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(-) Description

Title :  METHYLASPARTATE AMMONIA LYASE FROM CLOSTRIDIUM TETANOMORPHUM MUTANT Q73A
 
Authors :  H. Raj, W. Szymanski, J. De Villiers, H. J. Rozeboom, V. P. Veetil, C. R. Villiers, S. De Wildeman, F. J. Dekker, W. J. Quax, A. M. W. H. Thunniss B. L. Feringa, D. B. Janssen, G. J. Poelarends
Date :  25 Jul 11  (Deposition) - 02 May 12  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lyase, Enolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Raj, W. Szymanski, J. De Villiers, H. J. Rozeboom, V. P. Veetil, C. R. Reis, M. De Villiers, F. J. Dekker, S. De Wildeman, W. J. Quax, A. M. W. H. Thunnissen, B. L. Feringa, D. B. Janssen, G. J. Poelarends
Engineering Methylaspartate Ammonia Lyase For The Asymmetri Synthesis Of Unnatural Amino Acids.
Nat. Chem. V. 4 478 2012
PubMed-ID: 22614383  |  Reference-DOI: 10.1038/NCHEM.1338

(-) Compounds

Molecule 1 - METHYLASPARTATE AMMONIA-LYASE
    Atcc: 15920
    Chains: A
    EC Number: 4.3.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: TOP10
    Expression System Taxid: 562
    Expression System Vector: PBAD/MYC-HISA
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: CLOSTRIDIUM TETANOMORPHUM
    Organism Taxid: 1553
    Strain: H1
    Synonym: 3-METHYLASPARTATE AMMONIA LYASE, BETA-METHYLASPARTASE
 
Molecule 2 - METHYLASPARTATE AMMONIA-LYASE
    Atcc: 15920
    Chains: B
    EC Number: 4.3.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: TOP10
    Expression System Taxid: 562
    Expression System Vector: PBAD/MYC-HISA
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: CLOSTRIDIUM TETANOMORPHUM
    Organism Taxid: 1553
    Strain: H1
    Synonym: 3-METHYLASPARTATE AMMONIA LYASE, BETA-METHYLASPARTASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2CSO1Mod. Amino AcidS-HYDROXYCYSTEINE
3GOL5Ligand/IonGLYCEROL
4MG2Ligand/IonMAGNESIUM ION
5OCS1Mod. Amino AcidCYSTEINESULFONIC ACID

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:238 , GLU A:273 , ASP A:307 , HOH A:2180 , HOH A:2181 , HOH A:2182BINDING SITE FOR RESIDUE MG A 1421
2AC2SOFTWAREASP B:238 , GLU B:273 , ASP B:307 , HOH B:2182 , HOH B:2183 , HOH B:2184BINDING SITE FOR RESIDUE MG B 1421
3AC3SOFTWAREGLU A:401 , ARG A:404 , LEU A:408 , HOH A:2127BINDING SITE FOR RESIDUE GOL A 1416
4AC4SOFTWAREHOH A:2060 , GLU B:401 , ARG B:404 , LEU B:408 , HOH B:2116 , HOH B:2256BINDING SITE FOR RESIDUE GOL B 1416
5AC5SOFTWAREPRO A:10 , GLY A:11 , LYS A:49 , GLU A:51 , HOH A:2261 , ASN B:403BINDING SITE FOR RESIDUE GOL A 1417
6AC6SOFTWAREASN B:199 , GLU B:201 , GLU B:202BINDING SITE FOR RESIDUE GOL B 1417
7AC7SOFTWAREGLU A:308 , TRP A:309 , ASN A:311BINDING SITE FOR RESIDUE GOL A 1418
8AC8SOFTWARELYS A:2 , ASP B:176 , TYR B:178 , ASP B:179BINDING SITE FOR RESIDUE CL B 1418

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Leu A:192 -Pro A:193
2Lys A:266 -Pro A:267
3Lys A:386 -Pro A:387
4Leu B:192 -Pro B:193
5Lys B:266 -Pro B:267
6Lys B:386 -Pro B:387

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ZVH)

(-) 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:415
 aligned with MAAL_CLOTT | Q05514 from UniProtKB/Swiss-Prot  Length:413

    Alignment length:415
                                                                                                                                                                                                                                                                                                                                                                                                                                                      413  
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410  |  
           MAAL_CLOTT     1 MKIVDVLCTPGLTGFYFDDQRAIKKGAGHDGFTYTGSTVTEGFTQVRQKGESISVLLVLEDGQVAHGDCAAVQYSGAGGRDPLFLAKDFIPVIEKEIAPKLIGREITNFKPMAEEFDKMTVNGNRLHTAIRYGITQAILDAVAKTRKVTMAEVIRDEYNPGAEINAVPVFAQSGDDRYDNVDKMIIKEADVLPHALINNVEEKLGLKGEKLLEYVKWLRDRIIKLRVREDYAPIFHIDVYGTIGAAFDVDIKAMADYIQTLAEAAKPFHLRIEGPMDVEDRQKQMEAMRDLRAELDGRGVDAELVADEWCNTVEDVKFFTDNKAGHMVQIKTPDLGGVNNIADAIMYCKANGMGAYCGGTCNETNRSAEVTTNIGMACGARQVLAKPGMGVDEGMMIVKNEMNRVLALVGRRK--   -
               SCOP domains d3zvha1 A:1-160 automated matches                                                                                                                               d3zvha2 A:161-415 automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee....eeehhhhhhhh..ee..ee............eee..eeeeeeee....eeeeee...............hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhee..ee.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.........ee.......hhhhhhhhhhh..eeee....hhhhhhh..hhhhhhhhhhhhhhhhhhh.......eeeee..hhhhhhh..hhhhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhh....eeeehhhhhh.hhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zvh A   1 MKIVDVLCTPGLTGFYFDDQRAIKKGAGHDGFTYTGSTVTEGFTQVRQKGESISVLLVLEDGQVAHGDCAAVAYSGAGGRDPLFLAKDFIPVIEKEIAPKLIGREITNFKPMAEEFDKMTVNGNRLHTAIRYGITQAILDAVAKTRKVTMAEVIRDEYNPGAEINAVPVFAQSGDDRYDNVDKMIIKEADVLPHALINNVEEKLGLKGEKLLEYVKWLRDRIIKLRVREDYAPIFHIDVYGTIGAAFDVDIKAMADYIQTLAEAAKPFHLRIEGPMDVEDRQKQMEAMRDLRAELDGRGVDAELVADEWCNTVEDVKFFTDNKAGHMVQIKTPDLGGVNNIADAIMYCKANGMGAYCGGTcNETNRSAEVTTNIGMACGARQVLAKPGMGVDEGMMIVKNEMNRVLALVGRRKKL 415
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360|      370       380       390       400       410     
                                                                                                                                                                                                                                                                                                                                                                                                  361-CSO                                                  


Chain B from PDB  Type:PROTEIN  Length:415
 aligned with MAAL_CLOTT | Q05514 from UniProtKB/Swiss-Prot  Length:413

    Alignment length:415
                                                                                                                                                                                                                                                                                                                                                                                                                                                      413  
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410  |  
           MAAL_CLOTT     1 MKIVDVLCTPGLTGFYFDDQRAIKKGAGHDGFTYTGSTVTEGFTQVRQKGESISVLLVLEDGQVAHGDCAAVQYSGAGGRDPLFLAKDFIPVIEKEIAPKLIGREITNFKPMAEEFDKMTVNGNRLHTAIRYGITQAILDAVAKTRKVTMAEVIRDEYNPGAEINAVPVFAQSGDDRYDNVDKMIIKEADVLPHALINNVEEKLGLKGEKLLEYVKWLRDRIIKLRVREDYAPIFHIDVYGTIGAAFDVDIKAMADYIQTLAEAAKPFHLRIEGPMDVEDRQKQMEAMRDLRAELDGRGVDAELVADEWCNTVEDVKFFTDNKAGHMVQIKTPDLGGVNNIADAIMYCKANGMGAYCGGTCNETNRSAEVTTNIGMACGARQVLAKPGMGVDEGMMIVKNEMNRVLALVGRRK--   -
               SCOP domains d3zvhb1 B:1-160 automated matches                                                                                                                               d3zvhb2 B:161-415 automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeeeeehhhhhhhh..ee..ee............eeeeeeeeeeeee....eeeeee...............hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhee..ee.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.........ee.......hhhhhhhhhh...eeee....hhhhhh...hhhhhhhhhhhhhhhhhhh.......eeeee..hhhhhhh..hhhhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhh....eeee.......hhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zvh B   1 MKIVDVLCTPGLTGFYFDDQRAIKKGAGHDGFTYTGSTVTEGFTQVRQKGESISVLLVLEDGQVAHGDCAAVAYSGAGGRDPLFLAKDFIPVIEKEIAPKLIGREITNFKPMAEEFDKMTVNGNRLHTAIRYGITQAILDAVAKTRKVTMAEVIRDEYNPGAEINAVPVFAQSGDDRYDNVDKMIIKEADVLPHALINNVEEKLGLKGEKLLEYVKWLRDRIIKLRVREDYAPIFHIDVYGTIGAAFDVDIKAMADYIQTLAEAAKPFHLRIEGPMDVEDRQKQMEAMRDLRAELDGRGVDAELVADEWCNTVEDVKFFTDNKAGHMVQIKTPDLGGVNNIADAIMYCKANGMGAYCGGTcNETNRSAEVTTNIGMACGARQVLAKPGMGVDEGMMIVKNEMNRVLALVGRRKKL 415
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360|      370       380       390       400       410     
                                                                                                                                                                                                                                                                                                                                                                                                  361-OCS
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZVH)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MAAL_CLOTT | Q05514)
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:0031419    cobalamin binding    Interacting selectively and non-covalently with cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0050096    methylaspartate ammonia-lyase activity    Catalysis of the reaction: threo-3-methyl-L-aspartate = mesaconate + NH(4)(+).
biological process
    GO:0019553    glutamate catabolic process via L-citramalate    The chemical reactions and pathways resulting in the breakdown of glutamate, via the intermediate L-citramalate.
    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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  3zvh
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 Related Entries

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

UniProtKB/Swiss-Prot
        MAAL_CLOTT | Q05514: 1kcz 1kd0 3zvi

(-) Related Entries Specified in the PDB File

1kcz CRYSTAL STRUCTURE OF BETA-METHYLASPARTASE FROM CLOSTRIDIUM TETANOMORPHUM. MG-COMPLEX.
1kd0 CRYSTAL STRUCTURE OF BETA-METHYLASPARTASE FROM CLOSTRIDIUM TETANOMORPHUM. APO-STRUCTURE.
3zvi METHYLASPARTATE AMMONIA LYASE FROM CLOSTRIDIUM TETANOMORPHUM MUTANT L384A