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(-) Description

Title :  1.30 A CRYSTAL STRUCTURE OF DAPE ENZYME FROM NEISSERIA MENINGITIDIS MC58
 
Authors :  B. Nocek, A. Joachimiak, W. F. Anderson, Center For Structural Geno Infectious Diseases (Csgid)
Date :  02 Jan 17  (Deposition) - 01 Feb 17  (Release) - 08 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  M20 Peptidase, Zn-Dependent Enzyme, High Resolution, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Nocek, T. Heath, D. Becker, A. Joachimiak, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
1. 30 A Crystal Structure Of Dape Enzyme From Neisseria Meningitidis Mc58
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SUCCINYL-DIAMINOPIMELATE DESUCCINYLASE
    Chains: A, B
    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: 487
    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, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
2ZN5Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:68 , ASP A:101 , GLU A:164 , ZN A:402 , HOH A:857binding site for residue ZN A 401
02AC2SOFTWAREASP A:101 , GLU A:136 , HIS A:350 , ZN A:401 , HOH A:857binding site for residue ZN A 402
03AC3SOFTWAREARG A:179 , GLY A:325 , ASN A:346 , HOH A:539 , HOH A:634 , HOH A:665 , HOH A:748 , TYR B:198binding site for residue SO4 A 403
04AC4SOFTWARESER A:182 , ARG A:259 , SER A:291 , HOH A:523 , HOH A:602 , HOH A:673 , HOH A:765binding site for residue SO4 A 404
05AC5SOFTWAREASP B:101 , GLU B:136 , HIS B:350 , ZN B:402 , HOH B:863binding site for residue ZN B 401
06AC6SOFTWAREHIS B:68 , ASP B:101 , GLU B:164 , ZN B:401 , HOH B:863binding site for residue ZN B 402
07AC7SOFTWAREHIS B:120 , GLU B:223 , HOH B:793 , HOH B:882 , HOH B:965binding site for residue ZN B 403
08AC8SOFTWARESER B:182 , ARG B:259 , SER B:291 , HOH B:523 , HOH B:547 , HOH B:561 , HOH B:670 , HOH B:713 , HOH B:743 , HOH B:806binding site for residue SO4 B 404
09AC9SOFTWARETYR A:198 , ARG B:179 , GLY B:325 , HOH B:506 , HOH B:544 , HOH B:567 , HOH B:815binding site for residue SO4 B 405
10AD1SOFTWAREARG B:374 , HOH B:588binding site for residue SO4 B 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5UEJ)

(-) Cis Peptide Bonds  (6, 8)

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 5UEJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5UEJ)

(-) Exons   (0, 0)

(no "Exon" information available for 5UEJ)

(-) 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:375
                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.........hhhhhhhhhhhh...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
                 5uej A   3 ETQSLELAKELISRPSVTPDDRDCQKLLAERLHKIGFAAEELHFGDTKNIWLRRGTKAPVVCFAGHTDVVPTGPVEKWDSPPFEPAERDGRLYGRGAADMKTSIACFVTACERFVAKHPNHQGSIALLITSDEEGDALDGTTKVVDVLKARDELIDYCIVGEPTAVDKLGDMIKNGRRGSLSGNLTVKGKQGHIAYPHLAINPVHTFAPALLELTQEVWDEGNEYFPPTSFQISNINGGTGATNVIPGELNVKFNFRFSTESTEAGLKQRVHAILDKHGVQYDLQWSCSGQPFLTQAGKLTDVARAAIAETCGIEAELSTTGGTSDGRFIKAIAQELIELGPSNATIHQINENVRLNDIPKLSAVYEGILARLLA 377
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372     


Chain B from PDB  Type:PROTEIN  Length:376
                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.........hhhhhhhhhhhh...eeeeeee..eeeeeeee.....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
                 5uej B   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
   Legend:   → Mismatch (orange background)
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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 5UEJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5UEJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5UEJ)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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

(-) Related Entries Specified in the PDB File

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