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(-) Description

Title :  CRYSTAL STRUCTURE OF LACC FROM ENTEROCOCCUS FAECALIS
 
Authors :  J. Gorman, L. Shapiro, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  31 Aug 05  (Deposition) - 13 Sep 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Gorman, L. Shapiro
Crystal Structure Of Lacc From Enterococcus Faecalis
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TAGATOSE-6-PHOSPHATE KINASE
    Chains: A, B
    EC Number: 2.7.1.144
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: MODIFIED PET26B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: LACC
    Organism Scientific: ENTEROCOCCUS FAECALIS
    Organism Taxid: 1351
    Synonym: LACC

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 24)

Asymmetric/Biological Unit (2, 24)
No.NameCountTypeFull Name
1BR12Ligand/IonBROMIDE ION
2MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:38 , ARG A:88 , SER A:136BINDING SITE FOR RESIDUE BR A 401
02AC2SOFTWARELYS B:38 , ARG B:88 , SER B:136BINDING SITE FOR RESIDUE BR B 402
03AC3SOFTWAREALA A:312BINDING SITE FOR RESIDUE BR A 403
04AC4SOFTWAREARG A:44BINDING SITE FOR RESIDUE BR A 404
05AC5SOFTWARETHR B:164 , SER B:168 , LEU B:169BINDING SITE FOR RESIDUE BR B 405
06AC6SOFTWAREPRO B:212 , MSE B:213BINDING SITE FOR RESIDUE BR B 406
07AC7SOFTWAREALA B:105 , GLY B:106BINDING SITE FOR RESIDUE BR B 407
08AC8SOFTWAREALA A:105 , GLY A:106BINDING SITE FOR RESIDUE BR A 408
09AC9SOFTWAREARG B:44BINDING SITE FOR RESIDUE BR B 409
10BC1SOFTWAREGLN A:174 , HOH A:584BINDING SITE FOR RESIDUE BR A 410
11BC2SOFTWAREALA A:312 , LYS A:313 , GLN B:307BINDING SITE FOR RESIDUE BR A 411
12BC3SOFTWAREHOH A:562BINDING SITE FOR RESIDUE BR A 412

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2AWD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PFKB_KINASES_1PS00583 pfkB family of carbohydrate kinases signature 1.LACC_ENTFA36-60
 		  2A:36-60
B:36-60
2PFKB_KINASES_2PS00584 pfkB family of carbohydrate kinases signature 2.LACC_ENTFA249-262
 		  2A:249-262
B:249-262

(-) Exons   (0, 0)

(no "Exon" information available for 2AWD)

(-) 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    
   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:316
 aligned with LACC_ENTFA | Q833W9 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:316
                             1                                                                                                                                                                                                                                                                                                                     313  
                             |       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   |  
           LACC_ENTFA     - -MIVTVTMNPSIDISYLLDHLKLDTVNRTSQVTKTPGGKGLNVTRVIHDLGGDVIATGVLGGFHGAFIANELKKANIPQAFTSIKEETRDSIAILHEGNQTEILEAGPTVSPEEISNFLENFDQLIKQAEIVTISGSLAKGLPSDFYQELVQKAHAQEVKVLLDTSGDSLRQVLQGPWKPYLIKPNLEELEGLLGQDFSENPLAAVQTALTKPMFAGIEWIVISLGKDGAIAKHHDQFYRVKIPTIQAKNPVGSGDATIAGLAYGLAKDAPAAELLKWGMAAGMANAQERMTGHVDVENVKKHLMNIQVVEIAK--   -
               SCOP domains -d2awda1 A:1-313 Tagatose-6-phosphate kinase LacC                                                                                                                                                                                                                                                                         -- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeeeeee........eeee..eeeeeehhhhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhhhhh.....eee....eeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhh..eeeee..hhhhhhhhhh.....ee..hhhhhhhhhh......hhhhhhhhhhhhhhh...eeeee.hhh.eeeee..eeeeee..........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.......hhhhhhhhhh..eeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------PFKB_KINASES_1           --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2----------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2awd A   0 SLIVTVTmNPSIDISYLLDHLKLDTVNRTSQVTKTPGGKGLNVTRVIHDLGGDVIATGVLGGFHGAFIANELKKANIPQAFTSIKEETRDSIAILHEGNQTEILEAGPTVSPEEISNFLENFDQLIKQAEIVTISGSLAKGLPSDFYQELVQKAHAQEVKVLLDTSGDSLRQVLQGPWKPYLIKPNLEELEGLLGQDFSENPLAAVQTALTKPmFAGIEWIVISLGKDGAIAKHHDQFYRVKIPTIQAKNPVGSGDATIAGLAYGLAKDAPAAELLKWGmAAGmANAQERmTGHVDVENVKKHLmNIQVVEIAKEG 315
                                   | 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      
                                   7-MSE                                                                                                                                                                                                       213-MSE                                                           279-MSE      |           304-MSE       
                                                                                                                                                                                                                                                                                                                     283-MSE  |                         
                                                                                                                                                                                                                                                                                                                            290-MSE                     


Chain B from PDB  Type:PROTEIN  Length:313
 aligned with LACC_ENTFA | Q833W9 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:313
                             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   
           LACC_ENTFA     - -MIVTVTMNPSIDISYLLDHLKLDTVNRTSQVTKTPGGKGLNVTRVIHDLGGDVIATGVLGGFHGAFIANELKKANIPQAFTSIKEETRDSIAILHEGNQTEILEAGPTVSPEEISNFLENFDQLIKQAEIVTISGSLAKGLPSDFYQELVQKAHAQEVKVLLDTSGDSLRQVLQGPWKPYLIKPNLEELEGLLGQDFSENPLAAVQTALTKPMFAGIEWIVISLGKDGAIAKHHDQFYRVKIPTIQAKNPVGSGDATIAGLAYGLAKDAPAAELLKWGMAAGMANAQERMTGHVDVENVKKHLMNIQVVEIA 312
               SCOP domains d2awdb_ B: automated matches                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeeeeee........eeee..eeeeeehhhhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhhhh......eee....eeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhh.eeeee.........hhhhhhhhhhhhh..eeeee.hhhhhhhhhhh.....ee..hhhhhhhhhh.....hhhhhhhhhhhhhhhh...eeeee.hhh.eeeee..eeeeee..........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.......hhhhhhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------PFKB_KINASES_1           --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2-------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2awd B   0 SLIVTVTmNPSIDISYLLDHLKLDTVNRTSQVTKTPGGKGLNVTRVIHDLGGDVIATGVLGGFHGAFIANELKKANIPQAFTSIKEETRDSIAILHEGNQTEILEAGPTVSPEEISNFLENFDQLIKQAEIVTISGSLAKGLPSDFYQELVQKAHAQEVKVLLDTSGDSLRQVLQGPWKPYLIKPNLEELEGLLGQDFSENPLAAVQTALTKPmFAGIEWIVISLGKDGAIAKHHDQFYRVKIPTIQAKNPVGSGDATIAGLAYGLAKDAPAAELLKWGmAAGmANAQERmTGHVDVENVKKHLmNIQVVEIA 312
                                   | 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   
                                   7-MSE                                                                                                                                                                                                       213-MSE                                                           279-MSE      |           304-MSE    
                                                                                                                                                                                                                                                                                                                     283-MSE  |                      
                                                                                                                                                                                                                                                                                                                            290-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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2AWD)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (LACC_ENTFA | Q833W9)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016773    phosphotransferase activity, alcohol group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
    GO:0009024    tagatose-6-phosphate kinase activity    Catalysis of the reaction: ATP + D-tagatose 6-phosphate = ADP + D-tagatose 1,6-bisphosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:2001059    D-tagatose 6-phosphate catabolic process    The chemical reactions and pathways resulting in the breakdown of a D-tagatose 6-phosphate.
    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:0019512    lactose catabolic process via tagatose-6-phosphate    The chemical reactions and pathways resulting in the breakdown of lactose, via the intermediate tagatose-6-phosphate.
    GO:0005988    lactose metabolic process    The chemical reactions and pathways involving lactose, the disaccharide galactopyranosyl-glucose.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        LACC_ENTFA | Q833W9: 2f02

(-) Related Entries Specified in the PDB File

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