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(-) Description

Title :  CRYSTAL STRUCTURE OF A AMINOPEPTIDASE/GLUCANASE HOMOLOG
 
Authors :  Structural Genomix
Date :  01 Dec 03  (Deposition) - 30 Dec 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (12x)
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 - AMINOPEPTIDASE/GLUCANASE HOMOLOG
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: YSDC
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (12x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1MSE11Mod. Amino AcidSELENOMETHIONINE
2ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 11)
No.NameCountTypeFull Name
1MSE11Mod. Amino AcidSELENOMETHIONINE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 132)
No.NameCountTypeFull Name
1MSE132Mod. Amino AcidSELENOMETHIONINE
2ZN-1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:68 , ASP A:182 , ASP A:237 , HOH A:373 , HOH A:374BINDING SITE FOR RESIDUE ZN A 372

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asp A:182 -Asn A:183

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VHE)

(-) 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:365
 aligned with YSDC_BACSU | P94521 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:365
                                                                                                                                                                                                                                                                                                                                                                                                361      
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352        |-     
           YSDC_BACSU     3 KLDETLTMLKDLTDAKGIPGNEREVRQVMKSYIEPFADEVTTDRLGSLIAKKTGAENGPKIMIAGHLDEVGFMVTQITDKGFIRFQTVGGWWAQVMLAQRVTIVTKKGEITGVIGSKPPHILSPEARKKSVEIKDMFIDIGASSREEALEWGVLPGDMIVPHFEFTVMNNEKFLLAKAWDNRIGCAIAIDVLRNLQNTDHPNIVYGVGTVQEEVGLRGAKTAAHTIQPDIAFGVDVGIAGDTPGISEKEAQSKMGKGPQIIVYDASMVSHKGLRDAVVATAEEAGIPYQFDAIAGGGTDSGAIHLTANGVPALSITIATRYIHTHAAMLHRDDYENAVKLITEVIKKLDRKTVDEITYQ------   -
               SCOP domains d1vhea2 A:3-72,A:163-367 Hypothetical protein YsdC, catalytic domain  d1vhea1 A:73-162 Hypothetical protein YsdC                                                d1vhea2 A:3-72,A:163-367 Hypothetical protein YsdC, catalytic domain                                                                                                                                          SCOP domains
               CATH domains 1vheA01 A:3-74,A:165-367 Zn peptidases                                  --1vheA02 A:77-164 Aminopeptidase/glucanase lid domain; domain 2                          1vheA01 A:3-74,A:165-367 Zn peptidases                                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------Peptidase_M42-1vheA01 A:48-342                                                                                                                                                                                                                                                                         ------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.eeee.....eeeeee......eeeeeee....eeeeeee.....eeeeee...hhhhh...eeeeee..eeeeeeee..hhhhh.........hhhhheee....hhhhhhhh......eeee....ee.....eeee.hhhhhhhhhhhhhhhhhhhh.....eeeeeee......hhhhhhhhhhhh..eeeeeeeee....................eeeeee..ee.hhhhhhhhhhhhhhhh...eeeee.....hhhhhh.......eeeeeeee.......eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vhe A   3 KLDETLTmLKDLTDAKGIPGNEREVRQVmKSYIEPFADEVTTDRLGSLIAKKTGAENGPKImIAGHLDEVGFmVTQITDKGFIRFQTVGGWWAQVmLAQRVTIVTKKGEITGVIGSKPPHILSPEARKKSVEIKDmFIDIGASSREEALEWGVLPGDmIVPHFEFTVmNNEKFLLAKAWDNRIGCAIAIDVLRNLQNTDHPNIVYGVGTVQEEVGLRGAKTAAHTIQPDIAFGVDVGIAGDTPGISEKEAQSKmGKGPQIIVYDASmVSHKGLRDAVVATAEEAGIPYQFDAIAGGGTDSGAIHLTANGVPALSITIATRYIHTHAAmLHRDDYENAVKLITEVIKKLDRKTVDEITYQEGGSHH 367
                                   |12        22        32        42        52        62 |      72  |     82        92     | 102       112       122       132     | 142       152       162       172       182       192       202       212       222       232       242       252   |   262      |272       282       292       302       312       322       332       342       352       362     
                                  10-MSE               31-MSE                           64-MSE     75-MSE                 98-MSE                                 138-MSE               160-MSE   170-MSE                                                                               256-MSE      269-MSE                                                      330-MSE
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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) (23833)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Peptidase_MH (119)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (YSDC_BACSU | P94521)
molecular function
    GO:0004177    aminopeptidase activity    Catalysis of the hydrolysis of N-terminal amino acid residues from in a polypeptide chain.
    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: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:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
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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