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(-) Description

Title :  CRYSTAL STRUCTURE OF MONO-ZINC FORM OF SUCCINYL DIAMINOPIMELATE DESUCCINYLASE FROM NEISSERIA MENINGITIDIS MC58
 
Authors :  B. Nocek, R. Holz, W. F. Anderson, A. Joachimiak, Center For Structur Genomics Of Infectious Diseases (Csgid)
Date :  16 Dec 13  (Deposition) - 15 Jan 14  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dape, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Starus, B. Nocek, B. Bennett, J. A. Larrabee, D. L. Shaw, W. Sae-Lee, M. T. Russo, D. M. Gillner, M. Makowska-Grzyska, A. Joachimiak, R. C. Holz
Inhibition Of The Dape-Encoded N-Succinyl-L, L-Diaminopimeli Acid Desuccinylase From Neisseria Meningitidis By L-Captopril.
Biochemistry V. 54 4834 2015
PubMed-ID: 26186504  |  Reference-DOI: 10.1021/ACS.BIOCHEM.5B00475

(-) Compounds

Molecule 1 - SUCCINYL-DIAMINOPIMELATE DESUCCINYLASE
    Chains: A, B
    EC Number: 3.5.1.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: DAPE, NMB1530
    Organism Scientific: NEISSERIA MENINGITIDIS
    Organism Taxid: 122586
    Strain: MC58
    Synonym: SDAP DESUCCINYLASE, N-SUCCINYL-LL-2,6-DIAMINOHEPTANEDIOATE AMIDOHYDROLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2ZN3Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:68 , ASP A:101 , GLU A:164 , HOH A:609BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWAREHIS B:68 , ASP B:101 , GLU B:135 , GLU B:164 , HOH B:547BINDING SITE FOR RESIDUE ZN B 401
3AC3SOFTWAREASP B:101 , GLU B:136 , HIS B:350 , HOH B:547BINDING SITE FOR RESIDUE ZN B 402
4AC4SOFTWAREHIS A:195 , ASN A:246 , ARG B:259 , GLY B:325 , THR B:326BINDING SITE FOR RESIDUE SO4 B 403
5AC5SOFTWAREARG A:259 , HOH A:562 , HIS B:195 , ASN B:246BINDING SITE FOR RESIDUE SO4 B 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4O23)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Thr A:20 -Pro A:21
2Ala A:60 -Pro A:61
3Asp A:101 -Met A:102
4Thr B:20 -Pro B:21
5Ala B:60 -Pro B:61
6Asp B:101 -Met B:102

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4O23)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4O23)

(-) Exons   (0, 0)

(no "Exon" information available for 4O23)

(-) 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:376
                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.........hhhhhhhhhhhhhh.eeee.......eeeeee.....eeeeeee.......hhhhh.......eee..eee......hhhhhhhhhhhhhhhhhhh.....eeeeeee.........hhhhhhhhhhhh...eeeeee...........eee.ee.eeeeeeeeee...ee..hhhhh.hhhhhhhhhhhhhhhh............eeeeeeeee......ee..eeeeeeeeee....hhhhhhhhhhhhhhhh...eeeeeeeee..ee...hhhhhhhhhhhhhhhh...eee......hhhhhh..eeeeee.............eee.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o23 A   2 TETQSLELAKELISRPSVTPDDRDCQKLLAERLHKIGFAAEELHFGDTKNIWLRRGTKAPVVCFAGHTDVVPTGPVEKWDSPPFEPAERDGRLYGRGAADMKTSIACFVTACERFVAKHPNHQGSIALLITSDEEGDALDGTTKVVDVLKARDELIDYCIVGEPTAVDKLGDMIKNGRRGSLSGNLTVKGKQGHIAYPHLAINPVHTFAPALLELTQEVWDEGNEYFPPTSFQISNINGGTGATNVIPGELNVKFNFRFSTESTEAGLKQRVHAILDKHGVQYDLQWSCSGQPFLTQAGKLTDVARAAIAETCGIEAELSTTGGTSDGRFIKAIAQELIELGPSNATIHQINENVRLNDIPKLSAVYEGILARLLA 377
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371      


Chain B from PDB  Type:PROTEIN  Length:372
                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhh.........hhhhhhhhhhhh..............eeeeee.....eeeeeee...................ee....ee......hhhhhhhhhhhhhhhhhhh.....eeeeeee.........hhhhhhhhhhh....eeeeee...........eee.ee.eeeeeeeeee...ee..hhhhh.hhhhhhhhhhhhhhhh............eeeeeeeee......ee..eeeeeeeeee....hhhhhhhhhhhhhhhh...eeeeeeeee..ee...hhhhhhhhhhhhhhh....eee......hhhhhh..eeeeee.............ee..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4o23 B   5 QSLELAKELISRPSVTPDDRDCQKLLAERLHKIGFAAEELHFGDTKNIWLRRGTKAPVVCFAGHTDVVPTGPVEKWDSPPFEPAERDGRLYGRGAADMKTSIACFVTACERFVAKHPNHQGSIALLITSDEEGDALDGTTKVVDVLKARDELIDYCIVGEPTAVDKLGDMIKNGRRGSLSGNLTVKGKQGHIAYPHLAINPVHTFAPALLELTQEVWDEGNEYFPPTSFQISNINGGTGATNVIPGELNVKFNFRFSTESTEAGLKQRVHAILDKHGVQYDLQWSCSGQPFLTQAGKLTDVARAAIAETCGIEAELSTTGGTSDGRFIKAIAQELIELGPSNATIHQINENVRLNDIPKLSAVYEGILARLL 376
                                    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
   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  (0, 0)

(no "SCOP Domain" information available for 4O23)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4O23)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4O23)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:60 - Pro A:61   [ RasMol ]  
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  4o23
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 Related Entries

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

UniProtKB/Swiss-Prot
        DAPE_NEIMB | Q9JYL2: 1vgy 4ppz 4pqa 5uej

(-) Related Entries Specified in the PDB File

1vgy RELATED ID: IDP92725 RELATED DB: TARGETTRACK RELATED ID: CSGID-IDP92725 RELATED DB: TARGETTRACK
3isz