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(-) Description

Title :  CRYSTAL STRUCTURE OF ZINC-DEPENDENT PEPTIDASE FROM METHANOCORPUSCULUM LABREANUM (STRAIN Z), NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET MUR16
 
Authors :  A. Kuzin, S. Ashok, S Vorobiev, J. Seetharaman, P. Patel, R. Xiao, C. Ci D. Lee, J. K. Everett, R. Nair, T. B. Acton, B. Rost, G. T. Montelione, L. J. F. Hunt, Northeast Structural Genomics Consortium (Nesg)
Date :  29 Jan 10  (Deposition) - 16 Feb 10  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Mur16, A2Sqk8, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kuzin, S. Ashok, S Vorobiev, J. Seetharaman, P. Patel, R. Xiao, C. Ciccosanti, D. Lee, J. K. Everett, R. Nair, T. B. Acton, B. Rost, G. T. Montelione, L. Tong, J. F. Hunt
Northeast Structural Genomics Consortium Target Mur16
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PEPTIDASE, ZINC-DEPENDENT
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)+ MAGIC
    Expression System Taxid: 469008
    Expression System Vector: PET 21-23C
    Gene: MLAB_0438
    Organism Scientific: METHANOCORPUSCULUM LABREANUM
    Organism Taxid: 410358
    Strain: ATCC 43576 / DSM 4855 / Z

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1FE1Ligand/IonFE (III) ION
2MSE5Mod. Amino AcidSELENOMETHIONINE
3ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:160 , CYS A:165 , CYS A:184 , CYS A:187BINDING SITE FOR RESIDUE FE A 211
2AC2SOFTWAREHIS A:149 , HIS A:153 , HIS A:159 , HOH A:230BINDING SITE FOR RESIDUE ZN A 212

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LMC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LMC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LMC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LMC)

(-) Exons   (0, 0)

(no "Exon" information available for 3LMC)

(-) 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    
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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:191
 aligned with A2SQK8_METLZ | A2SQK8 from UniProtKB/TrEMBL  Length:202

    Alignment length:191
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191 
         A2SQK8_METLZ     2 GIHLFWDSRVPVGLSRPVSEELSAVLEMPVSRIDDGIFPLEGFDPVRNQYDAVKVLLKLDMFRRRMPQIFKPADMDLEFYNKFNHLHEKILLVTPGDLYEPLADFVFGLAYPKLGVAIVSPHRLQNEFYGKYADDSALIDRIVKEGAHEIGHLFGLGHCDNPGCIMYCPRNLDELDRKRKYFCGKCRVQLN 192
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------Peptidase_M54-3lmcA01 A:45-192                                                                                                                       Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhhhhhhh..eeee.........ee....eeehhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhheeeee....eee..eeee.eeeehhh.eeee.hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh................hhhhhhhh....hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lmc A   2 GIHLFWDSRVPVGLSRPVSEELSAVLEmPVSRIDDGIFPLEGFDPVRNQYDAVKVLLKLDmFRRRmPQIFKPADmDLEFYNKFNHLHEKILLVTPGDLYEPLADFVFGLAYPKLGVAIVSPHRLQNEFYGKYADDSALIDRIVKEGAHEIGHLFGLGHCDNPGCImYCPRNLDELDRKRKYFCGKCRVQLN 192
                                    11        21       |31        41        51        61|    |  71    |   81        91       101       111       121       131       141       151       161     | 171       181       191 
                                                      29-MSE                           62-MSE|       76-MSE                                                                                    167-MSE                     
                                                                                            67-MSE
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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 3LMC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LMC)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_MA (251)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (A2SQK8_METLZ | A2SQK8)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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