5ELM

Crystal structure of L-aspartate/glutamate specific racemase in complex with L-glutamate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural basis for an atypical active site of an l-aspartate/glutamate-specific racemase from Escherichia coli

Ahn, J.W., Chang, J.H., Kim, K.J.

(2015) FEBS Lett 589: 3842-3847

  • DOI: 10.1016/j.febslet.2015.11.003
  • Primary Citation of Related Structures:  
    5ELL, 5ELM

  • PubMed Abstract: 

    • We determined the crystal structure of EcL-DER to elucidate protein function and substrate specificity. Unlike other asp/glu racemases, EcL-DER has an unbalanced pair of catalytic residues, Thr83/Cys197, at the active site that is crucial for L- to D-unidirectional racemase activity ...

    We determined the crystal structure of EcL-DER to elucidate protein function and substrate specificity. Unlike other asp/glu racemases, EcL-DER has an unbalanced pair of catalytic residues, Thr83/Cys197, at the active site that is crucial for L- to D-unidirectional racemase activity. EcL-DER exhibited racemase activity for both L-glutamate and L-aspartate, but had threefold higher activity for L-glutamate. Based on the structure of the EcL-DER(C197S) mutant in complex with L-glutamate, we determined the binding mode of the L-glutamate substrate in EcL-DER and provide a structural basis for how the protein utilizes L-glutamate as a main substrate. The unidirectionality, despite an equilibrium constant of unity, can be understood in terms of the Haldane relationship.

    Organizational Affiliation: 

    School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea. Electronic address: kkim@knu.ac.kr.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Asp/Glu_racemase family proteinA, B, C, D238Escherichia coliMutation(s): 0 
Gene Names: 
ygeA, A6519_003952, A8W81_002760, A9X72_04945, ABE90_009660, ACN002_2857, ACN68_00635, ACN81_20060, ACU57_24110, AM270_00630, AM464_05915, AML23_09215, AT335_004404, AUQ29_19990, AW059_10980, B7C15_002233, BANRA_01362, BANRA_03912, BANRA_04263, BB545_23930, BFL24_19905, BHF52_09040, BHS81_17025, BJI68_00725, BK292_22760, BMT50_16000, BMT91_10770, BN17_27241, BOH76_11055, BON63_07900, BON70_18940, BON72_20970, BON73_20125, BON76_20320, BON94_07500, BON95_17930, BvCms2454_02110, BvCmsHHP019_01807, BvCmsHHP056_02041, BvCmsKKP036_04048, BvCmsKKP057_01872, BvCmsNSNP036_01023, BvCmsSIP082_01309, BVL39_12645, C2U48_19720, C3F40_22375, C5542_002864, C5F72_05655, C6B22_06105, C6N50_000475, C7B02_19705, C9114_10915, C9160_16455, C9E67_05505, C9Z62_02350, CCS08_05395, CD42_001519, CF32_001556, CG692_06710, CG831_002248, CIG67_09740, CN875_002063, CO706_12090, COD50_06860, CWS33_02795, D3O91_13735, D4V09_21370, D6T60_11185, D9D77_01025, D9F92_16440, D9H13_18730, D9H94_17895, D9J11_18030, D9K17_09330, DAH18_08565, DAH34_10670, DAH37_01025, DAH50_00340, DB282_03625, DEN89_06490, DEN95_06105, DIV22_30085, DM968_19855, DS732_21010, DTL43_07930, DXT69_09710, DXT73_07755, E0I42_10805, E2119_13900, E2127_11035, E2128_06070, E2129_11015, E5S34_04375, E5S38_03570, E5S52_07995, EAI46_05580, EAN77_05830, EC1094V2_843, EC3234A_49c00260, EC95NR1_02093, ECs3697, EH88_001006, EHD79_07070, EHH55_20505, EI021_14255, EIZ93_12150, EKI52_20250, EL79_0859, EL80_0862, ELT21_08765, ELV08_14885, ELY05_07795, ETECE36_01584, ETECE925_00991, EYX47_20030, EYX55_16400, F6U69_03460, F9400_11470, F9407_13615, F9V24_07155, F9X20_024570, F9X20_24860, FMP09_14895, FPS82_15405, FQE77_09475, FQF29_08830, FTV90_23605, FTV92_24240, FV293_15540, FVB16_08895, FY127_22655, G5632_02680, G5696_11845, G6Z99_05075, G7635_001799, G9448_19565, GBE29_11810, GIB53_15670, GKF86_10105, GKF89_09500, GKG12_00685, GNZ05_07280, GP662_05025, GP946_10800, GP954_11505, GQE64_12260, GQE87_11660, GQF58_02150, GQF59_02150, GQM04_06965, GQM06_14065, GQM10_02900, GQW76_04975, GRQ19_08735, GRW05_08465, GRW57_12805, GRW80_15180, GRW81_16315, GUC01_19940, H4P50_04650, H4P51_04700, HHG09_003327, HHH44_000146, HIE44_003398, HIR12_000780, HJN04_001916, HJO75_002241, HMS79_03210, HNO08_11395, HNV65_00885, HVW11_15675, HVY77_05425, HVZ33_04850, HX136_04740, HZ71_002353, I6H00_23525, I6H01_07895, NCTC10090_04116, NCTC11022_02926, NCTC13216_00889, NCTC4450_02970, NCTC8960_03712, NCTC9036_01070, NCTC9045_01146, NCTC9048_01096, ND22_001995, PGD_04267, PU06_01765, SAMEA3472043_01335, SAMEA3484427_03233, SAMEA3484429_03350, SAMEA3751407_04129, SAMEA3752386_04039, SAMEA3752557_03104, SAMEA3753064_02222, SAMEA3753290_02912, SAMEA3753300_01172, WP4S18E08_09490, WQ89_09855

EC: 5.1.1.13 (PDB Primary Data), 5.1.1.10 (UniProt), 5.1.1 (UniProt)
UniProt
Find proteins for C3SWD2 (Escherichia coli)
Explore C3SWD2 
Go to UniProtKB:  C3SWD2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC3SWD2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.53α = 90
b = 81.25β = 111.39
c = 83.96γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2016-01-13
    Changes: Database references