PDBsum entry: 2spt

Hydrolase(serine proteinase)

PDB id: 2spt

Contents

Protein chain

145 a.a. *

Ligands

NAG

Metals

_SR ×8

Waters ×90

* Residue conservation analysis

PDB id:

2spt

Name:

Hydrolase(serine proteinase)

Title:

Differences in the metal ion structure between sr-and ca-pro fragment 1

Structure:

Prothrombin. Chain: a. Engineered: yes

Source:

Bos taurus. Cattle. Organism_taxid: 9913

Resolution:

2.50Å R-factor: 0.167

Authors:

A.Tulinsky

Key ref:

T.P.Seshadri et al. (1994). Differences in the metal ion structure between Sr- and Ca-prothrombin fragment 1. Biochemistry, 33, 1087-1092. PubMed id: 8110739 DOI: 10.1021/bi00171a006

Date:

01-Feb-94 Release date: 31-May-94

Protein chain

P00735  (THRB_BOVIN) -  Prothrombin

Seq: 625 a.a.

Struc: 145 a.a.*

* PDB and UniProt seqs differ at 10 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.4.21.5 - Thrombin.
• Reaction: Preferential cleavage: Arg-|-Gly; activates fibrinogen to fibrin and releases fibrinopeptide A and B.

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular region (1 term)
• Biochemical function: calcium ion binding (1 term)

DOI no: 10.1021/bi00171a006

Biochemistry 33:1087-1092 (1994)

PubMed id: 8110739

Differences in the metal ion structure between Sr- and Ca-prothrombin fragment 1.

T.P.Seshadri, E.Skrzypczak-Jankun, M.Yin, A.Tulinsky.

ABSTRACT

The structure of Sr-prothrombin fragment 1 has been solved and refined by restrained least-squares methods at 2.5-A resolution to a crystallographic R value of 0.167. The protein structure is very similar to that of Ca-fragment 1. A polymeric array of five Sr2+ ions separated by about 4.0 A is buried among six gamma-carboxyglutamic acid (Gla) residues; three other Sr2+ ions interact with other Gla residues and are located further apart. One of these was not found in the Ca-fragment 1 structure. The coordination of the Sr2+ ions resembles that of Ca2+, but there are some significant differences between them. The most notable is the lack of water coordination with Sr2+ ions and two conformations for Gla 8, which change the coordination of Sr-2 and Sr-3. A hexose moiety of an oligosaccharide was located in the vicinity of Asn101 that was flexibly disordered in Ca-fragment 1. The new Sr2+ ion found may be involved in metal ion phospholipid binding interactions along with Sr-1, and Sr-7, Sr-8.