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(-) Description

Title :  STRUCTURAL GENOMICS OF CAENORHABDITIS ELEGANS: ADENYLOSUCCINATE LYASE
 
Authors :  J. Symersky, N. Schormann, S. Lu, Y. Zhang, E. Karpova, S. Qiu, W. Huang, J. Zhou, M. Luo, A. Arabshahi, A. Mckinstry, C. -H. Luan, D. Luo, D. John J. Tsao, L. Delucas, Q. Shang, R. Gray, S. Li, T. Bray, Y. -J. Chen, South Collaboratory For Structural Genomics (Secsg)
Date :  12 Jan 05  (Deposition) - 25 Jan 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Caenorhabditis; X-Ray Structure, Structural Genomics, Psi, Protein Structure Initiative, Southeast Collaboratory For Structural Genomics, Secsg, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Symersky, N. Schormann, S. Lu, Y. Zhang, E. Karpova, S. Qiu, W. Huang Z. Cao, J. Zhou, M. Luo, A. Arabshahi, A. Mckinstry, C. -H. Luan, D. Luo, D. Johnson, J. An, J. Tsao, L. Delucas, Q. Shang, R. Gray, S. Li, T. Bray, Y. -J. Chen
Structural Genomics Of Caenorhabditis Elegans: Adenylosuccinate Lyase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ADENYLOSUCCINATE LYASE
    Chains: A
    EC Number: 4.3.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21-AI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239
    Synonym: FUMARATE LYASE (53.6 KD) (1H824)

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 44)
No.NameCountTypeFull Name
1MSE40Mod. Amino AcidSELENOMETHIONINE
2SO44Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:106 , THR A:107 , PHE A:110 , ARG A:192 , GLY A:193 , ILE A:194 , LYS A:195 , GLY A:196 , PHE A:204BINDING SITE FOR RESIDUE SO4 A 1001

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:262 -A:300

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asp A:423 -Pro A:424

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FUMARATE_LYASESPS00163 Fumarate lyases signature.PUR8_CAEEL284-293  1A:291-293
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FUMARATE_LYASESPS00163 Fumarate lyases signature.PUR8_CAEEL284-293  4A:291-293

(-) Exons   (0, 0)

(no "Exon" information available for 1YIS)

(-) 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:421
 aligned with PUR8_CAEEL | Q21774 from UniProtKB/Swiss-Prot  Length:478

    Alignment length:467
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       
           PUR8_CAEEL     2 ASEDKFESVLSTRYCKNSPLVSILSETNKATLWRQLWIWLAEAEKELGLKQVTQDAIDEMKSNRDVFDWPFIRSEERKLKHDVMAHNHAFGKLCPTAAGIIHLGATSCFVQDNADLIAYRDSIDHILKRFATVIDRLAAFSLKNKEVVTVGRTHYQTASLVTVGKRGVLWAQELLMAFQSLSEFRDKMRFRGIKGATGTQDSFLTLFAGDESKVEALDELVTKKANFSNRFLITGQTYSRQQDSQLVFSLSLLGAAAKKVCTDIRVLQAFGELLEPFEKDQIGSSAMPYKKNPMKSERCCALSRKLINAPQEALTILADQGLERTLDDSAGRRMLIPDVLLTAEALLTTLQNIFEGLSVQTDNVKKIVEDEIAFLGLEKAMMMLTEEGVDRQQAHAVIRKTALEAKQLQATQKVDIRQTMADPFFDSVRDRVVGLVNNPINFTGRCVSQTESFIAKELKPTIDKYLD 468
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------1yisA02 A:105-468 Fumarase/aspartase (Central domain)                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains -----------Lyase_1-1yisA02 A:13-308                                                                                                                                                                                                                                                                                ---------------------------------------------------------------------ADSL_C-1                                 yisA01 A:378-455                     ------------- Pfam domains
         Sec.struct. author hhhhh..hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhh..hhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee..-------------...hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhhhhhhhhhhhhhh---------------------------------..........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FUMARATE_L------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yis A   2 ASEDKFESVLSTRYCKNSPLVSILSETNKATLWRQLWIWLAEAEKELGLKQVTQDAIDEmKSNRDVFDWPFIRSEERKLKHDVmAHNHAFGKLCPTAAGIIHLGATSCFVQDNADLIAYRDSIDHILKRFATVIDRLAAFSLKNKEVVTVGRTHYQTASLVTVGKRGVLWAQELLmAFQSLSEFRDKmRFRGIKGATGTQDSFLTLFAGDESKVEALDELVTKKANFSNRFLITGQTYSRQQDSQLVFSLSLLGAAAKKVCTDIRVLQAFGELLEP-------------KKNPmKSERCCALSRKLINAPQEALTILADQGLERTLDDSAGRRmLIPDVLLTAEALLTTLQNIFEGLSVQTDNVKKIVEDEIAFLGLEKAmmmL---------------------------------QTmADPFFDSVRDRVVGLVNNPINFTGRCVSQTESFIAKELKPTIDKYLD 468
                                    11        21        31        41        51        61        71        81   |    91       101       111       121       131       141       151       161       171     | 181       191       201       211       221       231       241       251       261       271     |   -       291   |   301       311       321       331   |   341       351       361       371       381||||     -         -         -       421       431       441       451       461       
                                                                                      61-MSE                  85-MSE                                                                                     177-MSE     189-MSE                                                                                 277           291   |                                     335-MSE                                        382-MSE                              419 |                                               
                                                                                                                                                                                                                                                                                                                               295-MSE                                                                                 383-MSE                               421-MSE                                           
                                                                                                                                                                                                                                                                                                                                                                                                                        384-MSE                                                                                
                                                                                                                                                                                                                                                                                                                                                                                                                         385
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  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 1YIS)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: ADSL_C] (6)
(-)
Clan: no clan defined [family: Lyase_1] (27)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (PUR8_CAEEL | Q21774)
molecular function
    GO:0070626    (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate AMP-lyase (fumarate-forming) activity    Catalysis of the reaction: (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate = fumarate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide.
    GO:0004018    N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity    Catalysis of the reaction: N6-(1,2-dicarboxyethyl)AMP = fumarate + AMP.
    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.
biological process
    GO:0044208    'de novo' AMP biosynthetic process    The chemical reactions and pathways resulting in the formation of adenosine monophosphate (AMP) from inosine 5'-monophosphate (IMP).
    GO:0006189    'de novo' IMP biosynthetic process    The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate, by the stepwise assembly of a purine ring on ribose 5-phosphate.
    GO:0051262    protein tetramerization    The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
    GO:0006164    purine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    GO:0006163    purine nucleotide metabolic process    The chemical reactions and pathways involving a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

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 Related Entries

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(-) Related Entries Specified in the PDB File

1c3c
1c3u
1dof RELATED ID: R06C7.5 RELATED DB: TARGETDB