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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF DAPE PROTEIN FROM V.CHOLEREA IN THE ZN BOUND FORM
 
Authors :  B. Nocek, M. Makowska-Grzyska, R. Jedrzejczak, W. F. Anderson, A. Joac Center For Structural Genomics Of Infectious Diseases (Csgi
Date :  04 Feb 14  (Deposition) - 23 Apr 14  (Release) - 23 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Aminopeptidase, M20, Csgid, Structural Genomics, Niaid, National Institute Of Allergy And Infectious Diseases, Center For Structural Genomics Of Infectious Diseases, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Nocek, A. Starus, M. Makowska-Grzyska, B. Gutierrez, S. Sanchez, R. Jedrzejczak, J. C. Mack, K. W. Olsen, A. Joachimiak, R. C. Holz
The Dimerization Domain In Dape Enzymes Is Required For Catalysis.
Plos One V. 9 93593 2014
PubMed-ID: 24806882  |  Reference-DOI: 10.1371/JOURNAL.PONE.0093593

(-) 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, VC_2152
    Organism Scientific: VIBRIO CHOLERAE O1 BIOVAR EL TOR
    Organism Taxid: 243277
    Strain: N16961
    Synonym: SDAP DESUCCINYLASE, N-SUCCINYL-LL-2,6-DIAMINOHEPTANEDIOATE AMIDOHYDROLASE

 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  (4, 18)

Asymmetric Unit (4, 18)
No.NameCountTypeFull Name
1BU16Ligand/Ion1,4-BUTANEDIOL
2EDO5Ligand/Ion1,2-ETHANEDIOL
3GOL3Ligand/IonGLYCEROL
4ZN4Ligand/IonZINC ION
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1BU14Ligand/Ion1,4-BUTANEDIOL
2EDO3Ligand/Ion1,2-ETHANEDIOL
3GOL2Ligand/IonGLYCEROL
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1BU12Ligand/Ion1,4-BUTANEDIOL
2EDO2Ligand/Ion1,2-ETHANEDIOL
3GOL1Ligand/IonGLYCEROL
4ZN-1Ligand/IonZINC ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:255 , GLN A:258 , LYS A:259 , ASN A:262BINDING SITE FOR RESIDUE EDO A 301
02AC2SOFTWAREASP A:101 , GLU A:136 , HIS A:239 , ZN A:303 , EDO A:311BINDING SITE FOR RESIDUE ZN A 302
03AC3SOFTWAREHIS A:68 , ASP A:101 , GLU A:135 , GLU A:136 , GLU A:164 , ZN A:302 , EDO A:311BINDING SITE FOR RESIDUE ZN A 303
04AC4SOFTWAREARG A:145 , GLU A:148 , THR A:149 , HOH A:438 , HOH A:458 , ARG B:179BINDING SITE FOR RESIDUE GOL A 304
05AC5SOFTWARELEU A:77 , TRP A:80 , HIS A:81 , VAL B:89 , ASP B:91 , GLY B:92BINDING SITE FOR RESIDUE BU1 A 305
06AC6SOFTWAREMET A:151 , GLU A:155 , ILE A:157 , MET A:224 , GLY A:225 , ALA A:226BINDING SITE FOR RESIDUE BU1 A 306
07AC7SOFTWARETHR A:212 , GLY A:213 , GLY A:214 , ARG A:219 , VAL A:228 , HOH A:527 , HOH A:640BINDING SITE FOR RESIDUE BU1 A 307
08AC8SOFTWARETHR A:188 , GLU A:190 , GLN A:227BINDING SITE FOR RESIDUE EDO A 308
09AC9SOFTWAREALA A:36 , LEU A:37 , GLY A:38 , ARG A:56BINDING SITE FOR RESIDUE GOL A 309
10BC1SOFTWAREASP A:91 , GLY A:92 , HOH A:529 , TRP B:80 , HIS B:81 , THR B:82 , PRO B:83BINDING SITE FOR RESIDUE BU1 A 310
11BC2SOFTWAREHIS A:68 , ASP A:101 , GLU A:135 , GLU A:136 , GLU A:164 , HIS A:239 , ZN A:302 , ZN A:303 , HOH A:454BINDING SITE FOR RESIDUE EDO A 311
12BC3SOFTWAREGLN B:258 , LYS B:259 , ASN B:262 , HOH B:518BINDING SITE FOR RESIDUE EDO B 301
13BC4SOFTWAREASP B:101 , GLU B:136 , HIS B:239 , ZN B:303 , HOH B:634 , HOH B:635BINDING SITE FOR RESIDUE ZN B 302
14BC5SOFTWAREHIS B:68 , ASP B:101 , GLU B:136 , GLU B:164 , ZN B:302 , HOH B:634BINDING SITE FOR RESIDUE ZN B 303
15BC6SOFTWAREARG A:179 , ARG B:145 , GLU B:148 , THR B:149 , HOH B:418 , HOH B:445BINDING SITE FOR RESIDUE GOL B 304
16BC7SOFTWAREGLU B:155 , LEU B:156 , ILE B:157 , MET B:224 , GLY B:225 , ALA B:226BINDING SITE FOR RESIDUE BU1 B 305
17BC8SOFTWARELYS B:176 , ASN B:177 , GLY B:178 , THR B:212 , GLY B:213 , GLY B:214 , GLY B:218 , GLU B:230 , HOH B:585BINDING SITE FOR RESIDUE BU1 B 306
18BC9SOFTWAREPRO B:61 , THR B:188 , GLU B:190 , GLN B:227BINDING SITE FOR RESIDUE EDO B 307

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4OP4)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Thr A:20 -Pro A:21
2Ser A:60 -Pro A:61
3Asp A:101 -Met A:102
4Thr B:20 -Pro B:21
5Ser 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 4OP4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OP4)

(-) Exons   (0, 0)

(no "Exon" information available for 4OP4)

(-) 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:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh........hhhhhhhhhhhh...eeeeeee..eeeeeeee.....eeeeeee.......hhhhh.......eee..eee......hhhhhhhhhhhhhhhhhhh.....eeeeeee.......hhhhhhhhhhh......eeee...........eeee.hhhhhh....hhhhhhhhhhhhhhhh...eee....hhhhhhhhhhh.eeee.............eeehhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4op4 A   2 TDSPVLALAKELISRQSVTPADAGCQDLMIERLKALGFEIESMVFEDTTNFWARRGTQSPLFVFAGHTDVVPAGPLSQWHTPPFEPTVIDGFLHGRGAADMKGSLACMIVAVERFIAEHPDHQGSIGFLITSDEEGPNGTVRVVETLMARNELIDMCIVGEPSSTLAVGDVVKNGRRGGGFLTDTGELLAAVVAAVEEVNHQAPALLTTGGTSDGRFIAQMGAQVVELGPVNATIHKVNECVRIADLEKLTDMYQKTLNHLLG 266
                                    11        21        31        41        51        61        71        81        91       101       111       121       131      |143       153       163       173       183       193       203       213       223       233       243       253       263   
                                                                                                                                                                  138|                                                                                                                             
                                                                                                                                                                   141                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:265
                                                                                                                                                                                                                                                                                                         
               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........hhhhhhhhhhhhh.....eeee...........eeee.hhhhhh....hhhhhhhhhhhhhhhh...eee....hhhhhhhhhh..eeee.............eeehhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4op4 B   2 TDSPVLALAKELISRQSVTPADAGCQDLMIERLKALGFEIESMVFEDTTNFWARRGTQSPLFVFAGHTDVVPAGPLSQWHTPPFEPTVIDGFLHGRGAADMKGSLACMIVAVERFIAEHPDHQGSIGFLITSDEEGPFINGTVRVVETLMARNELIDMCIVGEPSSTLAVGDVVKNGRRGGGFLTDTGELLAAVVAAVEEVNHQAPALLTTGGTSDGRFIAQMGAQVVELGPVNATIHKVNECVRIADLEKLTDMYQKTLNHLLG 266
                                    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
   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  (0, 0)

(no "SCOP Domain" information available for 4OP4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OP4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OP4)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        DAPE_VIBCH | Q9KQ52: 4onw

(-) Related Entries Specified in the PDB File

3isz RELATED ID: CSGID-IDP90246 RELATED DB: TARGETTRACK