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(-) Description

Title :  CRYSTAL STRUCTURE OF N-ACYL-D-GLUTAMATE DEACYLASE FROM BORDETELLA BRONCHISEPTICA COMPLEXED WITH ZINC, ACETATE AND FORMATE IONS.
 
Authors :  A. A. Fedorov, E. V. Fedorov, J. Cummings, F. M. Raushel, S. C. Almo
Date :  05 Mar 09  (Deposition) - 01 Sep 09  (Release) - 01 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  N-Acyl-D-Glutamate Deacylase, Amidohydrolase Family, Crystal Structure, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Cummings, A. A. Fedorov, C. Xu, S. Brown, E. Fedorov, P. C. Babbitt, S. C. Almo, F. M. Raushel
Annotating Enzymes Of Uncertain Function: The Deacylation Of D-Amino Acids By Members Of The Amidohydrolase Superfamily.
Biochemistry V. 48 6469 2009
PubMed-ID: 19518059  |  Reference-DOI: 10.1021/BI900661B
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - N-ACYL-D-GLUTAMATE DEACYLASE
    Chains: A, B
    EC Number: 3.5.1.82
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BB3285
    Organism Common: ALCALIGENES BRONCHISEPTICUS
    Organism Scientific: BORDETELLA BRONCHISEPTICA
    Organism Taxid: 518

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2FMT4Ligand/IonFORMIC ACID
3ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2FMT2Ligand/IonFORMIC ACID
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2FMT2Ligand/IonFORMIC ACID
3ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:68 , CYS A:95 , TYR A:190 , HIS A:218 , HIS A:248 , SER A:288 , ASP A:365 , FMT A:482 , ZN A:484BINDING SITE FOR RESIDUE ACY A 481
2AC2SOFTWAREHIS A:248 , LYS A:250 , TYR A:282 , SER A:287 , SER A:288 , ASP A:365 , ARG A:376 , ACY A:481BINDING SITE FOR RESIDUE FMT A 482
3AC3SOFTWAREMET A:252 , SER A:287 , ARG A:295 , TYR A:343 , HOH A:536BINDING SITE FOR RESIDUE FMT A 483
4AC4SOFTWARECYS A:95 , HIS A:218 , HIS A:248 , ACY A:481BINDING SITE FOR RESIDUE ZN A 484
5AC5SOFTWAREHIS B:66 , HIS B:68 , CYS B:95 , TYR B:190 , HIS B:218 , HIS B:248 , SER B:288 , THR B:289 , ASP B:365 , ZN B:484BINDING SITE FOR RESIDUE ACY B 481
6AC6SOFTWAREHIS B:248 , LYS B:250 , TYR B:282 , SER B:287 , SER B:288 , ASP B:365 , ARG B:376BINDING SITE FOR RESIDUE FMT B 482
7AC7SOFTWAREMET B:252 , SER B:287 , ARG B:295 , TYR B:343 , HOH B:534BINDING SITE FOR RESIDUE FMT B 483
8AC8SOFTWARECYS B:95 , HIS B:218 , HIS B:248 , ACY B:481BINDING SITE FOR RESIDUE ZN B 484

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GIP)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Ala A:100 -Pro A:101
2Gln A:191 -Pro A:192
3Ala A:337 -Pro A:338
4Phe A:463 -Pro A:464
5Ala B:100 -Pro B:101
6Gln B:191 -Pro B:192
7Ala B:337 -Pro B:338
8Phe B:463 -Pro B:464

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GIP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GIP)

(-) Exons   (0, 0)

(no "Exon" information available for 3GIP)

(-) 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:474
 aligned with A0A0H3LXD5_B | A0A0H3LXD5 from UniProtKB/TrEMBL  Length:480

    Alignment length:474
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474    
         A0A0H3LXD5_B     5 EKLDFKITGGWIIDGTGAPRRRADLGVRDGRIAAIGELGAHPARHAWDASGKIVAPGFIDVHGHDDLMFVEKPDLRWKTSQGITTVVVGNCGVSAAPAPLPGNTAAALALLGETPLFADVPAYFAALDAQRPMINVAALVGHANLRLAAMRDPQAAPTAAEQQAMQDMLQAALEAGAVGFSTGLAYQPGAVAQAAELEGLARVAAERRRLHTSHIRNEADGVEAAVEEVLAIGRGTGCATVVSHHKCMMPQNWGRSRATLANIDRAREQGVEVALDIYPYPGSSTILIPERAETIDDIRITWSTPHPECSGEYLADIAARWGCDKTTAARRLAPAGAIYFAMDEDEVKRIFQHPCCMVGSDGLPNDARPHPRLWGSFTRVLGRYVREARLMTLEQAVARMTALPARVFGFAERGVLQPGAWADVVVFDPDTVADRATWDEPTLASVGIAGVLVNGAEVFPQPPADGRPGQVLRA 478
               SCOP domains d3gipa1 A:5-60 automated matches                        d3gipa2 A:61-418 automated matches                                                                                                                                                                                                                                                                                                                                    d3gipa3 A:419-478 automated matches                          SCOP domains
               CATH domains 3gipA01 A:5-59,A:419-432,A:451-467                     3gipA02 A:60-286,A:344-413 Metal-dependent hydrolases                                                                                                                                                                              3gipA03 A:287-343 D-aminoacylase. Domain 3               3gipA02 A:60-286,A:344-413 Metal-dependent hydrolases                 -----3gipA01       ------------------3gipA01          ----------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee..ee........ee.eeeee..eeeeee......eeeeee....eeee.eee......hhhhhh..hhhhhh..eeeeee................hhhhhhh.......hhhhhhhhhhhh....eeeeeeehhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhh.eeee......hhhhhhhhhhhhhhhhhhhhh...eeeee.....eeee.hhhhh......eeeee..hhhhh..hhhhhhhhhh.hhhhhhhhhh.eeeee...hhhhhhhhhhh..eee............hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh..............eeee....................eeeeee..eeee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gip A   5 EKLDFKITGGWIIDGTGAPRRRADLGVRDGRIAAIGELGAHPARHAWDASGKIVAPGFIDVHGHDDLMFVEKPDLRWKTSQGITTVVVGNCGVSAAPAPLPGNTAAALALLGETPLFADVPAYFAALDAQRPMINVAALVGHANLRLAAMRDPQAAPTAAEQQAMQDMLQAALEAGAVGFSTGLAYQPGAVAQAAELEGLARVAAERRRLHTSHIRNEADGVEAAVEEVLAIGRGTGCATVVSHHKCMMPQNWGRSRATLANIDRAREQGVEVALDIYPYPGSSTILIPERAETIDDIRITWSTPHPECSGEYLADIAARWGCDKTTAARRLAPAGAIYFAMDEDEVKRIFQHPCCMVGSDGLPNDARPHPRLWGSFTRVLGRYVREARLMTLEQAVARMTALPARVFGFAERGVLQPGAWADVVVFDPDTVADRATWDEPTLASVGIAGVLVNGAEVFPQPPADGRPGQVLRA 478
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474    


Chain B from PDB  Type:PROTEIN  Length:474
 aligned with A0A0H3LXD5_B | A0A0H3LXD5 from UniProtKB/TrEMBL  Length:480

    Alignment length:474
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474    
         A0A0H3LXD5_B     5 EKLDFKITGGWIIDGTGAPRRRADLGVRDGRIAAIGELGAHPARHAWDASGKIVAPGFIDVHGHDDLMFVEKPDLRWKTSQGITTVVVGNCGVSAAPAPLPGNTAAALALLGETPLFADVPAYFAALDAQRPMINVAALVGHANLRLAAMRDPQAAPTAAEQQAMQDMLQAALEAGAVGFSTGLAYQPGAVAQAAELEGLARVAAERRRLHTSHIRNEADGVEAAVEEVLAIGRGTGCATVVSHHKCMMPQNWGRSRATLANIDRAREQGVEVALDIYPYPGSSTILIPERAETIDDIRITWSTPHPECSGEYLADIAARWGCDKTTAARRLAPAGAIYFAMDEDEVKRIFQHPCCMVGSDGLPNDARPHPRLWGSFTRVLGRYVREARLMTLEQAVARMTALPARVFGFAERGVLQPGAWADVVVFDPDTVADRATWDEPTLASVGIAGVLVNGAEVFPQPPADGRPGQVLRA 478
               SCOP domains d3gipb1 B:5-60 automated matches                        d3gipb2 B:61-418 automated matches                                                                                                                                                                                                                                                                                                                                    d3gipb3 B:419-478 automated matches                          SCOP domains
               CATH domains 3gipB01 B:5-59,B:419-432,B:451-467                     3gipB02 B:60-286,B:344-413 Metal-dependent hydrolases                                                                                                                                                                              3gipB03 B:287-343 D-aminoacylase. Domain 3               3gipB02 B:60-286,B:344-413 Metal-dependent hydrolases                 -----3gipB01       ------------------3gipB01          ----------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee..ee........ee.eeeee..eeeeee.........eee....eeee.eee......hhhhhh..hhhhhh..eeeeee................hhhhhhh.......hhhhhhhhhhhh....eeeeeeehhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhh.eeee......hhhhhhhhhhhhhhhhhhhhhh..eeeee.....eeee.hhhhh......eeeee..hhhhh..hhhhhhhhhh.hhhhhhhhhh.eeeee...hhhhhhhhhhh..eee............hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh..............eeee....................eeeeee..eeee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gip B   5 EKLDFKITGGWIIDGTGAPRRRADLGVRDGRIAAIGELGAHPARHAWDASGKIVAPGFIDVHGHDDLMFVEKPDLRWKTSQGITTVVVGNCGVSAAPAPLPGNTAAALALLGETPLFADVPAYFAALDAQRPMINVAALVGHANLRLAAMRDPQAAPTAAEQQAMQDMLQAALEAGAVGFSTGLAYQPGAVAQAAELEGLARVAAERRRLHTSHIRNEADGVEAAVEEVLAIGRGTGCATVVSHHKCMMPQNWGRSRATLANIDRAREQGVEVALDIYPYPGSSTILIPERAETIDDIRITWSTPHPECSGEYLADIAARWGCDKTTAARRLAPAGAIYFAMDEDEVKRIFQHPCCMVGSDGLPNDARPHPRLWGSFTRVLGRYVREARLMTLEQAVARMTALPARVFGFAERGVLQPGAWADVVVFDPDTVADRATWDEPTLASVGIAGVLVNGAEVFPQPPADGRPGQVLRA 478
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474
   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, 6)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GIP)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3GIP)

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        A0A0H3LXD5_B | A0A0H3LXD5: 3giq

(-) Related Entries Specified in the PDB File

3giq CRYSTAL STRUCTURE OF N-ACYL-D-GLUTAMATE DEACYLASE FROM BORDETELLA BRONCHISEPTICA COMPLEXED WITH ZINC AND PHOSPHONATE INHIBITOR, A MIMIC OF THE REACTION TETRAHEDRAL INTERMEDIATE.