Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D4  (3D View)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D4  (3D View)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 721.31 kDa 
• Atom Count: 48417 
• Modelled Residue Count: 6471 
• Deposited Residue Count: 6768 
• Unique protein chains: 1

3FEQ

Crystal structure of uncharacterized protein eah89906

• PDB DOI: 10.2210/pdb3FEQ/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): unidentified
• Mutation(s): No 


• Deposited: 2008-11-30 Released: 2008-12-16 
• Deposition Author(s): Patskovsky, Y., Bonanno, J., Romero, R., Freeman, J., Lau, C., Smith, D., Bain, K., Wasserman, S.R., Raushel, F., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free: 0.281 
• R-Value Work: 0.238 
• R-Value Observed: 0.239 

Literature

Functional identification and structure determination of two novel prolidases from cog1228 in the amidohydrolase superfamily .

Xiang, D.F., Patskovsky, Y., Xu, C., Fedorov, A.A., Fedorov, E.V., Sisco, A.A., Sauder, J.M., Burley, S.K., Almo, S.C., Raushel, F.M.

(2010) Biochemistry 49: 6791-6803

• PubMed: 20604542 
• DOI: 10.1021/bi100897u
• Primary Citation of Related Structures:  
  3FEQ, 3MKV, 3MTW, 3N2C


• PubMed Abstract: 
  

Two uncharacterized enzymes from the amidohydrolase superfamily belonging to cog1228 were cloned, expressed, and purified to homogeneity. The two proteins, Sgx9260c ( gi|44242006 ) and Sgx9260b ( gi|44479596 ), were derived from environmental DNA samples originating from the Sargasso Sea. The catalytic function and substrate profiles for Sgx9260c and Sgx9260b were determined using a comprehensive library of dipeptides and N-acyl derivative of l-amino acids. Sgx9260c catalyzes the hydrolysis of Gly-l-Pro, l-Ala-l-Pro, and N-acyl derivatives of l-Pro. The best substrate identified to date is N-acetyl-l-Pro with a value of k(cat)/K(m) of 3 x 10(5) M(-1) s(-1). Sgx9260b catalyzes the hydrolysis of l-hydrophobic l-Pro dipeptides and N-acyl derivatives of l-Pro. The best substrate identified to date is N-propionyl-l-Pro with a value of k(cat)/K(m) of 1 x 10(5) M(-1) s(-1). Three-dimensional structures of both proteins were determined by X-ray diffraction methods (PDB codes 3MKV and 3FEQ ). These proteins fold as distorted (beta/alpha)(8)-barrels with two divalent cations in the active site. The structure of Sgx9260c was also determined as a complex with the N-methylphosphonate derivative of l-Pro (PDB code 3N2C ). In this structure the phosphonate moiety bridges the binuclear metal center, and one oxygen atom interacts with His-140. The alpha-carboxylate of the inhibitor interacts with Tyr-231. The proline side chain occupies a small substrate binding cavity formed by residues contributed from the loop that follows beta-strand 7 within the (beta/alpha)(8)-barrel. A total of 38 other proteins from cog1228 are predicted to have the same substrate profile based on conservation of the substrate binding residues. The structure of an evolutionarily related protein, Cc2672 from Caulobacter crecentus, was determined as a complex with the N-methylphosphonate derivative of l-arginine (PDB code 3MTW ).

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Organizational Affiliation: 

Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUTATIVE AMIDOHYDROLASE	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	423	unidentified	Mutation(s): 0
UniProt
Find proteins for Q393A1 (Burkholderia lata (strain ATCC 17760 / DSM 23089 / LMG 22485 / NCIMB 9086 / R18194 / 383)) Explore Q393A1  Go to UniProtKB:  Q393A1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	AA [auth F], BA [auth F], CA [auth G], DA [auth G], EA [auth H], FA [auth H], GA [auth I], HA [auth I], IA [auth J], JA [auth J], KA [auth K], LA [auth K], MA [auth L], NA [auth L], OA [auth M], PA [auth M], Q [auth A], QA [auth N], R [auth A], RA [auth N], S [auth B], SA [auth O], T [auth B], TA [auth O], U [auth C], UA [auth P], V [auth C], VA [auth P], W [auth D], X [auth D], Y [auth E], Z [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free: 0.281 
• R-Value Work: 0.238 
• R-Value Observed: 0.239 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.208	α = 81.75
b = 108.048	β = 80.36
c = 171.132	γ = 74.4

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-11-30 
• Released Date: 2008-12-16 
Deposition Author(s): Patskovsky, Y., Bonanno, J., Romero, R., Freeman, J., Lau, C., Smith, D., Bain, K., Wasserman, S.R., Raushel, F., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-12-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-10-10
  Changes: Database references
• Version 1.3: 2018-11-21
  Changes: Data collection, Database references, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary