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(-) Description

Title :  CRYSTAL STRUCTURE OF ZINC-BOUND 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 :  27 Feb 14  (Deposition) - 26 Mar 14  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Dape, M20, Csgid, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Succinyl-Diaminopimelate Desuccinylase, Aminopeptidase, 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
    EC Number: 3.5.1.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    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

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:68 , ASP A:101 , GLU A:135 , GLU A:136 , GLU A:164 , ZN A:602 , HOH A:819BINDING SITE FOR RESIDUE ZN A 601
2AC2SOFTWAREASP A:101 , GLU A:136 , HIS A:350 , ZN A:601 , HOH A:819 , HOH A:841BINDING SITE FOR RESIDUE ZN A 602
3AC3SOFTWAREHIS A:195 , ASN A:246 , ARG A:259BINDING SITE FOR RESIDUE PO4 A 603

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Thr A:20 -Pro A:21
2Ala A:60 -Pro A:61
3Asp A:101 -Met A:102

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:375
                                                                                                                                                                                                                                                                                                                                                                                                                       
               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.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ppz A   2 TETQSLELAKELISRPSVTPDDRDCQKLLAERLHKIGFAAEELHFGDTKNIWLRRGTKAPVVCFAGHTDVVPTGPVEKWDSPPFEPAERDGRLYGRGAADMKTSIACFVTACERFVAKHPNHQGSIALLITSDEEGDALDGTTKVVDVLKARDELIDYCIVGEPTAVDKLGDMIKNGRRGSLSGNLTVKGKQGHIAYPHLAINPVHTFAPALLELTQEVWDEGNEYFPPTSFQISNINGGTGATNVIPGELNVKFNFRFSTESTEAGLKQRVHAILDKHGVQYDLQWSCSGQPFLTQAGKLTDVARAAIAETCGIEAELSTTGGTSDGRFIKAIAQELIELGPSNATIHQINENVRLNDIPKLSAVYEGILARLL 376
                                    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
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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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (10, 10)

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 Related Entries

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

UniProtKB/Swiss-Prot
        DAPE_NEIMB | Q9JYL2: 1vgy 4o23 4pqa 5uej

(-) Related Entries Specified in the PDB File

1vgy RELATED ID: CSGID-IDP92725 RELATED DB: TARGETTRACK
3isz
4o23