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: 
ygeAA6519_003952A8W81_002760A9X72_04945ABE90_009660ACN002_2857ACN68_00635ACN81_20060ACU57_24110AM270_00630AM464_05915AML23_09215AT335_004404AUQ29_19990AW059_10980B7C15_002233BANRA_01362BANRA_03912BANRA_04263BB545_23930BFL24_19905BHF52_09040BHS81_17025BJI68_00725BK292_22760BMT50_16000BMT91_10770BN17_27241BOH76_11055BON63_07900BON70_18940BON72_20970BON73_20125BON76_20320BON94_07500BON95_17930BvCms2454_02110BvCmsHHP019_01807BvCmsHHP056_02041BvCmsKKP036_04048BvCmsKKP057_01872BvCmsNSNP036_01023BvCmsSIP082_01309BVL39_12645C2U48_19720C3F40_22375C5542_002864C5F72_05655C6B22_06105C6N50_000475C7B02_19705C9114_10915C9160_16455C9E67_05505C9Z62_02350CCS08_05395CD42_001519CF32_001556CG692_06710CG831_002248CIG67_09740CN875_002063CO706_12090COD50_06860CWS33_02795D3O91_13735D4V09_21370D6T60_11185D9D77_01025D9F92_16440D9H13_18730D9H94_17895D9J11_18030D9K17_09330DAH18_08565DAH34_10670DAH37_01025DAH50_00340DB282_03625DEN89_06490DEN95_06105DIV22_30085DM968_19855DS732_21010DTL43_07930DXT69_09710DXT73_07755E0I42_10805E2119_13900E2127_11035E2128_06070E2129_11015E5S34_04375E5S38_03570E5S52_07995EAI46_05580EAN77_05830EC1094V2_843EC3234A_49c00260EC95NR1_02093ECs3697EH88_001006EHD79_07070EHH55_20505EI021_14255EIZ93_12150EKI52_20250EL79_0859EL80_0862ELT21_08765ELV08_14885ELY05_07795ETECE36_01584ETECE925_00991EYX47_20030EYX55_16400F6U69_03460F9400_11470F9407_13615F9V24_07155F9X20_024570F9X20_24860FMP09_14895FPS82_15405FQE77_09475FQF29_08830FTV90_23605FTV92_24240FV293_15540FVB16_08895FY127_22655G5632_02680G5696_11845G6Z99_05075G7635_001799G9448_19565GBE29_11810GIB53_15670GKF86_10105GKF89_09500GKG12_00685GNZ05_07280GP662_05025GP946_10800GP954_11505GQE64_12260GQE87_11660GQF58_02150GQF59_02150GQM04_06965GQM06_14065GQM10_02900GQW76_04975GRQ19_08735GRW05_08465GRW57_12805GRW80_15180GRW81_16315GUC01_19940H4P50_04650H4P51_04700HHG09_003327HHH44_000146HIE44_003398HIR12_000780HJN04_001916HJO75_002241HMS79_03210HNO08_11395HNV65_00885HVW11_15675HVY77_05425HVZ33_04850HX136_04740HZ71_002353I6H00_23525I6H01_07895NCTC10090_04116NCTC11022_02926NCTC13216_00889NCTC4450_02970NCTC8960_03712NCTC9036_01070NCTC9045_01146NCTC9048_01096ND22_001995PGD_04267PU06_01765SAMEA3472043_01335SAMEA3484427_03233SAMEA3484429_03350SAMEA3751407_04129SAMEA3752386_04039SAMEA3752557_03104SAMEA3753064_02222SAMEA3753290_02912SAMEA3753300_01172WP4S18E08_09490WQ89_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
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  • 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




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