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(-) Description

Title :  CRYSTAL STRUCTURE OF AN N-TERMINAL DELETION MUTANT OF ESCHERICHIA COLI GADB IN AN AUTOINHIBITED STATE (ALDAMINE)
 
Authors :  M. G. Gruetter, G. Capitani, H. Gut
Date :  14 Mar 06  (Deposition) - 20 Jun 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C,D,E,F  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A,B  (1x)
Biol. Unit 4:  E,F  (1x)
Biol. Unit 5:  D,E  (1x)
Biol. Unit 6:  A,F  (1x)
Keywords :  Gadb, Gadbd1-14, Autoinhibition, Substituted Aldamine, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Gut, E. Pennacchietti, R. A. John, F. Bossa, G. Capitani, D. De Biase, M. G. Gruetter
Escherichia Coli Acid Resistance: Ph-Sensing, Activation By Chloride And Autoinhibition In Gadb
Embo J. V. 25 2643 2006
PubMed-ID: 16675957  |  Reference-DOI: 10.1038/SJ.EMBOJ.7601107
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUTAMATE DECARBOXYLASE BETA
    Chains: A, B, C, D, E, F
    EC Number: 4.1.1.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE60
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: GADBD1-14
    Gene: GADB
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: JM109
    Synonym: GAD-BETA, GADB

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABCDEF
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x): AB    
Biological Unit 4 (1x):     EF
Biological Unit 5 (1x):    DE 
Biological Unit 6 (1x): A    F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 20)

Asymmetric Unit (3, 20)
No.NameCountTypeFull Name
1EDO8Ligand/Ion1,2-ETHANEDIOL
2PLP6Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3SO46Ligand/IonSULFATE ION
Biological Unit 1 (3, 20)
No.NameCountTypeFull Name
1EDO8Ligand/Ion1,2-ETHANEDIOL
2PLP6Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3SO46Ligand/IonSULFATE ION
Biological Unit 2 (3, 7)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3SO42Ligand/IonSULFATE ION
Biological Unit 3 (3, 7)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3SO42Ligand/IonSULFATE ION
Biological Unit 4 (3, 6)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3SO42Ligand/IonSULFATE ION
Biological Unit 5 (3, 6)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3SO42Ligand/IonSULFATE ION
Biological Unit 6 (3, 6)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3SO42Ligand/IonSULFATE ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:113 , LYS A:114 , ASP A:291 , GLU A:292 , HOH A:5007 , HOH A:5008BINDING SITE FOR RESIDUE SO4 A 4770
02AC2SOFTWARELYS B:114 , ASP B:291 , GLU B:292 , HOH B:4952 , HOH B:4994 , HOH B:5041BINDING SITE FOR RESIDUE SO4 B 4771
03AC3SOFTWARELYS C:114 , ASP C:291 , GLU C:292 , HOH C:4881 , HOH C:4889 , HOH C:4993BINDING SITE FOR RESIDUE SO4 C 4772
04AC4SOFTWAREPRO D:113 , LYS D:114 , ASP D:291 , GLU D:292 , HOH D:5003 , HOH D:5044 , HOH D:5045BINDING SITE FOR RESIDUE SO4 D 4773
05AC5SOFTWARELYS E:114 , ASP E:291 , GLU E:292BINDING SITE FOR RESIDUE SO4 E 4774
06AC6SOFTWARELYS F:114 , ASP F:291 , GLU F:292 , HOH F:4963BINDING SITE FOR RESIDUE SO4 F 4775
07AC7SOFTWAREGLY A:125 , SER A:126 , SER A:127 , GLN A:163 , CYS A:165 , THR A:208 , THR A:212 , ASP A:243 , ALA A:245 , SER A:273 , HIS A:275 , LYS A:276 , HIS A:465 , HOH A:4774 , HOH A:4783 , PHE B:317 , SER B:318BINDING SITE FOR RESIDUE PLP A 1500
08AC8SOFTWAREPHE A:317 , SER A:318 , GLY B:125 , SER B:126 , SER B:127 , GLN B:163 , THR B:208 , THR B:212 , ASP B:243 , ALA B:245 , SER B:273 , HIS B:275 , LYS B:276 , HIS B:465 , HOH B:4782 , HOH B:4888BINDING SITE FOR RESIDUE PLP B 1501
09AC9SOFTWAREGLY C:125 , SER C:126 , SER C:127 , GLN C:163 , THR C:208 , THR C:212 , ASP C:243 , ALA C:245 , SER C:273 , HIS C:275 , LYS C:276 , HIS C:465 , HOH C:4830 , PHE D:317 , SER D:318 , HOH D:4779BINDING SITE FOR RESIDUE PLP C 1502
10BC1SOFTWAREPHE C:317 , SER C:318 , GLY D:125 , SER D:126 , SER D:127 , GLN D:163 , CYS D:165 , THR D:208 , THR D:212 , ASP D:243 , ALA D:245 , SER D:273 , HIS D:275 , LYS D:276 , HIS D:465 , HOH D:4777 , HOH D:4825BINDING SITE FOR RESIDUE PLP D 1503
11BC2SOFTWAREGLY E:125 , SER E:126 , SER E:127 , GLN E:163 , CYS E:165 , THR E:208 , THR E:212 , ASP E:243 , ALA E:245 , SER E:273 , HIS E:275 , LYS E:276 , HIS E:465 , HOH E:4794 , HOH E:4824 , PHE F:317 , SER F:318BINDING SITE FOR RESIDUE PLP E 1504
12BC3SOFTWAREPHE E:317 , SER E:318 , HOH E:4790 , GLY F:125 , SER F:126 , SER F:127 , GLN F:163 , CYS F:165 , THR F:208 , GLY F:210 , THR F:212 , ASP F:243 , ALA F:245 , SER F:273 , HIS F:275 , LYS F:276 , HIS F:465 , HOH F:4898BINDING SITE FOR RESIDUE PLP F 1505
13BC4SOFTWAREASN A:81 , HOH A:4779 , ARG B:57 , ASP B:68 , TYR C:51BINDING SITE FOR RESIDUE EDO B 2191
14BC5SOFTWARETYR B:51 , ARG C:57 , ASP C:68 , HOH C:4982 , ASN D:81BINDING SITE FOR RESIDUE EDO C 2192
15BC6SOFTWAREGLN A:92 , ARG A:99 , HOH A:4970 , GLU B:49 , ASP C:432BINDING SITE FOR RESIDUE EDO A 2193
16BC7SOFTWAREGLU A:49 , GLN B:92 , ARG B:99 , HOH B:4808 , ASP F:432BINDING SITE FOR RESIDUE EDO B 2194
17BC8SOFTWAREGLN C:92 , ARG C:99 , HOH C:4988 , GLU D:49 , LEU D:52 , ASP E:432BINDING SITE FOR RESIDUE EDO C 2195
18BC9SOFTWAREASP B:432 , LEU B:436 , GLU C:49 , GLN D:92 , ARG D:99 , HOH D:4938BINDING SITE FOR RESIDUE EDO D 2196
19CC1SOFTWAREASP A:432 , GLN E:92 , ARG E:99 , HOH E:4879 , GLU F:49 , LEU F:52BINDING SITE FOR RESIDUE EDO E 2197
20CC2SOFTWAREASP D:432 , PHE D:433 , LEU D:436 , GLU E:49 , LEU E:52 , GLN F:92 , ARG F:99 , HOH F:4942BINDING SITE FOR RESIDUE EDO F 2198

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DGK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DGK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DGK)

(-) PROSITE Motifs  (1, 6)

Asymmetric Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DDC_GAD_HDC_YDCPS00392 DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site.DCEB_ECOLI269-290
 
 
 
 
 		  6A:269-290
B:269-290
C:269-290
D:269-290
E:269-290
F:269-290
Biological Unit 1 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DDC_GAD_HDC_YDCPS00392 DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site.DCEB_ECOLI269-290
 
 
 
 
 		  6A:269-290
B:269-290
C:269-290
D:269-290
E:269-290
F:269-290
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DDC_GAD_HDC_YDCPS00392 DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site.DCEB_ECOLI269-290
 
 
 
 
 		  2-
-
C:269-290
D:269-290
-
-
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DDC_GAD_HDC_YDCPS00392 DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site.DCEB_ECOLI269-290
 
 
 
 
 		  2A:269-290
B:269-290
-
-
-
-
Biological Unit 4 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DDC_GAD_HDC_YDCPS00392 DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site.DCEB_ECOLI269-290
 
 
 
 
 		  2-
-
-
-
E:269-290
F:269-290
Biological Unit 5 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DDC_GAD_HDC_YDCPS00392 DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site.DCEB_ECOLI269-290
 
 
 
 
 		  2-
-
-
D:269-290
E:269-290
-
Biological Unit 6 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DDC_GAD_HDC_YDCPS00392 DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site.DCEB_ECOLI269-290
 
 
 
 
 		  2A:269-290
-
-
-
-
F:269-290

(-) Exons   (0, 0)

(no "Exon" information available for 2DGK)

(-) Sequences/Alignments

Asymmetric 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:438
 aligned with DCEB_ECOLI | P69910 from UniProtKB/Swiss-Prot  Length:466

    Alignment length:438
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458        
           DCEB_ECOLI    29 SKRFPLHEMRDDVAFQIINDELYLDGNARQNLATFCQTWDDENVHKLMDLSINKNWIDKEEYPQSAAIDLRCVNMVADLWHAPAPKNGQAVGTNTIGSSEACMLGGMAMKWRWRKRMEAAGKPTDKPNLVCGPVQICWHKFARYWDVELREIPMRPGQLFMDPKRMIEACDENTIGVVPTFGVTYTGNYEFPQPLHDALDKFQADTGIDIDMHIDAASGGFLAPFVAPDIVWDFRLPRVKSISASGHKFGLAPLGCGWVIWRDEEALPQELVFNVDYLGGQIGTFAINFSRPAGQVIAQYYEFLRLGREGYTKVQNASYQVAAYLADEIAKLGPYEFICTGRPDEGIPAVCFKLKDGEDPGYTLYDLSERLRLRGWQVPAFTLGGEATDIVVMRIMCRRGFEMDFAELLLEDYKASLKYLSDHPKLQGIAQQNSFKHT 466
               SCOP domains d2dgka_ A: Glutamate decarboxylase beta, GadB                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhh...............hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh..........eeeee.hhhhhhhhhhhhhhhhhhhhhhhh.......eeee...hhhhhhhhhhh..eeee..........hhhhhhhhh...eeeee............hhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhh...........eeeeeee...........eeeee.hhhhhhhhhheee......eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee........eeeeee........hhhhhhhhhhhh.....eee........eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DDC_GAD_HDC_YDC       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2dgk A  29 SKRFPLHEMRDDVAFQIINDELYLDGNARQNLATFCQTWDDENVHKLMDLSINKNWIDKEEYPQSAAIDLRCVNMVADLWHAPAPKNGQAVGTNTIGSSEACMLGGMAMKWRWRKRMEAAGKPTDKPNLVCGPVQICWHKFARYWDVELREIPMRPGQLFMDPKRMIEACDENTIGVVPTFGVTYTGNYEFPQPLHDALDKFQADTGIDIDMHIDAASGGFLAPFVAPDIVWDFRLPRVKSISASGHKFGLAPLGCGWVIWRDEEALPQELVFNVDYLGGQIGTFAINFSRPAGQVIAQYYEFLRLGREGYTKVQNASYQVAAYLADEIAKLGPYEFICTGRPDEGIPAVCFKLKDGEDPGYTLYDLSERLRLRGWQVPAFTLGGEATDIVVMRIMCRRGFEMDFAELLLEDYKASLKYLSDHPKLQGIAQQNSFKHT 466
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458        


Chain B from PDB  Type:PROTEIN  Length:438
 aligned with DCEB_ECOLI | P69910 from UniProtKB/Swiss-Prot  Length:466

    Alignment length:438
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458        
           DCEB_ECOLI    29 SKRFPLHEMRDDVAFQIINDELYLDGNARQNLATFCQTWDDENVHKLMDLSINKNWIDKEEYPQSAAIDLRCVNMVADLWHAPAPKNGQAVGTNTIGSSEACMLGGMAMKWRWRKRMEAAGKPTDKPNLVCGPVQICWHKFARYWDVELREIPMRPGQLFMDPKRMIEACDENTIGVVPTFGVTYTGNYEFPQPLHDALDKFQADTGIDIDMHIDAASGGFLAPFVAPDIVWDFRLPRVKSISASGHKFGLAPLGCGWVIWRDEEALPQELVFNVDYLGGQIGTFAINFSRPAGQVIAQYYEFLRLGREGYTKVQNASYQVAAYLADEIAKLGPYEFICTGRPDEGIPAVCFKLKDGEDPGYTLYDLSERLRLRGWQVPAFTLGGEATDIVVMRIMCRRGFEMDFAELLLEDYKASLKYLSDHPKLQGIAQQNSFKHT 466
               SCOP domains d2dgkb_ B: Glutamate decarboxylase beta, GadB                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhh...............hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh..........eeeee.hhhhhhhhhhhhhhhhhhhhhhhh.......eeee...hhhhhhhhhhh..eeee..........hhhhhhhhh...eeeee............hhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhh...........eeeeeee...........eeeee.hhhhhhhhhheee......eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee........eeeeee........hhhhhhhhhhh......eee........eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DDC_GAD_HDC_YDC       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2dgk B  29 SKRFPLHEMRDDVAFQIINDELYLDGNARQNLATFCQTWDDENVHKLMDLSINKNWIDKEEYPQSAAIDLRCVNMVADLWHAPAPKNGQAVGTNTIGSSEACMLGGMAMKWRWRKRMEAAGKPTDKPNLVCGPVQICWHKFARYWDVELREIPMRPGQLFMDPKRMIEACDENTIGVVPTFGVTYTGNYEFPQPLHDALDKFQADTGIDIDMHIDAASGGFLAPFVAPDIVWDFRLPRVKSISASGHKFGLAPLGCGWVIWRDEEALPQELVFNVDYLGGQIGTFAINFSRPAGQVIAQYYEFLRLGREGYTKVQNASYQVAAYLADEIAKLGPYEFICTGRPDEGIPAVCFKLKDGEDPGYTLYDLSERLRLRGWQVPAFTLGGEATDIVVMRIMCRRGFEMDFAELLLEDYKASLKYLSDHPKLQGIAQQNSFKHT 466
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458        


Chain C from PDB  Type:PROTEIN  Length:437
 aligned with DCEB_ECOLI | P69910 from UniProtKB/Swiss-Prot  Length:466

    Alignment length:437
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       
           DCEB_ECOLI    30 KRFPLHEMRDDVAFQIINDELYLDGNARQNLATFCQTWDDENVHKLMDLSINKNWIDKEEYPQSAAIDLRCVNMVADLWHAPAPKNGQAVGTNTIGSSEACMLGGMAMKWRWRKRMEAAGKPTDKPNLVCGPVQICWHKFARYWDVELREIPMRPGQLFMDPKRMIEACDENTIGVVPTFGVTYTGNYEFPQPLHDALDKFQADTGIDIDMHIDAASGGFLAPFVAPDIVWDFRLPRVKSISASGHKFGLAPLGCGWVIWRDEEALPQELVFNVDYLGGQIGTFAINFSRPAGQVIAQYYEFLRLGREGYTKVQNASYQVAAYLADEIAKLGPYEFICTGRPDEGIPAVCFKLKDGEDPGYTLYDLSERLRLRGWQVPAFTLGGEATDIVVMRIMCRRGFEMDFAELLLEDYKASLKYLSDHPKLQGIAQQNSFKHT 466
               SCOP domains d2dgkc_ C: Glutamate decarboxylase beta, GadB                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhh...............hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh..........eeeee.hhhhhhhhhhhhhhhhhhhhhhhh.......eeee...hhhhhhhhhhh..eeee..........hhhhhhhhh...eeeee............hhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhh...........eeeeeee...........eeeee.hhhhhhhhhheee......eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee........eeeeee........hhhhhhhhhhhh.....eee........eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DDC_GAD_HDC_YDC       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dgk C  30 KRFPLHEMRDDVAFQIINDELYLDGNARQNLATFCQTWDDENVHKLMDLSINKNWIDKEEYPQSAAIDLRCVNMVADLWHAPAPKNGQAVGTNTIGSSEACMLGGMAMKWRWRKRMEAAGKPTDKPNLVCGPVQICWHKFARYWDVELREIPMRPGQLFMDPKRMIEACDENTIGVVPTFGVTYTGNYEFPQPLHDALDKFQADTGIDIDMHIDAASGGFLAPFVAPDIVWDFRLPRVKSISASGHKFGLAPLGCGWVIWRDEEALPQELVFNVDYLGGQIGTFAINFSRPAGQVIAQYYEFLRLGREGYTKVQNASYQVAAYLADEIAKLGPYEFICTGRPDEGIPAVCFKLKDGEDPGYTLYDLSERLRLRGWQVPAFTLGGEATDIVVMRIMCRRGFEMDFAELLLEDYKASLKYLSDHPKLQGIAQQNSFKHT 466
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       


Chain D from PDB  Type:PROTEIN  Length:438
 aligned with DCEB_ECOLI | P69910 from UniProtKB/Swiss-Prot  Length:466

    Alignment length:438
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458        
           DCEB_ECOLI    29 SKRFPLHEMRDDVAFQIINDELYLDGNARQNLATFCQTWDDENVHKLMDLSINKNWIDKEEYPQSAAIDLRCVNMVADLWHAPAPKNGQAVGTNTIGSSEACMLGGMAMKWRWRKRMEAAGKPTDKPNLVCGPVQICWHKFARYWDVELREIPMRPGQLFMDPKRMIEACDENTIGVVPTFGVTYTGNYEFPQPLHDALDKFQADTGIDIDMHIDAASGGFLAPFVAPDIVWDFRLPRVKSISASGHKFGLAPLGCGWVIWRDEEALPQELVFNVDYLGGQIGTFAINFSRPAGQVIAQYYEFLRLGREGYTKVQNASYQVAAYLADEIAKLGPYEFICTGRPDEGIPAVCFKLKDGEDPGYTLYDLSERLRLRGWQVPAFTLGGEATDIVVMRIMCRRGFEMDFAELLLEDYKASLKYLSDHPKLQGIAQQNSFKHT 466
               SCOP domains d2dgkd_ D: Glutamate decarboxylase beta, GadB                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhh...............hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh..........eeeee.hhhhhhhhhhhhhhhhhhhhhhhh.......eeee...hhhhhhhhhhh..eeee..........hhhhhhhhh...eeeee............hhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhh...........eeeeeee...........eeeee.hhhhhhhhhheee......eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee........eeeeee........hhhhhhhhhhh......eee........eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DDC_GAD_HDC_YDC       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2dgk D  29 SKRFPLHEMRDDVAFQIINDELYLDGNARQNLATFCQTWDDENVHKLMDLSINKNWIDKEEYPQSAAIDLRCVNMVADLWHAPAPKNGQAVGTNTIGSSEACMLGGMAMKWRWRKRMEAAGKPTDKPNLVCGPVQICWHKFARYWDVELREIPMRPGQLFMDPKRMIEACDENTIGVVPTFGVTYTGNYEFPQPLHDALDKFQADTGIDIDMHIDAASGGFLAPFVAPDIVWDFRLPRVKSISASGHKFGLAPLGCGWVIWRDEEALPQELVFNVDYLGGQIGTFAINFSRPAGQVIAQYYEFLRLGREGYTKVQNASYQVAAYLADEIAKLGPYEFICTGRPDEGIPAVCFKLKDGEDPGYTLYDLSERLRLRGWQVPAFTLGGEATDIVVMRIMCRRGFEMDFAELLLEDYKASLKYLSDHPKLQGIAQQNSFKHT 466
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458        


Chain E from PDB  Type:PROTEIN  Length:438
 aligned with DCEB_ECOLI | P69910 from UniProtKB/Swiss-Prot  Length:466

    Alignment length:438
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458        
           DCEB_ECOLI    29 SKRFPLHEMRDDVAFQIINDELYLDGNARQNLATFCQTWDDENVHKLMDLSINKNWIDKEEYPQSAAIDLRCVNMVADLWHAPAPKNGQAVGTNTIGSSEACMLGGMAMKWRWRKRMEAAGKPTDKPNLVCGPVQICWHKFARYWDVELREIPMRPGQLFMDPKRMIEACDENTIGVVPTFGVTYTGNYEFPQPLHDALDKFQADTGIDIDMHIDAASGGFLAPFVAPDIVWDFRLPRVKSISASGHKFGLAPLGCGWVIWRDEEALPQELVFNVDYLGGQIGTFAINFSRPAGQVIAQYYEFLRLGREGYTKVQNASYQVAAYLADEIAKLGPYEFICTGRPDEGIPAVCFKLKDGEDPGYTLYDLSERLRLRGWQVPAFTLGGEATDIVVMRIMCRRGFEMDFAELLLEDYKASLKYLSDHPKLQGIAQQNSFKHT 466
               SCOP domains d2dgke_ E: Glutamate decarboxylase beta, GadB                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhh.................hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh..........eeeee.hhhhhhhhhhhhhhhhhhhhhhhh.......eeee...hhhhhhhhhhh..eeee..........hhhhhhhhh...eeeee............hhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhh...........eeeeeee...........eeeee.hhhhhhhhhheee......eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee........eeeeee........hhhhhhhhhhhh.....eee.hhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DDC_GAD_HDC_YDC       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2dgk E  29 SKRFPLHEMRDDVAFQIINDELYLDGNARQNLATFCQTWDDENVHKLMDLSINKNWIDKEEYPQSAAIDLRCVNMVADLWHAPAPKNGQAVGTNTIGSSEACMLGGMAMKWRWRKRMEAAGKPTDKPNLVCGPVQICWHKFARYWDVELREIPMRPGQLFMDPKRMIEACDENTIGVVPTFGVTYTGNYEFPQPLHDALDKFQADTGIDIDMHIDAASGGFLAPFVAPDIVWDFRLPRVKSISASGHKFGLAPLGCGWVIWRDEEALPQELVFNVDYLGGQIGTFAINFSRPAGQVIAQYYEFLRLGREGYTKVQNASYQVAAYLADEIAKLGPYEFICTGRPDEGIPAVCFKLKDGEDPGYTLYDLSERLRLRGWQVPAFTLGGEATDIVVMRIMCRRGFEMDFAELLLEDYKASLKYLSDHPKLQGIAQQNSFKHT 466
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458        


Chain F from PDB  Type:PROTEIN  Length:438
 aligned with DCEB_ECOLI | P69910 from UniProtKB/Swiss-Prot  Length:466

    Alignment length:438
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458        
           DCEB_ECOLI    29 SKRFPLHEMRDDVAFQIINDELYLDGNARQNLATFCQTWDDENVHKLMDLSINKNWIDKEEYPQSAAIDLRCVNMVADLWHAPAPKNGQAVGTNTIGSSEACMLGGMAMKWRWRKRMEAAGKPTDKPNLVCGPVQICWHKFARYWDVELREIPMRPGQLFMDPKRMIEACDENTIGVVPTFGVTYTGNYEFPQPLHDALDKFQADTGIDIDMHIDAASGGFLAPFVAPDIVWDFRLPRVKSISASGHKFGLAPLGCGWVIWRDEEALPQELVFNVDYLGGQIGTFAINFSRPAGQVIAQYYEFLRLGREGYTKVQNASYQVAAYLADEIAKLGPYEFICTGRPDEGIPAVCFKLKDGEDPGYTLYDLSERLRLRGWQVPAFTLGGEATDIVVMRIMCRRGFEMDFAELLLEDYKASLKYLSDHPKLQGIAQQNSFKHT 466
               SCOP domains d2dgkf_ F: Glutamate decarboxylase beta, GadB                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhh...............hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh..........eeeee.hhhhhhhhhhhhhhhhhhhhhhhh.......eeee...hhhhhhhhhhh..eeee..........hhhhhhhhh...eeeee............hhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhh...........eeeeeee...........eeeee.hhhhhhhhhheee......eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee........eeeeee........hhhhhhhhhhhh.....eee.hhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DDC_GAD_HDC_YDC       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2dgk F  29 SKRFPLHEMRDDVAFQIINDELYLDGNARQNLATFCQTWDDENVHKLMDLSINKNWIDKEEYPQSAAIDLRCVNMVADLWHAPAPKNGQAVGTNTIGSSEACMLGGMAMKWRWRKRMEAAGKPTDKPNLVCGPVQICWHKFARYWDVELREIPMRPGQLFMDPKRMIEACDENTIGVVPTFGVTYTGNYEFPQPLHDALDKFQADTGIDIDMHIDAASGGFLAPFVAPDIVWDFRLPRVKSISASGHKFGLAPLGCGWVIWRDEEALPQELVFNVDYLGGQIGTFAINFSRPAGQVIAQYYEFLRLGREGYTKVQNASYQVAAYLADEIAKLGPYEFICTGRPDEGIPAVCFKLKDGEDPGYTLYDLSERLRLRGWQVPAFTLGGEATDIVVMRIMCRRGFEMDFAELLLEDYKASLKYLSDHPKLQGIAQQNSFKHT 466
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458
   Legend:   → Mismatch (orange background)
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 6)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DGK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DGK)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (DCEB_ECOLI | P69910)
molecular function
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
    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:0004351    glutamate decarboxylase activity    Catalysis of the reaction: L-glutamate = 4-aminobutanoate + CO2.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
biological process
    GO:0019752    carboxylic acid metabolic process    The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
    GO:0006536    glutamate metabolic process    The chemical reactions and pathways involving glutamate, the anion of 2-aminopentanedioic acid.
    GO:0051454    intracellular pH elevation    Any process that increases the internal pH of a cell, measured by the concentration of the hydrogen ion.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DCEB_ECOLI | P69910: 1pmm 1pmo 2dgl 2dgm 3fz6 3fz7 3fz8

(-) Related Entries Specified in the PDB File

1pmm CRYSTAL STRUCTURE OF ESCHERICHIA COLI GADB (LOW PH)
1pmo CRYSTAL STRUCTURE OF ESCHERICHIA COLI GADB (NEUTRAL PH)
2dgl THE SAME PROTEIN IN COMPLEX WITH BROMIDE
2dgm THE SAME PROTEIN IN COMPLEX WITH IODIDE