1K1E

Structure Of the cobalt-bound form of the deoxy-D-mannose-octulosonate 8-phosphate phosphatase (YrbI) From Haemophilus Influenzae (HI1679)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.178 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

From structure to function: YrbI from Haemophilus influenzae (HI1679) is a phosphatase.

Parsons, J.F.Lim, K.Tempczyk, A.Krajewski, W.Eisenstein, E.Herzberg, O.

(2002) Proteins 46: 393-404

  • DOI: 10.1002/prot.10057
  • Primary Citation of Related Structures:  
    1J8D, 1K1E

  • PubMed Abstract: 
  • The crystal structure of the YrbI protein from Haemophilus influenzae (HI1679) was determined at a 1.67-A resolution. The function of the protein had not been assigned previously, and it is annotated as hypothetical in sequence databases. The protein exhibits the alpha/beta-hydrolase fold (also termed the Rossmann fold) and resembles most closely the fold of the L-2-haloacid dehalogenase (HAD) superfamily ...

    The crystal structure of the YrbI protein from Haemophilus influenzae (HI1679) was determined at a 1.67-A resolution. The function of the protein had not been assigned previously, and it is annotated as hypothetical in sequence databases. The protein exhibits the alpha/beta-hydrolase fold (also termed the Rossmann fold) and resembles most closely the fold of the L-2-haloacid dehalogenase (HAD) superfamily. Following this observation, a detailed sequence analysis revealed remote homology to two members of the HAD superfamily, the P-domain of Ca(2+) ATPase and phosphoserine phosphatase. The 19-kDa chains of HI1679 form a tetramer both in solution and in the crystalline form. The four monomers are arranged in a ring such that four beta-hairpin loops, each inserted after the first beta-strand of the core alpha/beta-fold, form an eight-stranded barrel at the center of the assembly. Four active sites are located at the subunit interfaces. Each active site is occupied by a cobalt ion, a metal used for crystallization. The cobalt is octahedrally coordinated to two aspartate side-chains, a backbone oxygen, and three solvent molecules, indicating that the physiological metal may be magnesium. HI1679 hydrolyzes a number of phosphates, including 6-phosphogluconate and phosphotyrosine, suggesting that it functions as a phosphatase in vivo. The physiological substrate is yet to be identified; however the location of the gene on the yrb operon suggests involvement in sugar metabolism.


    Organizational Affiliation

    Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
deoxy-D-mannose-octulosonate 8-phosphate phosphatase
A, B, C, D, E, F, G, H, I, J, K, L
A, B, C, D, E, F, G, H, I, J, K, L
180Haemophilus influenzae Rd KW20Mutation(s): 0 
Gene Names: HI1679HI_1679
EC: 3.1.3 (PDB Primary Data), 3.1.3.45 (UniProt)
UniProt
Find proteins for P45314 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Explore P45314 
Go to UniProtKB:  P45314
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45314
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HG
Query on HG

Download Ideal Coordinates CCD File 
BA [auth D],
EA [auth E],
EB [auth K],
IA [auth F],
JB [auth L],
BA [auth D],
EA [auth E],
EB [auth K],
IA [auth F],
JB [auth L],
MA [auth G],
N [auth A],
QA [auth H],
S [auth B],
UA [auth I],
W [auth C],
ZA [auth J]
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

Download Ideal Coordinates CCD File 
CB [auth J],
SA [auth H],
Y [auth C]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AB [auth J],
BB [auth J],
CA [auth D],
FA [auth E],
FB [auth K],
AB [auth J],
BB [auth J],
CA [auth D],
FA [auth E],
FB [auth K],
GA [auth E],
JA [auth F],
KA [auth F],
KB [auth L],
NA [auth G],
O [auth A],
P [auth A],
RA [auth H],
T [auth B],
U [auth B],
VA [auth I],
WA [auth I],
X [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
GB [auth K],
HB [auth K],
OA [auth G],
Q [auth A],
XA [auth I],
GB [auth K],
HB [auth K],
OA [auth G],
Q [auth A],
XA [auth I],
Z [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CO
Query on CO

Download Ideal Coordinates CCD File 
AA [auth D],
DA [auth E],
DB [auth K],
HA [auth F],
IB [auth L],
AA [auth D],
DA [auth E],
DB [auth K],
HA [auth F],
IB [auth L],
LA [auth G],
M [auth A],
PA [auth H],
R [auth B],
TA [auth I],
V [auth C],
YA [auth J]
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.178 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.3α = 90
b = 109.1β = 107.6
c = 179.1γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
CNSrefinement
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-02-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance