PDBsum entry 4hcs

Signaling protein

PDB id: 4hcs

Contents

Protein chain

67 a.a.

Waters ×113

PDB id:

4hcs

Name:

Signaling protein

Title:

Structure of novel subfamily cx chemokine solved by sulfur sad

Structure:

Uncharacterized protein. Chain: a. Fragment: cxl-c24a. Engineered: yes

Source:

Danio rerio. Leopard danio,zebra danio,zebra fish. Organism_taxid: 7955. Gene: si:dkey-25o1.2. Expressed in: pichia. Expression_system_taxid: 4919

Resolution:

1.28Å R-factor: 0.184 R-free: 0.206

Authors:

D.Rajasekaran,C.Fan,W.Meng,J.W.Pflugrath,E.J.Lolis

Key ref:

D.Rajasekaran et al. (2014). Structural insight into the evolution of a new chemokine family from zebrafish. Proteins, 82, 708-716. PubMed id: 23900850 DOI: 10.1002/prot.24380

Date:

01-Oct-12 Release date: 16-Oct-13

Protein chain

F1Q6N2  (F1Q6N2_DANRE) -  CX chemokine ligand 34b, duplicate 11 from Danio rerio

Seq: 115 a.a.

Struc: 67 a.a.

DOI no: 10.1002/prot.24380

Proteins 82:708-716 (2014)

PubMed id: 23900850

Structural insight into the evolution of a new chemokine family from zebrafish.

D.Rajasekaran, C.Fan, W.Meng, J.W.Pflugrath, E.J.Lolis.

ABSTRACT

The mammalian chemokine family is segregated into four families - CC, CXC, CX3C, and XC-based on the arrangement of cysteines and the corresponding disulfides. Sequencing of the Danio rerio (zebrafish) genome has identified more than double the amount of human chemokines with the absence of the CX3C family and the presence of a new family, CX. The only other family with a single cysteine in the N-terminal region is the XC family. Human lymphotactin (XCL1) has two interconverting structures due to dynamic changes that occur in the protein. Similar to an experiment with XCL1 that identified the two structural forms, we probed for multiple forms of zCXL1 using heparin affinity. The results suggest only a single form of CXL1 is present. We used sulfur-SAD phasing to determine the three-dimensional structure CXL1. Zebrafish CXL1 (zCXL1) has three disulfides that appear to be important for a stable structure. One disulfide is common to all chemokines except those that belong to the XC family, another is similar to a subset of CC chemokines containing three disulfides, but the third disulfide is unique to the CX family. We analyzed the electrostatic potential of the zCXL1 structure and identified the likely heparin-binding site for glycosaminoglycans (GAGs). zCXL1 has a similar sequence identity with human CCL5 and CXCL12, but the structure is more related to CCL5. Our structural analysis supports the phylogenetic and genomic studies on the evolution of the CXL family. Proteins 2014; 82:708-716. © 2013 Wiley Periodicals, Inc.