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(-) Description

Title :  THE CRYSTAL STRUCTURE OF A PROBABLY AROMATIC AMINO ACID DEGRADATION PROTEIN FROM SINORHIZOBIUM MELILOTI 1021
 
Authors :  K. Tan, X. Xu, H. Cui, A. Savchenko, A. Edwards, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  01 Mar 10  (Deposition) - 16 Mar 10  (Release) - 16 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, X. Xu, H. Cui, S. Chin, A. Savchenko, A. Edwards, A. Joachimiak
The Crystal Structure Of A Probably Aromatic Amino Acid Degradation Protein From Sinorhizobium Meliloti 1021
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - FUMARYLACETOACETATE HYDROLASE FAMILY PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15TV LIC
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: R02938, SMC03207
    Organism Scientific: SINORHIZOBIUM MELILOTI
    Organism Taxid: 382
    Strain: 1021

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 44)

Asymmetric Unit (2, 44)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2MSE40Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 20)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE20Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 20)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE20Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:83 , GLU A:139 , GLU A:141 , ASP A:170 , HOH A:427 , HOH A:429BINDING SITE FOR RESIDUE CA A 339
2AC2SOFTWAREASP B:83 , GLU B:139 , GLU B:141 , ASP B:170 , LYS B:191 , HOH B:388 , HOH B:400BINDING SITE FOR RESIDUE CA B 339
3AC3SOFTWAREASP C:83 , GLU C:139 , GLU C:141 , ASP C:170 , HOH C:354BINDING SITE FOR RESIDUE CA C 339
4AC4SOFTWAREASP D:83 , GLU D:139 , GLU D:141 , ASP D:170 , HOH D:426BINDING SITE FOR RESIDUE CA D 339

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LZK)

(-) 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:340
 aligned with Q92LT4_RHIME | Q92LT4 from UniProtKB/TrEMBL  Length:338

    Alignment length:340
                               1                                                                                                                                                                                                                                                                                                                                                
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337
         Q92LT4_RHIME     - ---MKLATLKDSTRDGKLVVVSKDLTRCSEVGHIARTLQAALDDWAHAGPRLERVAEGIETGAQPTMRFHEHDAASPLPRAFQWADGSAYVNHVELVRKARNAEMPASFWTDPLIYQGGSDSFLGPRDPILMADDAWGIDMEGEAAVIVDDVPMGATLDEAKAAIRLVMLVNDVSLRGLIPGELAKGFGFYQSKPSSAFSPVAVTPEELGEAWDGGKLHLPLHVDLNGEPFGRANAGIDMTFDFPQLIVHAARTRPLSAGTIIGSGTVSNKLEGGPGRPVSEGGAGYSCIAELRMIETIEGGAPKTQFLKFGDVVRIEMKDRTGHSIFGAIEQKVGKYER 337
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.......eeeee.....eeee......hhhhhhhhhhhhhhhhhhhhhhhhhh....ee.hhhhh.........eeee..hhhhhhhhhhhh....hhhhhh...eeee...........eee......ee..eeeeeee.......hhhhhhhheeeeeeee..ee..hhhhhhhhh..........ee...eehhhhhhhhh........eeeee..eeee..........hhhhhhhhhh........eeee..............hhhhh.....hhhhhhhhhhhhhh...........eeeeee...........eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lzk A  -2 FQGmKLATLKDSTRDGKLVVVSKDLTRCSEVGHIARTLQAALDDWAHAGPRLERVAEGIETGAQPTmRFHEHDAASPLPRAFQWADGSAYVNHVELVRKARNAEmPASFWTDPLIYQGGSDSFLGPRDPILmADDAWGIDmEGEAAVIVDDVPmGATLDEAKAAIRLVmLVNDVSLRGLIPGELAKGFGFYQSKPSSAFSPVAVTPEELGEAWDGGKLHLPLHVDLNGEPFGRANAGIDmTFDFPQLIVHAARTRPLSAGTIIGSGTVSNKLEGGPGRPVSEGGAGYSCIAELRmIETIEGGAPKTQFLKFGDVVRIEmKDRTGHSIFGAIEQKVGKYER 337
                               |     7        17        27        37        47        57      | 67        77        87        97    |  107       117       127 |     137|      147   |   157       167       177       187       197       207       217       227       237       247       257       267       277       287    |  297       307       317       327       337
                               |                                                             64-MSE                               102-MSE                    129-MSE  138-MSE      151-MSE        166-MSE                                                                237-MSE                                                292-MSE                 316-MSE                 
                               1-MSE                                                                                                                                                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:339
 aligned with Q92LT4_RHIME | Q92LT4 from UniProtKB/TrEMBL  Length:338

    Alignment length:339
                              1                                                                                                                                                                                                                                                                                                                                                
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328         
         Q92LT4_RHIME     - --MKLATLKDSTRDGKLVVVSKDLTRCSEVGHIARTLQAALDDWAHAGPRLERVAEGIETGAQPTMRFHEHDAASPLPRAFQWADGSAYVNHVELVRKARNAEMPASFWTDPLIYQGGSDSFLGPRDPILMADDAWGIDMEGEAAVIVDDVPMGATLDEAKAAIRLVMLVNDVSLRGLIPGELAKGFGFYQSKPSSAFSPVAVTPEELGEAWDGGKLHLPLHVDLNGEPFGRANAGIDMTFDFPQLIVHAARTRPLSAGTIIGSGTVSNKLEGGPGRPVSEGGAGYSCIAELRMIETIEGGAPKTQFLKFGDVVRIEMKDRTGHSIFGAIEQKVGKYER 337
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.......eeeee.....eeee......hhhhhhhhhhhhhhhhhhhhhhhhhh....ee.hhhhh.........eeee..hhhhhhhhhhh.....hhhhhh...eee............eee.hhhh.ee..eeeeeee.......hhhhhhhheeeeeeee..ee..hhhhhhhhh..........ee...eehhhhhhhhh.......eeeeee..eeeeeee.......hhhhhhhhhh........eeee..............hhhhh.....hhhhhhhhhhhh.............eeeee............eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lzk B  -1 QGmKLATLKDSTRDGKLVVVSKDLTRCSEVGHIARTLQAALDDWAHAGPRLERVAEGIETGAQPTmRFHEHDAASPLPRAFQWADGSAYVNHVELVRKARNAEmPASFWTDPLIYQGGSDSFLGPRDPILmADDAWGIDmEGEAAVIVDDVPmGATLDEAKAAIRLVmLVNDVSLRGLIPGELAKGFGFYQSKPSSAFSPVAVTPEELGEAWDGGKLHLPLHVDLNGEPFGRANAGIDmTFDFPQLIVHAARTRPLSAGTIIGSGTVSNKLEGGPGRPVSEGGAGYSCIAELRmIETIEGGAPKTQFLKFGDVVRIEmKDRTGHSIFGAIEQKVGKYER 337
                              |      8        18        28        38        48        58     |  68        78        88        98   |   108       118       128|      138       148  |    158       168       178       188       198       208       218       228       238       248       258       268       278       288   |   298       308       318       328         
                              1-MSE                                                         64-MSE                               102-MSE                    129-MSE  138-MSE      151-MSE        166-MSE                                                                237-MSE                                                292-MSE                 316-MSE                 


Chain C from PDB  Type:PROTEIN  Length:343
 aligned with Q92LT4_RHIME | Q92LT4 from UniProtKB/TrEMBL  Length:338

    Alignment length:343
                                  1                                                                                                                                                                                                                                                                                                                                                
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334   
         Q92LT4_RHIME     - ------MKLATLKDSTRDGKLVVVSKDLTRCSEVGHIARTLQAALDDWAHAGPRLERVAEGIETGAQPTMRFHEHDAASPLPRAFQWADGSAYVNHVELVRKARNAEMPASFWTDPLIYQGGSDSFLGPRDPILMADDAWGIDMEGEAAVIVDDVPMGATLDEAKAAIRLVMLVNDVSLRGLIPGELAKGFGFYQSKPSSAFSPVAVTPEELGEAWDGGKLHLPLHVDLNGEPFGRANAGIDMTFDFPQLIVHAARTRPLSAGTIIGSGTVSNKLEGGPGRPVSEGGAGYSCIAELRMIETIEGGAPKTQFLKFGDVVRIEMKDRTGHSIFGAIEQKVGKYER 337
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee.......eeeee.....eeee......hhhhhhhhhhhhhhhhhhhhhhhhhh....ee.hhhhh.........eeee..hhhhhhhhhhh.....hhhhhh...eeee...........eee.hhhh.ee..eeeeeee.......hhhhhhhheeeeeeee..ee..hhhhhhhh...........ee...eehhhhhhhhh........eeeee..eeee..........hhhhhhhhhh........eeee..............hhhhh.....hhhhhhhhhhhhhh...........eeeeee...........eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lzk C  -5 NLYFQGmKLATLKDSTRDGKLVVVSKDLTRCSEVGHIARTLQAALDDWAHAGPRLERVAEGIETGAQPTmRFHEHDAASPLPRAFQWADGSAYVNHVELVRKARNAEmPASFWTDPLIYQGGSDSFLGPRDPILmADDAWGIDmEGEAAVIVDDVPmGATLDEAKAAIRLVmLVNDVSLRGLIPGELAKGFGFYQSKPSSAFSPVAVTPEELGEAWDGGKLHLPLHVDLNGEPFGRANAGIDmTFDFPQLIVHAARTRPLSAGTIIGSGTVSNKLEGGPGRPVSEGGAGYSCIAELRmIETIEGGAPKTQFLKFGDVVRIEmKDRTGHSIFGAIEQKVGKYER 337
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124    |  134   |   144      |154       164 |     174       184       194       204       214       224       234  |    244       254       264       274       284       294       304       314 |     324       334   
                                  1-MSE                                                         64-MSE                               102-MSE                    129-MSE  138-MSE      151-MSE        166-MSE                                                                237-MSE                                                292-MSE                 316-MSE                 


Chain D from PDB  Type:PROTEIN  Length:340
 aligned with Q92LT4_RHIME | Q92LT4 from UniProtKB/TrEMBL  Length:338

    Alignment length:340
                              1                                                                                                                                                                                                                                                                                                                                                 
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338
         Q92LT4_RHIME     - --MKLATLKDSTRDGKLVVVSKDLTRCSEVGHIARTLQAALDDWAHAGPRLERVAEGIETGAQPTMRFHEHDAASPLPRAFQWADGSAYVNHVELVRKARNAEMPASFWTDPLIYQGGSDSFLGPRDPILMADDAWGIDMEGEAAVIVDDVPMGATLDEAKAAIRLVMLVNDVSLRGLIPGELAKGFGFYQSKPSSAFSPVAVTPEELGEAWDGGKLHLPLHVDLNGEPFGRANAGIDMTFDFPQLIVHAARTRPLSAGTIIGSGTVSNKLEGGPGRPVSEGGAGYSCIAELRMIETIEGGAPKTQFLKFGDVVRIEMKDRTGHSIFGAIEQKVGKYERG 338
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------FAA_hydrolase-3lzkD01 D:80-333                                                                                                                                                                                                                                ----- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------FAA_hydrolase-3lzkD02 D:80-333                                                                                                                                                                                                                                ----- Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------FAA_hydrolase-3lzkD03 D:80-333                                                                                                                                                                                                                                ----- Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------FAA_hydrolase-3lzkD04 D:80-333                                                                                                                                                                                                                                ----- Pfam domains (4)
         Sec.struct. author ...eeeee.......eeeee.....eeee......hhhhhhhhhhhhhhhhhhhhhhhhhh....ee.hhhhh.........eeee..hhhhhhhhhhhh....hhhhhh...eee............eee......ee..eeeeeee.......hhhhhhhheeeeeeee..ee..hhhhhhhhh..........ee...eehhhhhhhhh........eeeee..eeee..........hhhhhhhhhh........eeee......ee..ee..hhhhh.....hhhhhhhhhhhhh............eeeeee...........eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lzk D  -1 QGmKLATLKDSTRDGKLVVVSKDLTRCSEVGHIARTLQAALDDWAHAGPRLERVAEGIETGAQPTmRFHEHDAASPLPRAFQWADGSAYVNHVELVRKARNAEmPASFWTDPLIYQGGSDSFLGPRDPILmADDAWGIDmEGEAAVIVDDVPmGATLDEAKAAIRLVmLVNDVSLRGLIPGELAKGFGFYQSKPSSAFSPVAVTPEELGEAWDGGKLHLPLHVDLNGEPFGRANAGIDmTFDFPQLIVHAARTRPLSAGTIIGSGTVSNKLEGGPGRPVSEGGAGYSCIAELRmIETIEGGAPKTQFLKFGDVVRIEmKDRTGHSIFGAIEQKVGKYERG 338
                              |      8        18        28        38        48        58     |  68        78        88        98   |   108       118       128|      138       148  |    158       168       178       188       198       208       218       228       238       248       258       268       278       288   |   298       308       318       328       338
                              1-MSE                                                         64-MSE                               102-MSE                    129-MSE  138-MSE      151-MSE        166-MSE                                                                237-MSE                                                292-MSE                 316-MSE
   Legend:   → Mismatch (orange background)
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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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: FAH (11)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q92LT4_RHIME | Q92LT4)
molecular function
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    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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