1C - CHIRONOMUS TENTANS (MIDGE).
H1C_HUMAN HISTONE H1C (H1.3) - HOMO SAPIENS (HUMAN).
H1E_STRPU HISTONE H1, EARLY EMBRYONIC - STRONGYLOCENTROTUS PURPURATUS (PURPLE SEA URCHIN).
H1_DROHY HISTONE H1 - DROSOPHILA HYDEI (FRUIT FLY).
H1_DROVI HISTONE H1 - DROSOPHILA VIRILIS (FRUIT FLY).
H1_PARAN HISTONE H1, GONADAL - PARECHINUS ANGULOSUS (ANGULATE SEA URCHIN).
O16277 F59A7.4 PROTEIN - CAENORHABDITIS ELEGANS.
O18317 HISTONE H1-II-2 - CHIRONOMUS THUMMI THUMMI (MIDGE).
O18319 HISTONE H1D - CHIRONOMUS TENTANS (MIDGE).
O18642 HISTONE H1 - CHAETOPTERUS VARIOPEDATUS.
O18649 HISTONE H1.2 - CAENORHABDITIS ELEGANS.
O65794 HISTONE H1 - TRITICUM AESTIVUM (WHEAT).
O65795 HISTONE H1 - TRITICUM AESTIVUM (WHEAT).
Q23792 HISTONE H1-II-2 - CHIRONOMUS THUMMI PIGER (MIDGE).
Q91369 H1A=SOMATIC H1 HISTONE - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
Q91760 LINKER HISTONE H1C - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
Q94555 HISTONE H1.2 - DROSOPHILA VIRILIS (FRUIT FLY).
Q94972 HISTONE H1.3 - DROSOPHILA VIRILIS (FRUIT FLY).

H101_CHICK HISTONE H1.01 - GALLUS GALLUS (CHICKEN).
H103_CHICK HISTONE H1.03 - GALLUS GALLUS (CHICKEN).
H110_CHICK HISTONE H1.10 (METHYLATED DNA BINDING PROTEIN-2-H1) (MDBP-2-H1) - GALLUS GALLUS (CHICKEN).
H11L_CHICK HISTONE H1.11L - GALLUS GALLUS (CHICKEN).
H11_CAEEL HISTONE H1.1 - CAENORHABDITIS ELEGANS.
H12_VOLCA HISTONE H1-II - VOLVOX CARTERI.
H15_MOUSE HISTONE H1.5 (H1 VAR.5) (H1B) - MUS MUSCULUS (MOUSE).
H162_TRYCR HISTONE H1.M6.2 - TRYPANOSOMA CRUZI.
H1A_HUMAN HISTONE H1A (H1.1) - HOMO SAPIENS (HUMAN).
H1A_PLADU HISTONE H1A, SPERM - PLATYNEREIS DUMERILII (DUMERIL'S CLAM WORM).
H1A_XENLA HISTONE H1A - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
H1B_CHITE HISTONE H1B - CHIRONOMUS TENTANS (MIDGE).
H1B_XENLA HISTONE H1B - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
H1C1_XENLA HISTONE H1C (CLONE XLHW2) - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
H1D_HUMAN HISTONE H1D (H1.2) - HOMO SAPIENS (HUMAN).
H1E_CHIPA HISTONE H1E - CHIRONOMUS PALLIDIVITTATUS (MIDGE).
H1E_CHITE HISTONE H1E - CHIRONOMUS TENTANS (MIDGE).
H1L_MYTCA SPERM-SPECIFIC PROTEIN PHI-2B (PL-II*) (SPERM-SPECIFIC HISTONE H1-LIKE PROTEIN) - MYTILUS CALIFORNIANUS (CALIFORNIA MUSSEL).
H1L_MYTTR SPERM-SPECIFIC PROTEIN PHI-2B (PL-II*) (SPERM-SPECIFIC HISTONE H1-LIKE PROTEIN) [CONTAINS: PROTEIN PHI-3 (PL-IV)] - MYTILUS TROSSULUS (BLUE MUSSEL).
H1O_CHITH HISTONE H1, ORPHON - CHIRONOMUS THUMMI THUMMI (MIDGE).
H1T_MOUSE HISTONE H1T (TESTICULAR H1 HISTONE) - MUS MUSCULUS (MOUSE).
H1T_RAT HISTONE H1T - RATTUS NORVEGICUS (RAT).
H1_ANAPL HISTONE H1 - ANAS PLATYRHYNCHOS (DOMESTIC DUCK).
H1_CHICK HISTONE H1 - GALLUS GALLUS (CHICKEN).
H1_DROME HISTONE H1 - DROSOPHILA MELANOGASTER (FRUIT FLY).
H1_LYCES HISTONE H1 - LYCOPERSICON ESCULENTUM (TOMATO).
H1_ONCMY HISTONE H1 - ONCORHYNCHUS MYKISS (RAINBOW TROUT) (SALMO GAIRDNERI).
H1_SALTR HISTONE H1 - SALMO TRUTTA (BROWN TROUT).
H1_WHEAT HISTONE H1 - TRITICUM AESTIVUM (WHEAT).
O01833 CODED FOR BY C. ELEGANS CDNA CEMSE95F - CAENORHABDITIS ELEGANS.
O18316 HISTONE H1-II-2 - CHIRONOMUS THUMMI THUMMI (MIDGE).
O22672 HISTONE H1 - APIUM GRAVEOLENS (CELERY).
Q14529 HISTONE H1.5 - HOMO SAPIENS (HUMAN).
Q18336 C30G7.1 PROTEIN - CAENORHABDITIS ELEGANS.
Q26072 SEA URCHIN (P. MILIARIS) HISTONES H4, H2B, H3, H2A AND H1 (IN THAT ORDER, CONTAINING MANY SEQUENCE GAPS). (SEE ALSO FOR ALLELIC SEQUENCE.) - PSAMMECHINUS MILIARIS (SAND SEA URCHIN).
Q40225 MEIOTIN-1 - LILIUM LONGIFLORUM (TRUMPET LILY).
Q93901 M163.3 PROTEIN - CAENORHABDITIS ELEGANS.
Scan History
OWL29_0    2  25   NSINGLE    
SPTR37_9f 2 97 NSINGLE
Initial Motifs
Motif 1  width=22
Element Seqn Id St Int Rpt
AKPKRSKALKKSTDHPKYSDMI H5A_XENLA 11 11 -
AKPRRSKASKKSTDHPKYSDMI H5B_XENLA 9 9 -
AKPKRVKASRRSASHPTYSEMI H5_CHICK 11 11 -
AKPKRAKAPRKPASHPSYSEMI H5_CAIMO 12 12 -
AKPKRARAPRKPASHPTYSEMI H5_ANSAN 12 12 -

Motif 2 width=18
Element Seqn Id St Int Rpt
AEKSRSGSSRQSIQKYIK H5A_XENLA 38 5 -
AKKSRSGSSRQSIQKYIK H5B_XENLA 36 5 -
AEKSRGGSSRQSIQKYIK H5_CHICK 38 5 -
AEKSRGGSSRQSIQKYVK H5_CAIMO 39 5 -
ADKSRGGSSRQSIQKYVK H5_ANSAN 39 5 -

Motif 3 width=19
Element Seqn Id St Int Rpt
YKVGENADSQIKLSIKRLV H5A_XENLA 58 2 -
YTVGENADSQIKLSIKRLV H5B_XENLA 56 2 -
YKVGHNADLQIKLSIRRLL H5_CHICK 58 2 -
YKVGQHADLQIKLSIRRLL H5_CAIMO 59 2 -
YKVGQHADLQIKLAIRRLL H5_ANSAN 59 2 -

Motif 4 width=25
Element Seqn Id St Int Rpt
GALKQTKGVGASGSFRLAKADEGKK H5A_XENLA 79 2 -
GTLKQTKGVGASGSFRLAKADEVKK H5B_XENLA 77 2 -
GVLKQTKGVGASGSFRLAKSDKAKR H5_CHICK 79 2 -
GVLKQTKGVGASGSYRLAKGDKAKK H5_CAIMO 80 2 -
GVLKQTKGVGASGSFRLAKGDKAKR H5_ANSAN 80 2 -

Motif 5 width=15
Element Seqn Id St Int Rpt
KKAVSPKKVAKPKKA H5A_XENLA 113 9 -
KKAVSPKKAAKPKKA H5B_XENLA 111 9 -
RRSTSPKKAARPRKA H5_CHICK 113 9 -
RRSTSPRKAARPRKA H5_CAIMO 117 12 -
RKSTSPKKAARPRKA H5_ANSAN 117 12 -

Motif 6 width=18
Element Seqn Id St Int Rpt
KPAPSPKKAKKTKTVKAK H5A_XENLA 151 23 -
KPAPSPRKAKKTKTVRAK H5B_XENLA 149 23 -
KSRASPKKAKKPKTVKAK H5_CHICK 144 16 -
KSRASPKKAKKPKTVKAK H5_CAIMO 148 16 -
KSRASPKKAKKPKTVKAK H5_ANSAN 148 16 -

Motif 7 width=20
Element Seqn Id St Int Rpt
SKVKKAKPSKPKAKASPKKS H5A_XENLA 173 4 -
SKAKKAKPSKPKAKASPKKS H5B_XENLA 171 4 -
SKAKKVKRSKPRAKSGARKS H5_CHICK 166 4 -
SKVKKAKRSKPRAKSGARKS H5_CAIMO 170 4 -
SKPKKARRSKPRAKSGARKS H5_ANSAN 170 4 -
Final Motifs
Motif 1  width=22
Element Seqn Id St Int Rpt
AKPKRAKASKKSTDHPKYSDMI H10_HUMAN 10 10 -
AKPKRSKALKKSTDHPKYSDMI H5A_XENLA 11 11 -
AKPKRAKAAKKSTDHPKYSDMI H10_RAT 10 10 -
AKPKRAKASKKSTDHPKYSDMI H10_MOUSE 10 10 -
AKPRRSKASKKSTDHPKYSDMI Q91759 9 9 -
AKPRRSKASKKSTDHPKYSDMI H5B_XENLA 9 9 -
AKPKRVKASRRSASHPTYSEMI H5_CHICK 11 11 -
AKPKRAKAPRKPASHPSYSEMI H5_CAIMO 12 12 -
AKPKRARAPRKPASHPTYSEMI H5_ANSAN 12 12 -

Motif 2 width=18
Element Seqn Id St Int Rpt
AEKNRAGSSRQSIQKYIK H10_HUMAN 37 5 -
AEKSRSGSSRQSIQKYIK H5A_XENLA 38 5 -
AEKNRAGSSRQSIQKYIK H10_RAT 37 5 -
AEKNRAGSSRQSIQKYIK H10_MOUSE 37 5 -
AEKSRSGSSRQSIQKYIK Q91759 36 5 -
AKKSRSGSSRQSIQKYIK H5B_XENLA 36 5 -
AEKSRGGSSRQSIQKYIK H5_CHICK 38 5 -
AEKSRGGSSRQSIQKYVK H5_CAIMO 39 5 -
ADKSRGGSSRQSIQKYVK H5_ANSAN 39 5 -

Motif 3 width=19
Element Seqn Id St Int Rpt
YKVGENADSQIKLSIKRLV H10_HUMAN 57 2 -
YKVGENADSQIKLSIKRLV H5A_XENLA 58 2 -
YKVGENADSQIKLSIKRLV H10_RAT 57 2 -
YKVGENADSQIKLSIKRLV H10_MOUSE 57 2 -
YTVGENADSQIKLSIKRLV Q91759 56 2 -
YTVGENADSQIKLSIKRLV H5B_XENLA 56 2 -
YKVGHNADLQIKLSIRRLL H5_CHICK 58 2 -
YKVGQHADLQIKLSIRRLL H5_CAIMO 59 2 -
YKVGQHADLQIKLAIRRLL H5_ANSAN 59 2 -

Motif 4 width=25
Element Seqn Id St Int Rpt
GVLKQTKGVGASGSFRLAKSDEPKK H10_HUMAN 78 2 -
GALKQTKGVGASGSFRLAKADEGKK H5A_XENLA 79 2 -
GVLKQTKGVGASGSFRLAKGDEPKR H10_RAT 78 2 -
GVLKQTKGVGASGSFRLAKGDEPKR H10_MOUSE 78 2 -
GTLKQTKGVGASGSFRLAKADEVKK Q91759 77 2 -
GTLKQTKGVGASGSFRLAKADEVKK H5B_XENLA 77 2 -
GVLKQTKGVGASGSFRLAKSDKAKR H5_CHICK 79 2 -
GVLKQTKGVGASGSYRLAKGDKAKK H5_CAIMO 80 2 -
GVLKQTKGVGASGSFRLAKGDKAKR H5_ANSAN 80 2 -

Motif 5 width=15
Element Seqn Id St Int Rpt
KKVATPKKASKPKKA H10_HUMAN 114 11 -
KKAVSPKKVAKPKKA H5A_XENLA 113 9 -
KKVATPKKAAKPKKA H10_RAT 114 11 -
KKVATPKKAAKPKKA H10_MOUSE 114 11 -
KKAVSPKKAAKPKKA Q91759 111 9 -
KKAVSPKKAAKPKKA H5B_XENLA 111 9 -
RRSTSPKKAARPRKA H5_CHICK 113 9 -
RRSTSPRKAARPRKA H5_CAIMO 117 12 -
RKSTSPKKAARPRKA H5_ANSAN 117 12 -

Motif 6 width=18
Element Seqn Id St Int Rpt
KLAATPKKAKKPKTVKAK H10_HUMAN 148 19 -
KPAPSPKKAKKTKTVKAK H5A_XENLA 151 23 -
KPAATPKKAKKPKIVKVK H10_RAT 148 19 -
KPAATPKKAKKPKVVKVK H10_MOUSE 148 19 -
KPAPSPRKAKKTKTVRAK Q91759 149 23 -
KPAPSPRKAKKTKTVRAK H5B_XENLA 149 23 -
KSRASPKKAKKPKTVKAK H5_CHICK 144 16 -
KSRASPKKAKKPKTVKAK H5_CAIMO 148 16 -
KSRASPKKAKKPKTVKAK H5_ANSAN 148 16 -

Motif 7 width=20
Element Seqn Id St Int Rpt
SKPKKAKPVKPKAKSSAKRA H10_HUMAN 170 4 -
SKVKKAKPSKPKAKASPKKS H5A_XENLA 173 4 -
SKPKKAKPVKPKAKSSAKRA H10_RAT 170 4 -
SKPKKAKTVKPKAKSSAKRA H10_MOUSE 170 4 -
SKAKKAKPSKPKAKASPKKS Q91759 171 4 -
SKAKKAKPSKPKAKASPKKS H5B_XENLA 171 4 -
SKAKKVKRSKPRAKSGARKS H5_CHICK 166 4 -
SKVKKAKRSKPRAKSGARKS H5_CAIMO 170 4 -
SKPKKARRSKPRAKSGARKS H5_ANSAN 170 4 -