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(-) Description

Title :  THE CRYSTAL STRUCTURE OF A PROTEIN IN THE GLYCOSYL HYDROLASE FAMILY 38 FROM ENTEROCOCCUS FAECALIS TO 2.55A
 
Authors :  A. J. Stein, T. A. Binkowski, A. Weger, M. Borovilos, S. Moy, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  22 Feb 10  (Deposition) - 16 Mar 10  (Release) - 16 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Glycosyl, Hydrolase, Psi, Mcsg, Structural Genomics, Midwest Center For Structural Genomics, Protein Structure Initiative (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. J. Stein, T. A. Binkowski, A. Weger, M. Borovilos, S. Moy, A. Joachimiak
The Crystal Structure Of A Protein In The Glycosyl Hydrolase Family 38 From Enterococcus Faecalis To 2. 55A
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLYCOSYL HYDROLASE, FAMILY 38
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: EF1707, EF_1707
    Organism Common: STREPTOCOCCUS FAECALIS
    Organism Scientific: ENTEROCOCCUS FAECALIS
    Organism Taxid: 226185
    Strain: V583

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 20)

Asymmetric Unit (2, 20)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2MSE19Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 19)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE19Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 38)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE38Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:247 , PHE A:250 , TYR A:253BINDING SITE FOR RESIDUE CA A 897

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:354 -A:356

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:84 -Pro A:85
2Leu A:473 -Pro A:474
3Thr A:875 -Pro A:876

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LVT)

(-) 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:833
 aligned with Q834E8_ENTFA | Q834E8 from UniProtKB/TrEMBL  Length:896

    Alignment length:896
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889      
         Q834E8_ENTFA     - -MTKKKVYIVSHSHWDREWYLPYEEHHMRLIELVDNVLDLIENDPEFNSFHLDGQTIILDDYLQVRPEKKEAVKKAVQAGKLKIGPFYILQDDFLISSESNVRNMLIGHLESQKWGAPVQLGYFPDTFGNMGQTPQMMQLANLPAAAFGRGVKPIGFDNQVLESDYSSQYSEMWWEGPDQTKIFGLLFANWYSNGNEIPSEKEAAIAFWKQKLADVERYASTNHLLMMNGVDHQPVQRDITKAIALANELFPEYEFIHSNFDDYLKAVQEELPEDLGTVTGELTSQETDGWYTLANTSSARVYLKQWNTKVQRQLENIAEPLAAMAYEVTGDYPHDQFDYAWKTLLQNHPHDSICGCSVDEVHRGMMTRFENANDVGHFLADEATRQLTEAIDTSVFPEKAHPFVLFNTSGYQKTEVVTVEVEIERLPFYTGKPEDLYHELKQKATPDYQVIDPTGKAVASRIVKEDVRFGYDLPKDAFRQPYMAKYLTVELSVKEMAPFSWDSFALIQGETKAFEGSLLAQPATNEMENEFIQVKIENNGSLTIADKKTGETFSKLLTFEDTGDIGNEYIFFKPTEDQGITTENVTAEITNKENSPVKASYQIKQTVMLPVAADERLEEEQKAVREFRERLAQRSTTLRPFEITTMVTMIKESNQLFFETTINNQIKDHRLRVLFPTGMVTETHEADSIYEVVTRPNQVSDTWENPTNPQHQQAFVNVHDQNKGVTIFNEGLNEYEVLADGTIAVTLIRCVGELGDWGYFATPEAQCQGEYTFKYGLSLHGKPEERFATYQQAYSAQIPFTAATTARHEGKLAPNHVYLTTAEGPIGWTAVKRQEQTNHLVVRGFNLTAQNIPCELHKETQPATCLTNVLEEPLTPAIEVDAPLRPFEIRTWRFE 895
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----Glyco_hydr    o_38-3lvtA01 A:5-281                                                                                                                                                                                                                                                              Alpha-mann_mid-3lvtA03 A:293-369                                             -------------------------------Glyco_hydro_38C-3lvtA02 A:401-893                                                                                                                                                                                                                                                                                                                                                                                                                                                                            -- Pfam domains
         Sec.struct. author ....eeeeeeeee..----..hhhhhhhhhhhhhhhhhhhhhhh.....ee....hhhhhhhhhhh..hhhhhhhhhhh..ee........hhhhhhhhhhhhhhhhhhhhhhhhh.....eee...---..hhhhhhhh....eeee.---------------------.eeeee.....eeeeee....----.....hhhhhhhhhhhhhhhhhhhh...eeeeeeee.------hhhhhhhhhhhhh..eeeee.hhhhhhhhhhhh..--..eee..-----------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeeee.....eeeeeeeeeeeeeee.hhhhhhhhhhhhhhh....eeee.....ee..eeeeeeeeeee...-----.eeeeeeeeeeeeeeee...eeeeeeeee...........ee....eee...eeeee.....eeeee.....eeeee.eeeeee................ee......eeeeeee...eeeeeeeeeeeee....hhhhhhhhh..hhhhh.......eeeeeeeeeeeee.....eeeeeeeee....eeeeeee.......eeeee....eeeee.-------.....ee...eeeee....eeeeee....eeee.....eeeeeeee...........hhhhhh.eeeeeeeeeeee.hhhhhhhhhhhhhhhh...eeee..........eee.ee.....eeeeeeee......eeeeeee..........ee..ee..eee.....................eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lvt A   0 AmTKKKVYIVSHSHW----YLPYEEHHmRLIELVDNVLDLIENDPEFNSFHLDGQTIILDDYLQVRPEKKEAVKKAVQAGKLKIGPFYILQDDFLISSESNVRNmLIGHLESQKWGAPVQLGYFPDT---mGQTPQmmQLANLPAAAFG---------------------SEmWWEGPDQTKIFGLLFANW----NEIPSEKEAAIAFWKQKLADVERYASTNHLLmmNGVD------DITKAIALANELFPEYEFIHSNFDDYLKAVQEELP--LGTVTGE-----------LANTSSARVYLKQWNTKVQRQLENIAEPLAAmAYEVTGDYPHDQFDYAWKTLLQNHPHDSICGCSVDEVHRGmmTRFENANDVGHFLADEATRQLTEAIDTSVFPEKAHPFVLFNTSGYQKTEVVTVEVEIERLPFYTGKPEDLYHELKQKATPDYQVIDPTGKAVASRIVKEDVRFGYDLP-----QPYmAKYLTVELSVKEmAPFSWDSFALIQGETKAFEGSLLAQPATNEmENEFIQVKIENNGSLTIADKKTGETFSKLLTFEDTGDIGNEYIFFKPTEDQGITTENVTAEITNKENSPVKASYQIKQTVmLPVAADERLEEEQKAVREFRERLAQRSTTLRPFEITTmVTmIKESNQLFFETTINNQIKDHRLRVLFPTGmVTETHEADSIYEVVTRPN-------NPTNPQHQQAFVNVHDQNKGVTIFNEGLNEYEVLADGTIAVTLIRCVGELGDWGYFATPEAQCQGEYTFKYGLSLHGKPEERFATYQQAYSAQIPFTAATTARHEGKLAPNHVYLTTAEGPIGWTAVKRQEQTNHLVVRGFNLTAQNIPCELHKETQPATCLTNVLEEPLTPAIEVDAPLRPFEIRTWRFE 895
                             |       9    |   19       |29        39        49        59        69        79        89        99    |  109       119      |  -|     |139        |-         -         -| |    179       189|    | 199       209       219      |229 |     239       249       259       269  |  | 279 |       -   |   299       309       319    |  329       339       349       359     ||369       379       389       399       409       419       429       439       449       459       469    |    -|  |   489      |499       509       519       529       539       549       559       569       579       589       599       609       619       629       639      |649       659       669       679       689       | -     | 709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889      
                             |           14   19      27-MSE                                                                      104-MSE               126   |     ||        148                   170 |               190  195                            226-MSE1    238                               272  |   281         293                            324-MSE                                  365-MSE                                                                                                      474   480  |          496-MSE                        527-MSE                                                                          608-MSE                               646-MSE                          679-MSE           697     705                                                                                                                                                                                              
                             1-MSE                                                                                                                          130-MSE ||                                172-MSE                                                227-MSE                                         275                                                                                        366-MSE                                                                                                              483-MSE                                                                                                                                                               649-MSE                                                                                                                                                                                                                                                  
                                                                                                                                                                  136-MSE                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
                                                                                                                                                                   137-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  (0, 0)

(no "SCOP Domain" information available for 3LVT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (3, 3)

Asymmetric Unit
(-)
Clan: GH_CE (28)
(-)
Clan: Gal_mutarotase (81)
(-)
Clan: no clan defined [family: Alpha-mann_mid] (17)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q834E8_ENTFA | Q834E8)
molecular function
    GO:0004559    alpha-mannosidase activity    Catalysis of the hydrolysis of terminal, non-reducing alpha-D-mannose residues in alpha-D-mannosides.
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
    GO:0015923    mannosidase activity    Catalysis of the hydrolysis of mannosyl compounds, substances containing a group derived from a cyclic form of mannose or a mannose derivative.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0006013    mannose metabolic process    The chemical reactions and pathways involving mannose, the aldohexose manno-hexose, the C-2 epimer of glucose. The D-(+)-form is widely distributed in mannans and hemicelluloses and is of major importance in the core oligosaccharide of N-linked oligosaccharides of glycoproteins.

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  3lvt
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 Related Entries

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        Q834E8_ENTFA | Q834E8: 5kbp

(-) Related Entries Specified in the PDB File

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