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
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(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: HI1679, HI_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

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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