Home Page for Calbindin D9k

Calbindin D9k

Primary information about calbindin D9k:
Basic chemical and physical information	Basic biological information	Basic genomic information	Metal ion binding constants	Interspecies sequence alignment	Information on function
Summary of structural studies	Information on the conformational change	List of available structures	Information about mutations	References about calbindin D9k	Other web resources about calbindin D9k
Additional information about calbindin D_9k
Two-dimensional "Sequence map"	Links to contact maps of calbindin	Links to NMR assignments for calbindin	Dihedral angles in apo and calcium-loaded calbindin	Per atom solvent accessible surface area in apo and calcium-loaded calbindin

Basic Information

Basic Chemical and Physical Information:
Additional names and abbreviations:	calbindin D9k: intestinal calcium-binding protein (ICaBP); 9 kDa cholecalcin
Isoforms:	No information about isoforms is stored in the database
Yeast Protein Database Entries:	No links to the YPD are stored in the database

Number of amino acids:	78 (all species) View a list of all sources stored in the database
Molecular weight:	8.787 kD (Bos taurus) - 8.907 kD (Rattus norvegicus) View a list of all sources stored in the database
pI:	calculated pI (Homo sapiens) = 4.7 (InfoCard)
Number of functional calcium binding sites:	Bos taurus: 2 (InfoCard) Sus scrofa: 2 (InfoCard)
Macroscopic calcium binding constants:	Bos taurus, low salt: K₁ = 1.6 x 10⁸; K₂ = 4 x 10⁸ (measured by: competitive chelator pH: 7.5 temperature: 25 degrees Celsius buffer: 0.002 M Tris-HCl ) (InfoCard) Bos taurus, medium salt: K₁ = 5 x 10⁶; K₂ = 1.6 x 10⁷ (measured by: competitive chelator pH: 7.5 temperature: 25 degrees Celsius salt: 50 mM KCl buffer: 0.002 M Tris-HCl ) (InfoCard) Bos taurus, medium salt: K₁ = 3.2 x 10⁶; K₂ = 6.3 x 10⁶ (measured by: competitive chelator pH: 7.5 temperature: 25 degrees Celsius salt: 100 mM KCl buffer: 0.002 M Tris-HCl ) (InfoCard) Bos taurus, high salt: K₁ = 2 x 10⁶; K₂ = 3.2 x 10⁶ (measured by: competitive chelator pH: 7.5 temperature: 25 degrees Celsius salt: 150 mM KCl buffer: 0.002 M Tris-HCl ) (InfoCard) Sus scrofa, low salt: K₁ = 8 x 10⁷ +/- 1.5 x 10⁷; K₂ = 1.8 x 10⁸ +/- 2 x 10⁷ (measured by: competitive chelator pH: 7.5 temperature: 25 degrees Celsius buffer: 0.002 M Tris-HCl ) (InfoCard)
Other metal binding constants:	not yet available in the data library
Protein stability:	Bos taurus: free energy of unfolding: 4.78 +/- 0.24 kcal/mol, cooperativity of unfolding: 0.908 kcal/(mol M) (measured by: urea denaturation pH: 7.1 temperature: 25 degrees Celsius buffer: 0.001 M EGTA, 0.02 M Pipes ) (InfoCard)
Post-translational modifications:	not yet available in the data library

Basic Biological Information:
Source organisms:	Bos taurus, Homo sapiens, Mus musculus, Sus scrofa, Rattus norvegicus View an annotated list of all sources stored in the database
Tissues:	mammals: intestine (InfoCard) Mus musculus: kidney (InfoCard) Mus musculus: yolk sac (InfoCard) Rattus norvegicus: uterus (InfoCard) Rattus norvegicus: yolk sac (InfoCard) Rattus norvegicus: lung (InfoCard) Rattus norvegicus: ameloblasts of teeth (InfoCard)
Subcellular localization:	not yet available in the data library
Regulation:	all sources: regulated by Vitamin D (upregulates expression) (InfoCard) Rattus norvegicus: regulated by estrogen (causes expression in uterine tissues of non-pregnant rats, but only partially mimics effects of pregnancy on calbindin distribution in the uterus) (InfoCard)

Genomic Information:
GenBank entries:	View a list of GenBank entries stored in the database
Gene length:	Rattus norvegicus, expressed (GenBank code X16635): 2.5 kb (InfoCard)
Gene structure:	Rattus norvegicus, expressed: GenBank code X16635; intron 1 is in the 5'-untranslated region, intron 2 precedes residue 45; intron 1 is 306 bp, intron 2 is 1806 bp (InfoCard)
Promoter:	Rattus norvegicus, (GenBank code X16635): promoter contains CCAAT-like element, 72 bp upstream from transcription start site (putative) (InfoCard) Rattus norvegicus, (GenBank code X16635): promoter contains inversed CCAAT-like element, 146 bp upstream from transcription start site (putative) (InfoCard) Rattus norvegicus, (GenBank code X16635): promoter contains TATA box, 31-25 bp upstream from transcription start site (InfoCard)
Gene copies:	not yet available in the data library
Alleles:	no alleles are currently stored in the data library
Chromosomal localization:	Homo sapiens, expressed (GenBank code X76451): p22.2 region of chromosome X (not linked to hypophosphathemic rickets) (InfoCard)

Interspecies Sequence Alignment



                |-helixA-|--loop1------|helixB| 
                 En**nn**nX**Y*Z**#Ix**zn**nn*n          

BOVINE  :    KSPEELKGIFEKYAAKEGDPNQLSKEELKLLLQTEFPSLLKGGS
HUMAN   : STKKSPEELKRIFEKYAAKEGDPDQLSKDELKLLIQAEFPSLLKGPN
PORCINE : SAQKSPAELKSIFEKYAAKEGDPNQLSKEELKQLIQAEFPSLLKGPR
RAT     : SAKKSPEEMKSIFQKYAAKEGDPNQLSKEELKLLIQSEFPSLLKASS


         |-helixC-|--loop2-----|helixD| 
          En**nn**nX*Y*ZG#Ix**zn**nn*n

BOVINE  : TLDELFEELDKNGDGEVSFEEFQVLVKKISQ                      
HUMAN   : TLDDLFQELDKNGDGEVSFEEFQVLVKKISQ                      
PORCINE : TLDDLFQELDKNGNGEVSFEEFQVLVKKISQ                      
RAT     : TLDNLFKELDKNGDGEVSYEEFEVFFKKLSQ

Sequence alignment for the entire S100 subfamily

Functional Information:

General information:

no general functional information is currently stored in the database

Biological roles:

fetal calcium uptake (Movement of calcium across the placenta increase dramatically in the last trimester, when fetal skeletal mineralization is occuring)
immunocytochemical or immunohistochemical evidence in Rattus norvegicus: calbindin D9k is found in epithelial and myometrial cells only in pregnant rats (InfoCard)
biochemical evidence in Rattus norvegicus: calbindin D9k is found in uterine tissues from pregnant rats, but not from non-pregnant rats (InfoCard)
uterine contractions: is found in myometrial fibers, where it may help regulate the strengthm duration, and frequency of contractions by altering the free calcium levels in the cytoplasm
immunocytochemical or immunohistochemical evidence in Rattus norvegicus: calbindin D9k is found in myometrial fibers (InfoCard)
calcification of bone
immunocytochemical or immunohistochemical evidence in Rattus norvegicus: calbindin D9k is found in the correct locations to support activity in calcification of bone (InfoCard)
calcification of teeth
immunocytochemical or immunohistochemical evidence in Rattus norvegicus: calbindin D9k is found in the correct locations to support activity in calcification of teeth (InfoCard)
calcium transport and uptake in mammalian intestine
biochemical evidence in Rattus norvegicus: Active transport of calcium across the intestine is directly proportional to levels of calbindin D9k (InfoCard)

Disease states:

not yet available in the data library

Target molecules:

not yet available in the data library

Structural Information:

Calcium-coordination:
Bos taurus:	EF1 ; X = A14 O; Y = E17 O; Z = D19 O; -X = H₂O; -Y = Q22 O; -Z1 = E27 OE1; -Z2 = E27 OE2 EF2 ; X = D54 OD1; Y = N56 OD1; Z = D58 OD1; -X = H₂O; -Y = E60 O; -Z1 = E65 OE1; -Z2 = E65 OE2 (InfoCard)

Nature of the conformational changes:
Conformational change between apo and two calcium ions bound states:	The conformational change is very minor. The overall fold remains the same. There are some changes in the packing of helix IV. (InfoCard)
Conformational change between apo and one magnesium ion bound states:	One magnesium ion binds to site II. The conformation of the Mg1 state is distinct form the apo or Ca2 state. Helical packing is more compact. In particular, the angle between helix III and IV is ~25 degrees less in the Mg1 state than in the calcium-loaded or apo states. (InfoCard)
Conformational change between apo and one manganese ion bound states:	One manganese ion binds to site II. The conformation of the Mn1 state is distinct form the apo or Ca2 state, but very similar to the Mg1 state. Helical packing is more compact than in the apo or Ca2 states. In particular, the angle between helix III and IV is ~25 degrees less in the Mn1 state than in the calcium-loaded or apo states. (InfoCard)

Secondary structure: (as reported in the PDB file and its accompanying reference)
Bos taurus, apo state:	Helices: helix 1: 3 - 15, helix 2: 25 - 35, helix 3: 46 - 53, helix 4: 63 - 74 Beta strands: strand 1: 21 - 24, strand 2: 59 - 62 (pdb code 1CLB: InfoCard)
Bos taurus, one cadmium ion bound state:	Helices: helix 1: 3 - 15, helix 2: 25 - 35, helix 3: 46 - 53, helix 4: 63 - 73 (pdb code 1CDN: InfoCard)
Bos taurus, one magnesium ion bound state:	Helices: helix 1: 2 - 14, helix 2: 24 - 35, helix 3: 45 - 54, helix 4: 62 - 73 (pdb code 5ICB: InfoCard)
Bos taurus, one manganese ion bound state:	Helices: helix 1: 2 - 14, helix 2: 24 - 35, helix 3: 45 - 54, helix 4: 62 - 73 (pdb code 6ICB: InfoCard)
Bos taurus, two calcium ions bound state:	Helices: helix 1: 2 - 15, helix 2: 24 - 36, helix 3: 45 - 54, helix 4: 62 - 75 (pdb code 4ICB: InfoCard)

Additional structural information:
View a table of interhelical angles from various structures View a table of interhelical contacts from various structures View a table of hydrogen bonds observed in various structures

Available structures: (follow the links from the PDB code to the retrieve the PDB files)
Apo Structures:	1CLB: Bos taurus, full length protein, pH 5.3 NMR solution structure, 33 models, 28.44 restraints per residue (InfoCard)
Calcium Loaded Structures:	2BCB: Bos taurus, full length protein, pH 6 NMR solution structure, 33 models, 15.68 restraints per residue 2 Ca ions bound (InfoCard) 1B1G: Bos taurus, full length protein, pH 6 NMR solution structure, 10 models, 15.68 restraints per residue (InfoCard) 4ICB: Bos taurus, full length protein, Crystal structure, 1.6 angstrom resolution, R-value = 18.8 2 Ca ions bound (InfoCard) 3ICB: Bos taurus, full length protein, Crystal structure, 2.3 angstrom resolution, R-value = 17.8 2 Ca ions bound (InfoCard) 1CB1: Sus scrofa, full length protein, pH 6 NMR solution structure, 13 models, 7.28 restraints per residue 2 Ca ions bound (InfoCard)
Other Metal Bound Structures:	1CDN: Bos taurus, full length protein, pH 6 NMR solution structure, 24 models, 13.55 restraints per residue 1 Cd ion bound (InfoCard) 5ICB: Bos taurus, full length protein, Crystal structure, 1.6 angstrom resolution, R-value = 19.5, R-free = 28.5 1 Mg ion bound (InfoCard) 6ICB: Bos taurus, full length protein, Crystal structure, 1.9 angstrom resolution, R-value = 19, R-free = 25.8 1 Mn ion bound (InfoCard)
Mutant Structures:	1BOD: Bos taurus, full length protein, NMR solution structure, 24 models 2 Ca ions bound Mutations: A14 deleted + A15D + P20G + N21 deleted + P43M (InfoCard) 1BOC: Bos taurus, full length protein, NMR solution structure, 29 models 2 Ca ions bound Mutations: A15D + P20G + P43M (InfoCard)

Information about mutants:

P43G (Bos taurus)
P43M (Bos taurus)
A14 deleted + A15D + P20G + N21 deleted + P43M (Bos taurus)
A15D + P20G + P43M (Bos taurus)
Y13F (Bos taurus)
P20G (Bos taurus)
E17Q (Bos taurus)
P20 deleted (Bos taurus)
P20G + N21 deleted (Bos taurus)
E60D (Bos taurus)
L6V + P43M (Bos taurus)
F10A + P43M (Bos taurus)
L23A + P43M (Bos taurus)
L23G + P43M (Bos taurus)
L28A + P43M (Bos taurus)
P43M + V61A (Bos taurus)
P43M + F66W (Bos taurus)
P43M + F66A (Bos taurus)
P43M + V70L (Bos taurus)
P43M + I73V (Bos taurus)
P43M + V61G (Bos taurus)