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(-) Description

Title :  CRYSTAL STRUCTURE OF CITROBACTER AMALONATICUS METHYLASPARTATE AMMONIA LYASE CONTAINING (2S,3S)-3-METHYLASPARTIC ACID
 
Authors :  C. W. Levy, P. A. Buckley, S. Sedelnikova, K. Kato, Y. Asano, D. W. Rice, P
Date :  10 Dec 01  (Deposition) - 30 Jan 02  (Release) - 19 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Methylaspartate Ammonia Lyase, Enolase Superfamily, Tim Barrel, Substrate Complex, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. W. Levy, P. A. Buckley, S. Sedelnikova, Y. Kato, Y. Asano, D. W. Rice, P. J. Baker
Insights Into Enzyme Evolution Revealed By The Structure Of Methylaspartate Ammonia Lyase.
Structure V. 10 105 2002
PubMed-ID: 11796115  |  Reference-DOI: 10.1016/S0969-2126(01)00696-7

(-) Compounds

Molecule 1 - 3-METHYLASPARTATE AMMONIA-LYASE
    Chains: A, B
    EC Number: 4.3.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL
    Expression System Strain: DL41
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MAL
    Organism Scientific: CITROBACTER AMALONATICUS
    Organism Taxid: 35703

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 24)

Asymmetric/Biological Unit (3, 24)
No.NameCountTypeFull Name
12AS2Ligand/Ion(2S,3S)-3-METHYL-ASPARTIC ACID
2MG2Ligand/IonMAGNESIUM ION
3MSE20Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:238 , GLU A:273 , ASP A:307 , 2AS A:801 , HOH A:1070 , HOH A:1124BINDING SITE FOR RESIDUE MG A 501
2AC2SOFTWARE2AS A:800 , ASP B:238 , GLU B:273 , ASP B:307 , HOH B:527 , HOH B:536BINDING SITE FOR RESIDUE MG B 501
3AC3SOFTWAREHOH A:904 , HOH A:1016 , HOH A:1032 , GLN B:172 , HIS B:194 , ASP B:238 , TYR B:240 , GLU B:273 , ASP B:307 , GLN B:329 , LYS B:331 , GLY B:359 , THR B:360 , CYS B:361 , MG B:501 , HOH B:508 , HOH B:527BINDING SITE FOR RESIDUE 2AS A 800
4AC4SOFTWAREGLN A:172 , HIS A:194 , ASP A:238 , GLU A:273 , ASP A:307 , GLN A:329 , LYS A:331 , GLY A:359 , THR A:360 , CYS A:361 , MG A:501 , HOH A:815 , HOH A:1072BINDING SITE FOR RESIDUE 2AS A 801

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:155 -A:162
2B:155 -B:162

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KKR)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1KKR)

(-) 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:411
 aligned with MAAL_CITAM | O66145 from UniProtKB/Swiss-Prot  Length:413

    Alignment length:411
                                    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_CITAM     1 MKIKQALFTAGYSSFYFDDQQAIKNGAGHDGFIYTGDPVTPGFTSVRQAGECVSVQLILENGAVAVGDCAAVQYSGAGGRDPLFLAEHFIPFLNDHIKPLLEGRDVDAFLPNARFFDKLRIDGNLLHTAVRYGLSQALLDATALASGRLKTEVVCDEWQLPCVPEAIPLFGQSGDDRYIAVDKMILKGVDVLPHALINNVEEKLGFKGEKLREYVRWLSDRILSLRSSPRYHPTLHIDVYGTIGLIFDMDPVRCAEYIASLEKEAQGLPLYIEGPVDAGNKPDQIRMLTAITKELTRLGSGVKIVADEWCNTYQDIVDFTDAGSCHMVQIKTPDLGGIHNIVDAVLYCNKHGMEAYQGGTCNETEISARTCVHVALAARPMRMLIKPGMGFDEGLNIVFNEMNRTIALLQT 411
               SCOP domains d1kkra2 A:1-160 beta-Methylaspartase                                                                                                                            d1kkra1 A:161-411 beta-Methylaspartase                                                                                                                                                                                                                      SCOP domains
               CATH domains -1kkrA01 A:2-164 Enolase-like, N-terminal domain                                                                                                                    1kkrA02 A:165-401 Enolase superfamily                                                                                                                                                                                                        ---------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeeeeehhhhhhh...ee..ee............eeeeeeeeeeeee....eeeeee...............hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhee..ee.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..........ee.......hhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhh.......eeeee..hhhhhhh..hhhhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kkr A   1 mKIKQALFTAGYSSFYFDDQQAIKNGAGHDGFIYTGDPVTPGFTSVRQAGECVSVQLILENGAVAVGDCAAVQYSGAGGRDPLFLAEHFIPFLNDHIKPLLEGRDVDAFLPNARFFDKLRIDGNLLHTAVRYGLSQALLDATALASGRLKTEVVCDEWQLPCVPEAIPLFGQSGDDRYIAVDKmILKGVDVLPHALINNVEEKLGFKGEKLREYVRWLSDRILSLRSSPRYHPTLHIDVYGTIGLIFDmDPVRCAEYIASLEKEAQGLPLYIEGPVDAGNKPDQIRmLTAITKELTRLGSGVKIVADEWCNTYQDIVDFTDAGSCHmVQIKTPDLGGIHNIVDAVLYCNKHGmEAYQGGTCNETEISARTCVHVALAARPmRmLIKPGmGFDEGLNIVFNEmNRTIALLQT 411
                            |       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 
                            |                                                                                                                                                                                    184-MSE                                                          249-MSE                               287-MSE                                 327-MSE                   353-MSE                     381-MSE   |          402-MSE     
                            1-MSE                                                                                                                                                                                                                                                                                                                                                                                       383-MSE |                      
                                                                                                                                                                                                                                                                                                                                                                                                                              389-MSE                  


Chain B from PDB  Type:PROTEIN  Length:411
 aligned with MAAL_CITAM | O66145 from UniProtKB/Swiss-Prot  Length:413

    Alignment length:411
                                    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_CITAM     1 MKIKQALFTAGYSSFYFDDQQAIKNGAGHDGFIYTGDPVTPGFTSVRQAGECVSVQLILENGAVAVGDCAAVQYSGAGGRDPLFLAEHFIPFLNDHIKPLLEGRDVDAFLPNARFFDKLRIDGNLLHTAVRYGLSQALLDATALASGRLKTEVVCDEWQLPCVPEAIPLFGQSGDDRYIAVDKMILKGVDVLPHALINNVEEKLGFKGEKLREYVRWLSDRILSLRSSPRYHPTLHIDVYGTIGLIFDMDPVRCAEYIASLEKEAQGLPLYIEGPVDAGNKPDQIRMLTAITKELTRLGSGVKIVADEWCNTYQDIVDFTDAGSCHMVQIKTPDLGGIHNIVDAVLYCNKHGMEAYQGGTCNETEISARTCVHVALAARPMRMLIKPGMGFDEGLNIVFNEMNRTIALLQT 411
               SCOP domains d1kkrb2 B:1-160 beta-Methylaspartase                                                                                                                            d1kkrb1 B:161-411 beta-Methylaspartase                                                                                                                                                                                                                      SCOP domains
               CATH domains -1kkrB01 B:2-164 Enolase-like, N-terminal domain                                                                                                                    1kkrB02 B:165-401 Enolase superfamily                                                                                                                                                                                                        ---------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeeeee...hhhhhheee..eee...........eeeeeeeeeeeee....eeeeee...............hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhee..ee.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.........ee.......hhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhh.......eeeee..hhhhhhh..hhhhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kkr B   1 mKIKQALFTAGYSSFYFDDQQAIKNGAGHDGFIYTGDPVTPGFTSVRQAGECVSVQLILENGAVAVGDCAAVQYSGAGGRDPLFLAEHFIPFLNDHIKPLLEGRDVDAFLPNARFFDKLRIDGNLLHTAVRYGLSQALLDATALASGRLKTEVVCDEWQLPCVPEAIPLFGQSGDDRYIAVDKmILKGVDVLPHALINNVEEKLGFKGEKLREYVRWLSDRILSLRSSPRYHPTLHIDVYGTIGLIFDmDPVRCAEYIASLEKEAQGLPLYIEGPVDAGNKPDQIRmLTAITKELTRLGSGVKIVADEWCNTYQDIVDFTDAGSCHmVQIKTPDLGGIHNIVDAVLYCNKHGmEAYQGGTCNETEISARTCVHVALAARPmRmLIKPGmGFDEGLNIVFNEmNRTIALLQT 411
                            |       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                                                                                                                                                                                184-MSE                                                          249-MSE                               287-MSE                                 327-MSE                   353-MSE                     381-MSE   |          402-MSE     
                                                                                                                                                                                                                                                                                                                                                                                                                        383-MSE |                      
                                                                                                                                                                                                                                                                                                                                                                                                                              389-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  (0, 0)

(no "Pfam Domain" information available for 1KKR)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MAAL_CITAM | O66145)
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: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_CITAM | O66145: 1kko

(-) Related Entries Specified in the PDB File

1kko CRYSTAL STRUCTURE OF CITROBACTER AMALONATICUS METHYLASPARTATE AMMONIA LYASE