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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF SUCCINYL-DIAMINOPIMELATE DESUCCINYLASE FROM HAEMOPHILUS INFLUENZAE
 
Authors :  B. Nocek, R. Jedrzejczak, M. Makowska-Grzyska, A. Starus, R. Holz, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  12 Sep 12  (Deposition) - 21 Nov 12  (Release) - 26 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.84
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Dape, Mcsg, Psi-Biology, Structural Genomics, Midwest Center For Structural Genomics, Hydrolase, Zinc-Dependent 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: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PMCSG7
    Gene: DAPE, HI_0102
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 71421
    Strain: ATCC 51907 / DSM 11121 / KW20 / RD
    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  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:67 , ASP A:100 , GLU A:134 , GLU A:163 , ZN A:1002 , HOH A:1101BINDING SITE FOR RESIDUE ZN A 1001
2AC2SOFTWAREASP A:100 , GLU A:135 , HIS A:238 , ZN A:1001 , HOH A:1101BINDING SITE FOR RESIDUE ZN A 1002
3AC3SOFTWAREHIS B:67 , ASP B:100 , GLU B:134 , GLU B:163 , ZN B:1002 , HOH B:1101BINDING SITE FOR RESIDUE ZN B 1001
4AC4SOFTWAREASP B:100 , GLU B:135 , HIS B:238 , ZN B:1001 , HOH B:1101BINDING SITE FOR RESIDUE ZN B 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H2K)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Ser A:19 -Pro A:20
2Glu A:59 -Pro A:60
3Asp A:100 -Met A:101
4Ser B:19 -Pro B:20
5Glu B:59 -Pro B:60
6Asp B:100 -Met B:101

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H2K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H2K)

(-) Exons   (0, 0)

(no "Exon" information available for 4H2K)

(-) 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:258
                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh.........hhhhhhhhhhhh...eeee.......eeeeee.....eeeeeee.......hhhhh........ee..eee......hhhhhhhhhhhhhhhhhhh.....eeeeeee.........hhhhhhhhhhhh.....eeee...........eee.......hhhhhhhhhhhhhhh...eee..hhhhhhhhh...eeee.............eeehhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4h2k A  -1 NAMKEKVVSLAQDLIRRPSISPNDEGCQQIIAERLEKLGFQIEWMPFNDTLNLWAKHGTSEPVIAFAGHTDVVPTGDENQWSSPPFSAEIIDGMLYGRGAADMKGSLAAMIVAAEEYVKANPNHKGTIALLITSDEEATAKDGTIHVVETLMARDEKITYCMVGEPSSAKNLGDVVKNGRRGGGKLLDSITSAIEETIGITPKAETGTSDGRFIALMGAEVVEFGPLNSTIHKVNECVSVEDLGKCGEIYHKMLVNLL 264
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178  ||   194       204     ||216       226       236       246       256        
                                                                                                                                                                                                                181|                   210|                                                   
                                                                                                                                                                                                                 188                    213                                                   


Chain B from PDB  Type:PROTEIN  Length:253
                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.........hhhhhhhhhhhhh..eeee.......eeeeee.....eeeeeee.......hhhhh........ee..eee......hhhhhhhhhhhhhhhhhhh.....eeeeeee.........hhhhhhhhhhhh.....eeee...........eee..hhhhhhhhhhhhhhhh...eee..hhhhhhhhh...eeee.............eeehhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h2k B   1 MKEKVVSLAQDLIRRPSISPNDEGCQQIIAERLEKLGFQIEWMPFNDTLNLWAKHGTSEPVIAFAGHTDVVPTGDENQWSSPPFSAEIIDGMLYGRGAADMKGSLAAMIVAAEEYVKANPNHKGTIALLITSDEEATAKDGTIHVVETLMARDEKITYCMVGEPSSAKNLGDVVKNPGKLLDSITSAIEETIGITPKAETGTSDGRFIALMGAEVVEFGPLNSTIHKVNECVSVEDLGKCGEIYHKMLVNLLD 265
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     ||190       200       210|      222       232       242       252       262   
                                                                                                                                                                                                         176|                    210|                                                    
                                                                                                                                                                                                          187                     213
   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 4H2K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4H2K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H2K)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

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  4h2k
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  DAPE_HAEIN | P44514
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  3.5.1.18
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 Related Entries

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

UniProtKB/Swiss-Prot
        DAPE_HAEIN | P44514: 3ic1 3isz

(-) Related Entries Specified in the PDB File

3ic1 RELATED ID: MCSG-APC107340 RELATED DB: TARGETTRACK
3isz