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(-) Description

Title :  L-ALA-D/L-GLU EPIMERASE
 
Authors :  A. M. Gulick, D. M. Z. Schmidt, J. A. Gerlt, I. Rayment
Date :  02 Aug 01  (Deposition) - 21 Dec 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Enolase Superfamily, Muconate Lactonizing Subgroup, Alpha-Beta Barrel, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. Gulick, D. M. Schmidt, J. A. Gerlt, I. Rayment
Evolution Of Enzymatic Activities In The Enolase Superfamily: Crystal Structures Of The L-Ala-D/L-Glu Epimerases From Escherichia Coli And Bacillus Subtilis.
Biochemistry V. 40 15716 2001
PubMed-ID: 11747448  |  Reference-DOI: 10.1021/BI011641P

(-) Compounds

Molecule 1 - L-ALA-D/L-GLU EPIMERASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PET
    Fragment: L-ALA-D/L-GLU EPIMERASE
    Gene: YKFB
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MG4Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP D:191 , GLU D:219 , ASP D:244 , HOH D:1032 , HOH D:1056 , HOH D:1091BINDING SITE FOR RESIDUE MG D 1001
2AC2SOFTWAREASP B:191 , GLU B:219 , ASP B:244 , HOH B:1125 , HOH B:1126 , HOH B:1127BINDING SITE FOR RESIDUE MG B 1002
3AC3SOFTWAREASP A:191 , GLU A:219 , ASP A:244 , HOH A:2039 , HOH A:2040 , HOH A:2041BINDING SITE FOR RESIDUE MG A 1003
4AC4SOFTWAREASP C:191 , GLU C:219 , ASP C:244 , HOH C:1058 , HOH C:1059 , HOH C:1094BINDING SITE FOR RESIDUE MG C 1004
5AC5SOFTWAREALA A:42 , VAL A:43 , TRP A:45 , GLN A:113 , ILE A:354 , SER C:40 , GLY C:41BINDING SITE FOR RESIDUE GOL A 2001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1JPM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JPM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JPM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1JPM)

(-) Exons   (0, 0)

(no "Exon" information available for 1JPM)

(-) 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:359
 aligned with AEEP_BACSU | O34508 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:359
                                    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       340       350         
           AEEP_BACSU     1 MKIIRIETSRIAVPLTKPFKTALRTVYTAESVIVRITYDSGAVGWGEAPPTLVITGDSMDSIESAIHHVLKPALLGKSLAGYEAILHDIQHLLTGNMSAKAAVEMALYDGWAQMCGLPLYQMLGGYRDTLETDYTVSVNSPEEMAADAENYLKQGFQTLKIKVGKDDIATDIARIQEIRKRVGSAVKLRLDANQGWRPKEAVTAIRKMEDAGLGIELVEQPVHKDDLAGLKKVTDATDTPIMADESVFTPRQAFEVLQTRSADLINIKLMKAGGISGAEKINAMAEACGVECMVGSMIETKLGITAAAHFAASKRNITRFDFDAPLMLKTDVFNGGITYSGSTISMPGKPGLGIIGAAL 359
               SCOP domains d1jpma2 A:1-125 L-Ala-D/L-Glu epimerase                                                                                      d1jpma1 A:126-359 L-Ala-D/L-Glu epimerase                                                                                                                                                                                                  SCOP domains
               CATH domains 1jpmA01 A:1-115 Enolase-like, N-terminal domain                                                                    1jpmA02 A:116-359 Enolase superfamily                                                                                                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeeeeeee......................eeeeee.........hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhh.....eee..eee...hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhh...eee.....hhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhhhhh..eeee..hhhhhh....eee..eee..eee........eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jpm A   1 MKIIRIETSRIAVPLTKPFKTALRTVYTAESVIVRITYDSGAVGWGEAPPTLVITGDSMDSIESAIHHVLKPALLGKSLAGYEAILHDIQHLLTGNMSAKAAVEMALYDGWAQMCGLPLYQMLGGYRDTLETDYTVSVNSPEEMAADAENYLKQGFQTLKIKVGKDDIATDIARIQEIRKRVGSAVKLRLDANQGWRPKEAVTAIRKMEDAGLGIELVEQPVHKDDLAGLKKVTDATDTPIMADESVFTPRQAFEVLQTRSADLINIKLMKAGGISGAEKINAMAEACGVECMVGSMIETKLGITAAAHFAASKRNITRFDFDAPLMLKTDVFNGGITYSGSTISMPGKPGLGIIGAAL 359
                                    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       340       350         


Chain B from PDB  Type:PROTEIN  Length:359
 aligned with AEEP_BACSU | O34508 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:359
                                    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       340       350         
           AEEP_BACSU     1 MKIIRIETSRIAVPLTKPFKTALRTVYTAESVIVRITYDSGAVGWGEAPPTLVITGDSMDSIESAIHHVLKPALLGKSLAGYEAILHDIQHLLTGNMSAKAAVEMALYDGWAQMCGLPLYQMLGGYRDTLETDYTVSVNSPEEMAADAENYLKQGFQTLKIKVGKDDIATDIARIQEIRKRVGSAVKLRLDANQGWRPKEAVTAIRKMEDAGLGIELVEQPVHKDDLAGLKKVTDATDTPIMADESVFTPRQAFEVLQTRSADLINIKLMKAGGISGAEKINAMAEACGVECMVGSMIETKLGITAAAHFAASKRNITRFDFDAPLMLKTDVFNGGITYSGSTISMPGKPGLGIIGAAL 359
               SCOP domains d1jpmb2 B:1-125 L-Ala-D/L-Glu epimerase                                                                                      d1jpmb1 B:126-359 L-Ala-D/L-Glu epimerase                                                                                                                                                                                                  SCOP domains
               CATH domains 1jpmB01 B:1-115 Enolase-like, N-terminal domain                                                                    1jpmB02 B:116-359 Enolase superfamily                                                                                                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................eeeeeeeeeeeeee....eeeeee.........hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.hhhhhh.....eee..ee....hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhh...eee.....hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhhhhh..eeee..hhhhhh....eee..eee..eee........eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jpm B   1 MKIIRIETSRIAVPLTKPFKTALRTVYTAESVIVRITYDSGAVGWGEAPPTLVITGDSMDSIESAIHHVLKPALLGKSLAGYEAILHDIQHLLTGNMSAKAAVEMALYDGWAQMCGLPLYQMLGGYRDTLETDYTVSVNSPEEMAADAENYLKQGFQTLKIKVGKDDIATDIARIQEIRKRVGSAVKLRLDANQGWRPKEAVTAIRKMEDAGLGIELVEQPVHKDDLAGLKKVTDATDTPIMADESVFTPRQAFEVLQTRSADLINIKLMKAGGISGAEKINAMAEACGVECMVGSMIETKLGITAAAHFAASKRNITRFDFDAPLMLKTDVFNGGITYSGSTISMPGKPGLGIIGAAL 359
                                    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       340       350         


Chain C from PDB  Type:PROTEIN  Length:358
 aligned with AEEP_BACSU | O34508 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:358
                                    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       340       350        
           AEEP_BACSU     1 MKIIRIETSRIAVPLTKPFKTALRTVYTAESVIVRITYDSGAVGWGEAPPTLVITGDSMDSIESAIHHVLKPALLGKSLAGYEAILHDIQHLLTGNMSAKAAVEMALYDGWAQMCGLPLYQMLGGYRDTLETDYTVSVNSPEEMAADAENYLKQGFQTLKIKVGKDDIATDIARIQEIRKRVGSAVKLRLDANQGWRPKEAVTAIRKMEDAGLGIELVEQPVHKDDLAGLKKVTDATDTPIMADESVFTPRQAFEVLQTRSADLINIKLMKAGGISGAEKINAMAEACGVECMVGSMIETKLGITAAAHFAASKRNITRFDFDAPLMLKTDVFNGGITYSGSTISMPGKPGLGIIGAA 358
               SCOP domains d1jpmc2 C:1-125 L-Ala-D/L-Glu epimerase                                                                                      d1jpmc1 C:126-358 L-Ala-D/L-Glu epimerase                                                                                                                                                                                                 SCOP domains
               CATH domains 1jpmC01 C:1-115 Enolase-like, N-terminal domain                                                                    1jpmC02 C:116-358 Enolase superfamily                                                                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................eeeeeeeeeeeeee....eeeeee.........hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.hhhhhh.....eee..ee....hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhh...eee.....hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhhhhh..eeee..hhhhhh....eee..eee..eee........eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jpm C   1 MKIIRIETSRIAVPLTKPFKTALRTVYTAESVIVRITYDSGAVGWGEAPPTLVITGDSMDSIESAIHHVLKPALLGKSLAGYEAILHDIQHLLTGNMSAKAAVEMALYDGWAQMCGLPLYQMLGGYRDTLETDYTVSVNSPEEMAADAENYLKQGFQTLKIKVGKDDIATDIARIQEIRKRVGSAVKLRLDANQGWRPKEAVTAIRKMEDAGLGIELVEQPVHKDDLAGLKKVTDATDTPIMADESVFTPRQAFEVLQTRSADLINIKLMKAGGISGAEKINAMAEACGVECMVGSMIETKLGITAAAHFAASKRNITRFDFDAPLMLKTDVFNGGITYSGSTISMPGKPGLGIIGAA 358
                                    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       340       350        


Chain D from PDB  Type:PROTEIN  Length:358
 aligned with AEEP_BACSU | O34508 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:358
                                    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       340       350        
           AEEP_BACSU     1 MKIIRIETSRIAVPLTKPFKTALRTVYTAESVIVRITYDSGAVGWGEAPPTLVITGDSMDSIESAIHHVLKPALLGKSLAGYEAILHDIQHLLTGNMSAKAAVEMALYDGWAQMCGLPLYQMLGGYRDTLETDYTVSVNSPEEMAADAENYLKQGFQTLKIKVGKDDIATDIARIQEIRKRVGSAVKLRLDANQGWRPKEAVTAIRKMEDAGLGIELVEQPVHKDDLAGLKKVTDATDTPIMADESVFTPRQAFEVLQTRSADLINIKLMKAGGISGAEKINAMAEACGVECMVGSMIETKLGITAAAHFAASKRNITRFDFDAPLMLKTDVFNGGITYSGSTISMPGKPGLGIIGAA 358
               SCOP domains d1jpmd2 D:1-125 L-Ala-D/L-Glu epimerase                                                                                      d1jpmd1 D:126-358 L-Ala-D/L-Glu epimerase                                                                                                                                                                                                 SCOP domains
               CATH domains 1jpmD01 D:1-115 Enolase-like, N-terminal domain                                                                    1jpmD02 D:116-358 Enolase superfamily                                                                                                                                                                                                               CATH domains
           Pfam domains (1) ---MR_MLE_N-1jpmD01 D:4-124                                                                                                 -----------------------------------------------------------------------------------------------------------------------MR_MLE_C-1jpmD05 D:244-355                                                                                      --- Pfam domains (1)
           Pfam domains (2) ---MR_MLE_N-1jpmD02 D:4-124                                                                                                 -----------------------------------------------------------------------------------------------------------------------MR_MLE_C-1jpmD06 D:244-355                                                                                      --- Pfam domains (2)
           Pfam domains (3) ---MR_MLE_N-1jpmD03 D:4-124                                                                                                 -----------------------------------------------------------------------------------------------------------------------MR_MLE_C-1jpmD07 D:244-355                                                                                      --- Pfam domains (3)
           Pfam domains (4) ---MR_MLE_N-1jpmD04 D:4-124                                                                                                 -----------------------------------------------------------------------------------------------------------------------MR_MLE_C-1jpmD08 D:244-355                                                                                      --- Pfam domains (4)
         Sec.struct. author ..........................................eeeeee.........hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhh.....eee..ee....hhhhhhhhhhhhhhh...eeeee.....................hhheeeee.....hhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhh...eee.....hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhhhhh..eeee..hhhhhh....eee..eee..eee........eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jpm D   1 MKIIRIETSRIAVPLTKPFKTALRTVYTAESVIVRITYDSGAVGWGEAPPTLVITGDSMDSIESAIHHVLKPALLGKSLAGYEAILHDIQHLLTGNMSAKAAVEMALYDGWAQMCGLPLYQMLGGYRDTLETDYTVSVNSPEEMAADAENYLKQGFQTLKIKVGKDDIATDIARIQEIRKRVGSAVKLRLDANQGWRPKEAVTAIRKMEDAGLGIELVEQPVHKDDLAGLKKVTDATDTPIMADESVFTPRQAFEVLQTRSADLINIKLMKAGGISGAEKINAMAEACGVECMVGSMIETKLGITAAAHFAASKRNITRFDFDAPLMLKTDVFNGGITYSGSTISMPGKPGLGIIGAA 358
                                    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       340       350
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (2, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 8)

Asymmetric/Biological Unit
(-)
Clan: Enolase_N (69)
(-)
Clan: Enolase_TIM (82)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (AEEP_BACSU | O34508)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0016998    cell wall macromolecule catabolic process    The chemical reactions and pathways resulting in the breakdown of macromolecules that form part of a cell wall.
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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  1jpm
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  AEEP_BACSU | O34508
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 Related Entries

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

UniProtKB/Swiss-Prot
        AEEP_BACSU | O34508: 1tkk

(-) Related Entries Specified in the PDB File

1fhv O-SUCCINYLBENZOATE SYNTHASE
1jpd L-ALA-L/D-GLU EPIMERASE, E.COLI
1muc MUCONATE LACTONIZING ENZYME