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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE GAMMA-D-GLUTAMYL-L-DIAMINO ACID ENDOPEPTIDASE (NPUN_R0659) FROM NOSTOC PUNCTIFORME PCC 73102 AT 1.60 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  31 Oct 05  (Deposition) - 22 Nov 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Putative Gamma-D-Glutamyl-L-Diamino Acid Endopeptidase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Xu, S. Sudek, D. Mcmullan, M. D. Miller, B. Geierstanger, D. H. Jones S. S. Krishna, G. Spraggon, B. Bursalay, P. Abdubek, C. Acosta, E. Ambing, T. Astakhova, H. L. Axelrod, D. Carlton, J. Caruthers, H. J. Chiu, T. Clayton, M. C. Deller, L. Duan, Y. Elias, M. A. Elsliger, J. Feuerhelm, S. K. Grzechnik, J. Hale, G. Won Han, J. Haugen, L. Jaroszewski, K. K. Jin, H. E. Klock, M. W. Knuth, P. Kozbial, A. Kumar D. Marciano, A. T. Morse, E. Nigoghossian, L. Okach, S. Oommachen, J. Paulsen, R. Reyes, C. L. Rife, C. V. Trout, H. Van Den Bedem, D. Weekes, A. White, G. Wolf, C. Zubieta, K. O. Hodgson, J. Wooley, A. M. Deacon, A. Godzik, S. A. Lesley, I. A. Wilson
Structural Basis Of Murein Peptide Specificity Of A Gamma-D-Glutamyl-L-Diamino Acid Endopeptidase.
Structure V. 17 303 2009
PubMed-ID: 19217401  |  Reference-DOI: 10.1016/J.STR.2008.12.008

(-) Compounds

Molecule 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: 53686717
    Organism Scientific: NOSTOC PUNCTIFORME
    Organism Taxid: 63737
    Strain: PCC 73102

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO5Ligand/Ion1,2-ETHANEDIOL
3MSE2Mod. Amino AcidSELENOMETHIONINE
4NA1Ligand/IonSODIUM ION
Biological Unit 1 (2, 14)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO10Ligand/Ion1,2-ETHANEDIOL
3MSE4Mod. Amino AcidSELENOMETHIONINE
4NA-1Ligand/IonSODIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:27 , SER A:28 , CYS A:31 , THR A:32 , ARG A:33BINDING SITE FOR RESIDUE CL A 235
2AC2SOFTWAREGLU A:99 , ALA A:162 , LEU A:181BINDING SITE FOR RESIDUE NA A 236
3AC3SOFTWARETHR A:119 , GLN A:131 , ALA A:132 , TRP A:140 , HOH A:244 , HOH A:292BINDING SITE FOR RESIDUE EDO A 237
4AC4SOFTWAREASN A:112 , ARG A:196 , ASP A:197 , GLY A:198 , ILE A:199 , HOH A:276 , HOH A:371 , HOH A:520 , HOH A:528BINDING SITE FOR RESIDUE EDO A 238
5AC5SOFTWAREASP A:22 , LEU A:23 , ASN A:24 , ASP A:72 , HOH A:434BINDING SITE FOR RESIDUE EDO A 239
6AC6SOFTWARETHR A:32 , GLN A:37 , GLY A:121 , PRO A:122 , ASN A:123 , HOH A:246 , HOH A:300 , HOH A:324BINDING SITE FOR RESIDUE EDO A 240
7AC7SOFTWAREGLN A:84 , ALA A:85 , THR A:87 , GLU A:92 , GLU A:230BINDING SITE FOR RESIDUE EDO A 241

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2EVR)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:121 -Pro A:122
2Arg A:233 -Arg A:234

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2EVR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2EVR)

(-) Exons   (0, 0)

(no "Exon" information available for 2EVR)

(-) 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:222
 aligned with B2J9B4_NOSP7 | B2J9B4 from UniProtKB/TrEMBL  Length:242

    Alignment length:222
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240  
         B2J9B4_NOSP7    21 KLGEYQCLADLNLFDSPECTRLATQSASGRHLWVTSNHQNLAVEVYLCEDDYPGWLSLSDFDSLQPATVPYQAATFSESEIKKLLAEVIAFTQKAMQQSNYYLWGGTVGPNYDCSGLMQAAFASVGIWLPRDAYQQEGFTQPITIAELVAGDLVFFGTSQKATHVGLYLADGYYIHSSGKDQGRDGIGIDILSEQGDAVSLSYYQQLRGAGRVFKSYEPQRR 242
               SCOP domains d2evra1 A:13-86 Cell wall-associated hydrolase Spr N-terminal domain      d2evra2 A:87-234 Cell wall-associated hydrolase Spr C-terminal domain                                                                                SCOP domains
               CATH domains 2evrA01 A:13-86 SH3 Domains                                               2evrA02 A:87-234 endopeptidase domain like (from Nostoc punctiforme)                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...eeee.......eeeee....eeeeeeeee..eeeeee.....eeeee.hhhh.eee..........hhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhh.......hhhhhhhhheeehhhhh....eeeee....eeeeeee....eeeeee.......eeeeee.....hhhhhhhhh.eeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2evr A  13 KLGEYQCLADLNLFDSPECTRLATQSASGRHLWVTSNHQNLAVEVYLCEDDYPGWLSLSDFDSLQPATVPYQAATFSESEIKKLLAEVIAFTQKAmQQSNYYLWGGTVGPNYDCSGLmQAAFASVGIWLPRDAYQQEGFTQPITIAELVAGDLVFFGTSQKATHVGLYLADGYYIHSSGKDQGRDGIGIDILSEQGDAVSLSYYQQLRGAGRVFKSYEPQRR 234
                                    22        32        42        52        62        72        82        92       102     | 112       122       132       142       152       162       172       182       192       202       212       222       232  
                                                                                                                         108-MSE               130-MSE
   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  (2, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2EVR)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2EVR)

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  Cis Peptide Bonds
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