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(-) Description

Title :  CRYSTAL STRUCTURE OF A DUCK-DELTA-CRYSTALLIN-1 DOUBLE LOOP MUTANT (DLM) IN COMPLEX WITH SULFATE
 
Authors :  M. Tsai, L. M. Sampaleanu, C. Greene, L. Creagh, C. Haynes, P. L. Howell
Date :  14 Jul 04  (Deposition) - 05 Oct 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Eye Lens Protein, Duck-Delta-Crystallin, Argininosuccinate Lyase, Enzyme Mechanism, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Tsai, L. M. Sampaleanu, C. Greene, L. Creagh, C. Haynes, P. L. Howell
A Duck Delta1 Crystallin Double Loop Mutant Provides Insigh Into Residues Important For Argininosuccinate Lyase Activity.
Biochemistry V. 43 11672 2004
PubMed-ID: 15362851  |  Reference-DOI: 10.1021/BI0489006

(-) Compounds

Molecule 1 - DELTA CRYSTALLIN I
    Chains: A
    EC Number: 4.3.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-3D
    Expression System Strain: BB101
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: ANAS PLATYRHYNCHOS
    Organism Taxid: 8839

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MES4Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3SO44Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:114 , THR A:159 , HIS A:160 , SER A:281 , MET A:284 , LYS A:287 , ASN A:289 , HOH A:2143 , HOH A:2278 , HOH A:2305BINDING SITE FOR RESIDUE SO4 A 1001
2AC2SOFTWARELYS A:414 , SER A:421BINDING SITE FOR RESIDUE CL A 1002
3AC3SOFTWARELYS A:357BINDING SITE FOR RESIDUE CL A 1004
4AC4SOFTWARELYS A:69 , GLU A:98 , LEU A:99 , ASN A:406 , LEU A:408 , THR A:409 , LEU A:410 , LEU A:413 , SER A:425 , HOH A:2173 , HOH A:2184BINDING SITE FOR RESIDUE MES A 2119

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U16)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser A:319 -Thr A:320

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U16)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FUMARATE_LYASESPS00163 Fumarate lyases signature.ARLY1_ANAPL280-289  1A:280-289
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FUMARATE_LYASESPS00163 Fumarate lyases signature.ARLY1_ANAPL280-289  4A:280-289

(-) Exons   (0, 0)

(no "Exon" information available for 1U16)

(-) 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:449
 aligned with ARLY1_ANAPL | P24057 from UniProtKB/Swiss-Prot  Length:466

    Alignment length:449
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455         
          ARLY1_ANAPL    16 STDPIMQMLSTSISTEQRLSEVDIQASIAYAKALEKAGILTKTELEKILSGLEKISEELSKGVIVVTQSDEDIQTANERRLKELIGDIAGKLHTGRSRNEQVVTDLKLFMKNSLSIISTHLLQLIKTLVERAAIEIDVILPGYTHLQKAQPIRWSQFLLSHAVALTRDSERLGEVKKRINVLPLGSGALAGNPLDIDREMLRSELEFASISLNSMDAISERDFVVEFLSVATLLLIHLSKMAEDLIIYSTSEFGFLTLSDAFSTGSSLMPQKKNPDSLELIRSKAGRVFGRLASILMVLKGLPSTYNKDLQEDKEAVIDVVDTLTAVLQVATGVISTLQISKENMEKALTPEMLATDLALYLVRKGMPFRQAHTASGKAVHLAETKGIAINNLTLEDLKSISPLFSSDVSQVFNFVNSVEQYTALGGTAKSSVTTQIEQLRELMKKQKE 464
               SCOP domains d1u16a_ A: Argininosuccinate lyase/delta-crystallin                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -----------1u16A01 A:27-123,A:195-234 Fumarase/aspartase (N-terminal domain)                                1u16A02 A:124-194,A:235-364,A:437-463                                  1u16A01 A:27-123,A:195-234              1u16A02 A:124-194,A:235-364,A:437-463 Fumarase/aspartase (Central domain)                                                         1u16A03 A:365-436 Fumarase/aspartase (C-terminal domain)                1u16A02                    - CATH domains
               Pfam domains Lyase_1-1u16A01 A:16-305                                                                                                                                                                                                                                                                          --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhee..............hhhhhhhhhh..ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......ee.hhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheehhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhh.hhhhhhh........hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FUMARATE_L------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u16 A  16 STDPIMEKLNSSIAYDQRLSEVDIQASIAYAKALEKAGILTKTELEKILSGLEKISEEWSKGVFVVKQSDEDIHTANERRLKELIGDIAGKLHTGRSRNEQVVTDLKLFMKNSLSIISTHLLQLIKTLVERAAIEIDVILPGYTHLQKAQPIRWSQFLLSHAVALTRDSERLGEVKKRINVLPLGSGALAGNPLDIDREMLRSELEFASISLNSMDAISERDFVVEFLSVATLLLIHLSKMAEDLIIYSTSEFGFLTLSDAFSTGSSLMPQKKNPDSLELIRSKAGRVFGRLASILMVLKGLPSTYNKDLQEDKEAVIDVVDTLTAVLQVATGVISTLQISKENMEKALTPEMLATDLALYLVRKGMPFRQAHTASGKAVHLAETKGIAINNLTLEDLKSISPLFSSDVSQVFNFVNSVEQYTALGGTAKSSVTTQIEQLRELMKKQKE 464
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455
   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  (1, 1)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (3, 3)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (ARLY1_ANAPL | P24057)
molecular function
    GO:0004056    argininosuccinate lyase activity    Catalysis of the reaction: N-(L-arginino)succinate = fumarate + L-arginine.
    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:0005212    structural constituent of eye lens    The action of a molecule that contributes to the structural integrity of the lens of an eye.
biological process
    GO:0042450    arginine biosynthetic process via ornithine    The chemical reactions and pathways resulting in the formation of arginine (2-amino-5-guanidinopentanoic acid) via the intermediate compound ornithine.

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  1u16
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  ARLY1_ANAPL | P24057
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  4.3.2.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        ARLY1_ANAPL | P24057: 1hy0 1u15

(-) Related Entries Specified in the PDB File

1hy0 CRYSTAL STRUCTURE OF THE WILD TYPE DUCK-DELTA-CRYSTALLIN-1 ENZYME
1hy1 CRYSTAL STRUCTURE OF THE WILD TYPE DUCK-DELTA-CRYSTALLIN-2 ENZYME
1u15