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(-) Description

Title :  CRYSTAL STRUCTURE OF UREIDOGLYCOLATE DEHYDROGENASE IN TERNARY COMPLEX WITH NADH AND GLYOXYLATE
 
Authors :  M. I. Kim, S. Rhee
Date :  12 Jun 12  (Deposition) - 16 Jan 13  (Release) - 16 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alld, Nad(P)H-Dependent Oxidoreductase, Ureide Pathway, Ureidoglycolate, Oxalurate, Antiparallel Beta-Sheet Fold, Ureidoglycolate Dehydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. I. Kim, I. Shin, S. Cho, J. Lee, S. Rhee
Structural And Functional Insights Into (S)-Ureidoglycolate Dehydrogenase, A Metabolic Branch Point Enzyme In Nitrogen Utilization.
Plos One V. 7 52066 2012
PubMed-ID: 23284870  |  Reference-DOI: 10.1371/JOURNAL.PONE.0052066

(-) Compounds

Molecule 1 - UREIDOGLYCOLATE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.154
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ALLD, ECDH10B_0473
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 316385
    Strain: DH10B

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1GLV1Ligand/IonGLYOXYLIC ACID
2NAI2Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:41 , HIS A:44 , HIS A:116 , GLY A:118 , ILE A:120 , SER A:140 , THR A:156 , PRO A:158 , PHE A:173 , ASP A:174 , MET A:175 , ALA A:176 , TYR A:303 , TYR A:304 , GLY A:306 , ASP A:308 , GLN A:309 , GLV A:402 , HOH A:519 , HOH A:530 , HOH A:535 , HOH A:539 , HOH A:540 , HOH A:541 , HOH A:549 , HOH A:563 , HOH A:635 , HOH A:748 , PHE B:147 , PRO B:223 , LYS B:224BINDING SITE FOR RESIDUE NAI A 401
2AC2SOFTWAREARG A:48 , HIS A:116 , SER A:140 , ASP A:141 , MET A:251 , NAI A:401 , HOH A:698BINDING SITE FOR RESIDUE GLV A 402
3AC3SOFTWAREPHE A:147 , PRO A:223 , LYS A:224 , HOH A:517 , HOH A:776 , HIS B:44 , HIS B:116 , GLY B:118 , ILE B:120 , SER B:140 , THR B:156 , PRO B:158 , PHE B:173 , ASP B:174 , ALA B:176 , ALA B:181 , TYR B:303 , TYR B:304 , PRO B:305 , GLY B:306 , ASP B:308 , GLN B:309 , HOH B:513 , HOH B:536 , HOH B:617 , HOH B:679 , HOH B:819BINDING SITE FOR RESIDUE NAI B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4FJU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4FJU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4FJU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FJU)

(-) Exons   (0, 0)

(no "Exon" information available for 4FJU)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:338
                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4fjua_ A: automated matches                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee..eeeee....hhhhhhhhhhhhhhhhhhhhheeeeeeeee.....hhhhhhhhhhh..eeeeee....................eeeeee.....eeeeee......hhhhhhhhhh........ee..............ee....hhhhhhhhhhhhhhhhhhhh..hhhhh............eeeeeeee.hhhh.hhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhee.hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fju A   1 MKISRETLHQLIENKLCQAGLKREHAATVAEVLVYADARGIHSHGAVRVEYYAERISKGGTNREPEFRLEETGPCSAILHADNAAGQVAAKMGMEHAIKTAQQNGVAVVGISRMGHSGAISYFVQQAARAGFIGISMCQSDPMVVPFGGAEIYYGTNPLAFAAPGEGDEILTFDMATTVQAWGKVLDARSRNMSIPDTWAVDKNGVPTTDPFAVHALLPAAGPKGYGLMMMIDVLSGVLLGLPFGRQVSSMYDDLHAGRNLGQLHIVINPNFFSSSELFRQHLSQTMRELNAITPAPGFNQVYYPGQDQDIKQRKAAVEGIEIVDDIYQYLISDALYN 338
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330        


Chain B from PDB  Type:PROTEIN  Length:312
                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4fjub_ B: automated matches                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.........eeeeee..eeeeeeeeehhhhhhhhhhhhhhhhhhhhheeeeeeeee.....hhhhhhhhhhh..eeeeee....................eeeeee.....eeeeee......hhhhhhhhhh........ee..............ee....hhhhhhhhhhhhhhhhhhhh..hhhhh............eeeeeeee.hhhh.hhhhhhhhhhhhhhhhhh.............hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4fju B   4 SRETLHQLIENKLCQAGLKREHAATVAEVLVYADARGIHSHGAVRVEYYAERISKGGTNREPEFRLEETGPCSAILHADNAAGQVAAKMGMEHAIKTAQQNGVAVVGISRMGHSGAISYFVQQAARAGFIGISMCQSDPMVVPFGGAEIYYGTNPLAFAAPGEGDEILTFDMATTVQAWGKVLDARSRNMSIPDTWAVDKNGVPTTDPFAVHALLPAAGPKGYGLMMMIDVLSGVLLGLPFGRQVSSMYDDLHAGRNLGQLHIVINPNFFSSSELFRQHLSQTMRELNAITPAPGFNQVYYPGQDQDIKQRK 315
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4FJU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FJU)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4FJU)

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  4fju
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  1.1.1.154
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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(-) Related Entries Specified in the PDB File

4fjt 4h8a