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(-) Description

Title :  CRYSTAL STRUCTURE OF THE GLYCOSIDE HYDROLASE, FAMILY 43 YXIA PROTEIN FROM BACILLUS LICHENIFORMIS. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET BIR14.
 
Authors :  S. Vorobiev, M. Abashidze, J. Seetharaman, Rl. Belote, C. Ciccosanti, S. Sahdev, R. Xiao, T. B. Acton, J. K. Everett, G. T. Montelione, L. Tong, J. F. Hunt, Northeast Structural Genomics Consortium (Nesg)
Date :  19 Feb 10  (Deposition) - 09 Mar 10  (Release) - 09 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (1x),B (1x)
Keywords :  Glycoside Hydrolase, Similar To Arabinan Endo-1, 5-Alpha-L- Arabinosidase, Nesg, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Vorobiev, M. Abashidze, J. Seetharaman, Rl. Belote, C. Ciccosanti, S. Sahdev, R. Xiao, T. B. Acton, J. K. Everett, G. T. Montelione, L. Tong, J. F. Hunt
Crystal Structure Of The Glycoside Hydrolase, Family 43 Yxia Protein From Bacillus Licheniformis.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLYCOSIDE HYDROLASE YXIA
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 21-23C
    Expression System Strain: BL21 (DE3) + MAGIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BL00219, BLI04220, YXIA
    Organism Scientific: BACILLUS LICHENIFORMIS
    Organism Taxid: 279010
    Strain: DSM 13/ATCC 14580
    Synonym: YXIA, FAMILY 43 YXIA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 30)

Asymmetric Unit (3, 30)
No.NameCountTypeFull Name
1ACT5Ligand/IonACETATE ION
2CA5Ligand/IonCALCIUM ION
3MSE20Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 13)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 12)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (2, 13)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:318 , HOH A:702 , HOH A:703 , HOH A:707 , HOH A:709 , HOH A:714 , HOH A:734BINDING SITE FOR RESIDUE CA A 501
02AC2SOFTWAREASN A:308 , GLU A:385 , GLU A:402 , HOH A:732 , HOH A:1046 , HOH A:1162BINDING SITE FOR RESIDUE CA A 504
03AC3SOFTWAREGLU A:274 , HOH A:815 , HOH A:861 , HOH A:925 , HOH A:1110 , HOH A:1137 , HOH A:1270BINDING SITE FOR RESIDUE CA A 505
04AC4SOFTWARETYR A:52 , TYR A:331 , HOH A:1120BINDING SITE FOR RESIDUE ACT A 601
05AC5SOFTWAREARG A:129 , MSE A:155 , ASP A:156 , HOH A:1239 , HIS B:424 , HOH B:1370BINDING SITE FOR RESIDUE ACT A 602
06AC6SOFTWARETYR A:193 , SER A:194 , HIS A:224BINDING SITE FOR RESIDUE ACT A 605
07AC7SOFTWAREHIS B:318 , HOH B:706 , HOH B:711 , HOH B:713 , HOH B:726 , HOH B:741 , HOH B:773BINDING SITE FOR RESIDUE CA B 502
08AC8SOFTWAREASN B:308 , GLU B:385 , GLU B:402 , HOH B:817 , HOH B:951 , HOH B:985 , HOH B:1146BINDING SITE FOR RESIDUE CA B 503
09AC9SOFTWARETYR B:193 , SER B:194 , HIS B:224 , HOH B:749BINDING SITE FOR RESIDUE ACT B 603
10BC1SOFTWAREARG B:129 , MSE B:155 , ASP B:156BINDING SITE FOR RESIDUE ACT B 604

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LV4)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:142 -Pro A:143
2Gly A:268 -Pro A:269
3Gly B:142 -Pro B:143
4Gly B:268 -Pro B:269

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LV4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LV4)

(-) Exons   (0, 0)

(no "Exon" information available for 3LV4)

(-) 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:441
 aligned with Q65D31_BACLD | Q65D31 from UniProtKB/TrEMBL  Length:475

    Alignment length:441
                                    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       381       391       401       411       421       431       441       451       461       471 
         Q65D31_BACLD    32 KPVFSEVTVHDPSIIKANGTYYVFGSHLASAKSTDLMNWTQISSSVHDGNPLIPNVYEELKETFEWAESDTLWAPDVTQLEDGKFYMYYNACRGDSPRSALGLAVADDIEGPYKNKGIFLKSGMDGISNDGTPYDATKHPNVVDPHTFFDQNGKLWMVYGSYSGGIFILEMDKKTGFPLPGQGYGKKLIGGNHSRIEGAYILYHPETQYYYLYMSFGGLAADGGYNIRVARSKNPDGPYYDAEGHAMIDVRGKEGTLFDDRSIEPYGVKLMGNFSFNNKNGYVSPGHNSAFYDEKSGKSYLIFHTRFPGRGEEHEVRVHQLLMNKQGWPVVAPHRYAGEKLEKVKKSDVIGDYELVRHGKDISADIKESKEIRLNQNGKITGAVAGTWKNTGHNKIELKIDGKTYDGVFLRQWDAASERKVMTFSALSREGDAVWGSSLKR 472
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee..eeeeeehhheeeee......eeee...........hhhhhhhhhhhhhh.......eeee.....eeeeeeee......eeeeeeee.......eeeeeeeee.......................eeee.....eeeee......eeeeee..............eeee......eeeeeeeee....eeeeeeee.........eeeeeee.............hhhhh........hhhhhh...eeee..eee..eeeeeeeeeeeeee......eeeeeeee........eeeeeeeee.....eee.............hhhhhheeeeeeeee.......ee.eeeee....eeee...eeeeee...eeeeee..eeeeeeeeeeee....eeeeeeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lv4 A  32 KPVFSEVTVHDPSIIKANGTYYVFGSHLASAKSTDLmNWTQISSSVHDGNPLIPNVYEELKETFEWAESDTLWAPDVTQLEDGKFYmYYNACRGDSPRSALGLAVADDIEGPYKNKGIFLKSGmDGISNDGTPYDATKHPNVVDPHTFFDQNGKLWmVYGSYSGGIFILEmDKKTGFPLPGQGYGKKLIGGNHSRIEGAYILYHPETQYYYLYmSFGGLAADGGYNIRVARSKNPDGPYYDAEGHAmIDVRGKEGTLFDDRSIEPYGVKLmGNFSFNNKNGYVSPGHNSAFYDEKSGKSYLIFHTRFPGRGEEHEVRVHQLLmNKQGWPVVAPHRYAGEKLEKVKKSDVIGDYELVRHGKDISADIKESKEIRLNQNGKITGAVAGTWKNTGHNKIELKIDGKTYDGVFLRQWDAASERKVmTFSALSREGDAVWGSSLKR 472
                                    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       381       391       401       411       421       431       441       451 |     461       471 
                                                               68-MSE                                           118-MSE                              155-MSE                          188-MSE       202-MSE                                    245-MSE                          278-MSE                 302-MSE                                             354-MSE                                                                                            453-MSE               


Chain B from PDB  Type:PROTEIN  Length:439
 aligned with Q65D31_BACLD | Q65D31 from UniProtKB/TrEMBL  Length:475

    Alignment length:439
                                    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       381       391       401       411       421       431       441       451       461         
         Q65D31_BACLD    32 KPVFSEVTVHDPSIIKANGTYYVFGSHLASAKSTDLMNWTQISSSVHDGNPLIPNVYEELKETFEWAESDTLWAPDVTQLEDGKFYMYYNACRGDSPRSALGLAVADDIEGPYKNKGIFLKSGMDGISNDGTPYDATKHPNVVDPHTFFDQNGKLWMVYGSYSGGIFILEMDKKTGFPLPGQGYGKKLIGGNHSRIEGAYILYHPETQYYYLYMSFGGLAADGGYNIRVARSKNPDGPYYDAEGHAMIDVRGKEGTLFDDRSIEPYGVKLMGNFSFNNKNGYVSPGHNSAFYDEKSGKSYLIFHTRFPGRGEEHEVRVHQLLMNKQGWPVVAPHRYAGEKLEKVKKSDVIGDYELVRHGKDISADIKESKEIRLNQNGKITGAVAGTWKNTGHNKIELKIDGKTYDGVFLRQWDAASERKVMTFSALSREGDAVWGSSL 470
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Glyco_hydro_43-3lv4B01 B:32-360                                                                                                                                                                                                                                                                                                          -------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) Glyco_hydro_43-3lv4B02 B:32-360                                                                                                                                                                                                                                                                                                          -------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ............eeeee..eeeee.hhh.eeee......eeee...........hhhhhhhhhhhhhh.......eeee.....eeeeeeee......eeeeeeee.......eeeeeeeee.......................eeee.....eeeee......eeeeee..............eeee......eeeeeeee......eeeeeee.........eeeeeee.............hhhhh........hhhhhh...eeee..eee..eeeeeeeeeeeeee......eeeeeeee........eeeeeeeee.....eee.............hhhhhheeeeeeeee.......ee.eeeee....eeee...eeeeee...eeeeee..eeeeeeeeeeee....eeeeeeeeee....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lv4 B  32 KPVFSEVTVHDPSIIKANGTYYVFGSHLASAKSTDLmNWTQISSSVHDGNPLIPNVYEELKETFEWAESDTLWAPDVTQLEDGKFYmYYNACRGDSPRSALGLAVADDIEGPYKNKGIFLKSGmDGISNDGTPYDATKHPNVVDPHTFFDQNGKLWmVYGSYSGGIFILEmDKKTGFPLPGQGYGKKLIGGNHSRIEGAYILYHPETQYYYLYmSFGGLAADGGYNIRVARSKNPDGPYYDAEGHAmIDVRGKEGTLFDDRSIEPYGVKLmGNFSFNNKNGYVSPGHNSAFYDEKSGKSYLIFHTRFPGRGEEHEVRVHQLLmNKQGWPVVAPHRYAGEKLEKVKKSDVIGDYELVRHGKDISADIKESKEIRLNQNGKITGAVAGTWKNTGHNKIELKIDGKTYDGVFLRQWDAASERKVmTFSALSREGDAVWGSSL 470
                                    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       381       391       401       411       421       431       441       451 |     461         
                                                               68-MSE                                           118-MSE                              155-MSE                          188-MSE       202-MSE                                    245-MSE                          278-MSE                 302-MSE                                             354-MSE                                                                                            453-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 3LV4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LV4)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: B_Fructosidase (34)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q65D31_BACLD | Q65D31)
molecular function
    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:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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: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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