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(-) Description

Title :  CRYSTAL STRUCTURE OF BETA-METHYLASPARTASE FROM CLOSTRIDIUM TETANOMORPHUM. APO-STRUCTURE.
 
Authors :  M. Asuncion, W. Blankenfeldt, J. N. Barlow, D. Gani, J. H. Naismith
Date :  12 Nov 01  (Deposition) - 19 Dec 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta Zigzag, Alpha/Beta-Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Asuncion, W. Blankenfeldt, J. N. Barlow, D. Gani, J. H. Naismith
The Structure Of 3-Methylaspartase From Clostridium Tetanomorphum Functions Via The Common Enolase Chemical Step.
J. Biol. Chem. V. 277 8306 2002
PubMed-ID: 11748244  |  Reference-DOI: 10.1074/JBC.M111180200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-METHYLASPARTASE
    Chains: A, B
    EC Number: 4.3.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGETITA
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: CLOSTRIDIUM TETANOMORPHUM
    Organism Taxid: 1553
    Synonym: METHYLASPARTATE AMMONIA-LYASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 36)

Asymmetric/Biological Unit (2, 36)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2MSE34Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:401 , ARG A:404 , HOH A:719 , HOH A:737 , HOH A:992BINDING SITE FOR RESIDUE EDO A 701
2AC2SOFTWAREGLU B:401 , ARG B:404 , HOH B:727 , HOH B:749BINDING SITE FOR RESIDUE EDO B 702

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KD0)

(-) 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 1KD0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1KD0)

(-) Exons   (0, 0)

(no "Exon" information available for 1KD0)

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

    Alignment length: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 413
               SCOP domains d1kd0a2 A:1-160 beta-Methylaspartase                                                                                                                            d1kd0a1 A:161-413 beta-Methylaspartase                                                                                                                                                                                                                        SCOP domains
               CATH domains -1kd0A01 A:2-164 Enolase-like, N-terminal domain                                                                                                                    1kd0A02 A:165-413 Enolase superfamily                                                                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee....eeehhhhhhh..eee..eee...........eee..eeeeeeee....eeeeee...............hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhee..ee.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.........ee.......hhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhh.......eeeee..hhhhhhh..hhhhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kd0 A   1 mKIVDVLCTPGLTGFYFDDQRAIKKGAGHDGFTYTGSTVTEGFTQVRQKGESISVLLVLEDGQVAHGDCAAVQYSGAGGRDPLFLAKDFIPVIEKEIAPKLIGREITNFKPmAEEFDKmTVNGNRLHTAIRYGITQAILDAVAKTRKVTmAEVIRDEYNPGAEINAVPVFAQSGDDRYDNVDKmIIKEADVLPHALINNVEEKLGLKGEKLLEYVKWLRDRIIKLRVREDYAPIFHIDVYGTIGAAFDVDIKAmADYIQTLAEAAKPFHLRIEGPmDVEDRQKQmEAmRDLRAELDGRGVDAELVADEWCNTVEDVKFFTDNKAGHmVQIKTPDLGGVNNIADAImYCKANGmGAYCGGTCNETNRSAEVTTNIGmACGARQVLAKPGmGVDEGmmIVKNEmNRVLALVGRRK 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   
                            |                                                                                                            112-MSE  |                            150-MSE                           184-MSE                                                               254-MSE               276-MSE  285-MSE                                   327-MSE            346-MSE  |                    376-MSE      389-MSE ||     |           
                            1-MSE                                                                                                               119-MSE                                                                                                                                                                  288-MSE                                                          353-MSE                                   395-MSE  |           
                                                                                                                                                                                                                                                                                                                                                                                                                                     396-MSE |           
                                                                                                                                                                                                                                                                                                                                                                                                                                           402-MSE       


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

    Alignment length: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 413
               SCOP domains d1kd0b2 B:1-160 beta-Methylaspartase                                                                                                                            d1kd0b1 B:161-413 beta-Methylaspartase                                                                                                                                                                                                                        SCOP domains
               CATH domains -1kd0B01 B:2-164 Enolase-like, N-terminal domain                                                                                                                    1kd0B02 B:165-398 Enolase superfamily                                                                                                                                                                                                     --------------- CATH domains
           Pfam domains (1) MAAL_N-1kd0B01 B:1-160                                                                                                                                          MAAL_C-1kd0B03 B:161-411                                                                                                                                                                                                                                   -- Pfam domains (1)
           Pfam domains (2) MAAL_N-1kd0B02 B:1-160                                                                                                                                          MAAL_C-1kd0B04 B:161-411                                                                                                                                                                                                                                   -- Pfam domains (2)
         Sec.struct. author ..eeeeeeeee....eeehhhhhhhh..ee..ee............eee..eeeeeeee....eeeeee...............hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhee..ee.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.........ee.......hhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhh.......eeeee..hhhhhhhh.hhhhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhh....eeeehhhhhh.hhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kd0 B   1 mKIVDVLCTPGLTGFYFDDQRAIKKGAGHDGFTYTGSTVTEGFTQVRQKGESISVLLVLEDGQVAHGDCAAVQYSGAGGRDPLFLAKDFIPVIEKEIAPKLIGREITNFKPmAEEFDKmTVNGNRLHTAIRYGITQAILDAVAKTRKVTmAEVIRDEYNPGAEINAVPVFAQSGDDRYDNVDKmIIKEADVLPHALINNVEEKLGLKGEKLLEYVKWLRDRIIKLRVREDYAPIFHIDVYGTIGAAFDVDIKAmADYIQTLAEAAKPFHLRIEGPmDVEDRQKQmEAmRDLRAELDGRGVDAELVADEWCNTVEDVKFFTDNKAGHmVQIKTPDLGGVNNIADAImYCKANGmGAYCGGTCNETNRSAEVTTNIGmACGARQVLAKPGmGVDEGmmIVKNEmNRVLALVGRRK 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   
                            1-MSE                                                                                                        112-MSE  |                            150-MSE                           184-MSE                                                               254-MSE               276-MSE  285-MSE                                   327-MSE            346-MSE  |                    376-MSE      389-MSE ||     |           
                                                                                                                                                119-MSE                                                                                                                                                                  288-MSE                                                          353-MSE                                   395-MSE  |           
                                                                                                                                                                                                                                                                                                                                                                                                                                     396-MSE |           
                                                                                                                                                                                                                                                                                                                                                                                                                                           402-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, 4)

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

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Enolase_N (69)
(-)
Clan: Enolase_TIM (82)

(-) 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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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1kcz 1KCZ IS THE MG-COMPLEX.