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(-) Description

Title :  CRYSTAL STRUCTURE OF SUCCINYL DIAMINOPIMELATE DESUCCINYLASE
 
Authors :  Structural Genomix
Date :  03 Nov 03  (Deposition) - 25 Nov 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Badger, J. M. Sauder, J. M. Adams, S. Antonysamy, K. Bain, M. G. Bergseid, S. G. Buchanan, M. D. Buchanan, Y. Batiyenko, J. A. Christopher, S. Emtage, A. Eroshkina, I. Feil, E. B. Furlong, K. S. Gajiwala, X. Gao, D. He, J. Hendle, A. Huber, K. Hoda, P. Kearins, C. Kissinger, B. Laubert, H. A. Lewis, J. Lin, K. Loomis, D. Lorimer, G. Louie, M. Maletic, C. D. Marsh, I. Miller, J. Molinari, H. J. Muller-Dieckmann, J. M. Newman, B. W. Noland, B. Pagarigan, F. Park, T. S. Peat, K. W. Post, S. Radojicic, A. Ramos, R. Romero, M. E. Rutter, W. E. Sanderson, K. D. Schwinn, J. Tresser, J. Winhoven, T. A. Wright, L. Wu, J. Xu, T. J. Harris
Structural Analysis Of A Set Of Proteins Resulting From A Bacterial Genomics Project
Proteins V. 60 787 2005
PubMed-ID: 16021622  |  Reference-DOI: 10.1002/PROT.20541

(-) Compounds

Molecule 1 - SUCCINYL-DIAMINOPIMELATE DESUCCINYLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DAPE
    Mutation: YES
    Organism Scientific: NEISSERIA MENINGITIDIS
    Organism Taxid: 122586
    Strain: MC58

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric/Biological Unit (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1VGY)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VGY)

(-) 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 -Mse A:102
4Thr B:20 -Pro B:21
5Ala B:60 -Pro B:61
6Asp B:101 -Mse B:102

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VGY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VGY)

(-) Exons   (0, 0)

(no "Exon" information available for 1VGY)

(-) 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
 aligned with DAPE_NEIMB | Q9JYL2 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:375
                                    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     
           DAPE_NEIMB     2 TETQSLELAKELISRPSVTPDDRDCQKLLAERLHKIGFAAEELHFGDTKNIWLRRGTKAPVVCFAGHTDVVPTGPVEKWDSPPFEPAERDGRLYGRGAADMKTSIACFVTACERFVAKHPNHQGSIALLITSDEEGDALDGTTKVVDVLKARDELIDYCIVGEPTAVDKLGDMIKNGRRGSLSGNLTVKGKQGHIAYPHLAINPVHTFAPALLELTQEVWDEGNEYFPPTSFQISNINGGTGATNVIPGELNVKFNFRFSTESTEAGLKQRVHAILDKHGVQYDLQWSCSGQPFLTQAGKLTDVARAAIAETCGIEAELSTTGGTSDGRFIKAIAQELIELGPSNATIHQINENVRLNDIPKLSAVYEGILARLL 376
               SCOP domains d1vgya1 A:2-180,A:294-376 Succinyl-diaminopimelate desuccinylase, catalytic domain                                                                                                 d1vgya2 A:181-293 Succinyl-diaminopimelate desuccinylase                                                         d1vgya1 A:2-180,A:294-376 Succinyl-diaminopimelate desuccinylase, catalytic domain  SCOP domains
               CATH domains 1vgyA01 A:2-179,A:294-376 Zn peptidases                                                                                                                                           1vgyA02 A:180-293  [code=3.30.70.360, no name defined]                                                            1vgyA01 A:2-179,A:294-376 Zn peptidases                                             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.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vgy A   2 TETQSLELAKELISRPSVTPDDRDCQKLmAERLHKIGFAAEEmHFGNTKNIWLRRGTKAPVVCFAGHTDVVPTGPVEKWDSPPFEPAERDGRLYGRGAADmKTSIACFVTACERFVAKHPNHQGSIALLITSDEEGDALDGTTKVVDVLKARDELIDYCIVGEPTAVDKLGDmIKNGRRGSLSGNLTVKGKQGHIAYPHLAINPVHTFAPALLELTQEVWDEGNEYFPPTSFQISNINGGTGATNVIPGELNVKFNFRFSTESTEAGLKQRVHAILDKHGVQYDLQWSCSGQPFLTQAGKLTDVARAAIAETCGIEAELSTTGGTSDGRFIKAmAQELIELGPSNATIHQINENVRLNDIPKLSAVYEGILVRLL 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     
                                                       30-MSE        44-MSE                                                   102-MSE                                                                 174-MSE                                                                                                                                                          335-MSE                                     


Chain B from PDB  Type:PROTEIN  Length:375
 aligned with DAPE_NEIMB | Q9JYL2 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:375
                                    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     
           DAPE_NEIMB     2 TETQSLELAKELISRPSVTPDDRDCQKLLAERLHKIGFAAEELHFGDTKNIWLRRGTKAPVVCFAGHTDVVPTGPVEKWDSPPFEPAERDGRLYGRGAADMKTSIACFVTACERFVAKHPNHQGSIALLITSDEEGDALDGTTKVVDVLKARDELIDYCIVGEPTAVDKLGDMIKNGRRGSLSGNLTVKGKQGHIAYPHLAINPVHTFAPALLELTQEVWDEGNEYFPPTSFQISNINGGTGATNVIPGELNVKFNFRFSTESTEAGLKQRVHAILDKHGVQYDLQWSCSGQPFLTQAGKLTDVARAAIAETCGIEAELSTTGGTSDGRFIKAIAQELIELGPSNATIHQINENVRLNDIPKLSAVYEGILARLL 376
               SCOP domains d1vgyb1 B:2-180,B:294-376 Succinyl-diaminopimelate desuccinylase, catalytic domain                                                                                                 d1vgyb2 B:181-293 Succinyl-diaminopimelate desuccinylase                                                         d1vgyb1 B:2-180,B:294-376 Succinyl-diaminopimelate desuccinylase, catalytic domain  SCOP domains
               CATH domains 1vgyB01 B:2-179,B:294-376 Zn peptidases                                                                                                                                           1vgyB02 B:180-293  [code=3.30.70.360, no name defined]                                                            1vgyB01 B:2-179,B:294-376 Zn peptidases                                             CATH domains
           Pfam domains (1) --------------------------------------------------------------Peptidase_M20-1vgyB01 B:64-374                                                                                                                                                                                                                                                                                         -- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------Peptidase_M20-1vgyB02 B:64-374                                                                                                                                                                                                                                                                                         -- Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------M20_dimer-1vgyB03 B:177-285                                                                                  ------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------M20_dimer-1vgyB04 B:177-285                                                                                  ------------------------------------------------------------------------------------------- Pfam domains (4)
         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.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vgy B   2 TETQSLELAKELISRPSVTPDDRDCQKLmAERLHKIGFAAEEmHFGNTKNIWLRRGTKAPVVCFAGHTDVVPTGPVEKWDSPPFEPAERDGRLYGRGAADmKTSIACFVTACERFVAKHPNHQGSIALLITSDEEGDALDGTTKVVDVLKARDELIDYCIVGEPTAVDKLGDmIKNGRRGSLSGNLTVKGKQGHIAYPHLAINPVHTFAPALLELTQEVWDEGNEYFPPTSFQISNINGGTGATNVIPGELNVKFNFRFSTESTEAGLKQRVHAILDKHGVQYDLQWSCSGQPFLTQAGKLTDVARAAIAETCGIEAELSTTGGTSDGRFIKAmAQELIELGPSNATIHQINENVRLNDIPKLSAVYEGILVRLL 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     
                                                       30-MSE        44-MSE                                                   102-MSE                                                                 174-MSE                                                                                                                                                          335-MSE
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_MH (119)
(-)
Clan: no clan defined [family: M20_dimer] (13)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DAPE_NEIMB | Q9JYL2)
molecular function
    GO:0050897    cobalt ion binding    Interacting selectively and non-covalently with a cobalt (Co) ion.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0009014    succinyl-diaminopimelate desuccinylase activity    Catalysis of the reaction: N-succinyl-LL-2,6-diaminopimelate + H(2)O = LL-2,6-diaminopimelate + succinate.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0019877    diaminopimelate biosynthetic process    The chemical reactions and pathways resulting in the formation of diaminopimelate, both as an intermediate in lysine biosynthesis and as a component (as meso-diaminopimelate) of the peptidoglycan of Gram-negative bacterial cell walls.
    GO:0009085    lysine biosynthetic process    The chemical reactions and pathways resulting in the formation of lysine, 2,6-diaminohexanoic acid.
    GO:0009089    lysine biosynthetic process via diaminopimelate    The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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