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(-) Description

Title :  CRYSTAL STRUCTURE OF DEOXYGENATED LIMULUS POLYPHEMUS SUBUNIT II HEMOCYANIN AT 2.18 ANGSTROMS RESOLUTION: CLUES FOR A MECHANISM FOR ALLOSTERIC REGULATION
 
Authors :  B. Hazes, W. G. J. Hol
Date :  07 Sep 92  (Deposition) - 31 Jan 94  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.18
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxygen Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Hazes, K. A. Magnus, C. Bonaventura, J. Bonaventura, Z. Dauter, K. H. Kalk, W. G. Hol
Crystal Structure Of Deoxygenated Limulus Polyphemus Subunit Ii Hemocyanin At 2. 18 A Resolution: Clues For A Mechanism For Allosteric Regulation.
Protein Sci. V. 2 597 1993
PubMed-ID: 8518732
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEMOCYANIN (SUBUNIT TYPE II)
    Chains: A
    Engineered: YES
    Organism Common: ATLANTIC HORSESHOE CRAB
    Organism Scientific: LIMULUS POLYPHEMUS
    Organism Taxid: 6850

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2CU2Ligand/IonCOPPER (II) ION
3NA1Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:173 , HIS A:177 , HIS A:204BINDING SITE FOR RESIDUE CU A 629
2AC2SOFTWAREHIS A:324 , HIS A:328 , HIS A:364BINDING SITE FOR RESIDUE CU A 630
3AC3SOFTWARESER A:507 , THR A:510 , SER A:512 , ASP A:578 , HOH A:875 , HOH A:889BINDING SITE FOR RESIDUE NA A 631
4AC4SOFTWARESER A:47 , ARG A:333 , SER A:349BINDING SITE FOR RESIDUE CL A 632

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:534 -A:576
2A:536 -A:583

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:309 -Ser A:310
2Phe A:598 -Pro A:599

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEMOCYANIN_1PS00209 Arthropod hemocyanins / insect LSPs signature 1.HCY2_LIMPO162-181  1A:162-181
2HEMOCYANIN_2PS00210 Arthropod hemocyanins / insect LSPs signature 2.HCY2_LIMPO353-361  1A:353-361
3TYROSINASE_2PS00498 Tyrosinase and hemocyanins CuB-binding region signature.HCY2_LIMPO357-368  1A:357-368

(-) Exons   (0, 0)

(no "Exon" information available for 1LLA)

(-) 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:600
 aligned with HCY2_LIMPO | P04253 from UniProtKB/Swiss-Prot  Length:628

    Alignment length:627
                                    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       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       
           HCY2_LIMPO     2 LHDKQIRVCHLFEQLSSATVIGDGDKHKHSDRLKNVGKLQPGAIFSCFHPDHLEEARHLYEVFWEAGDFNDFIEIAKEARTFVNEGLFAFAAEVAVLHRDDCKGLYVPPVQEIFPDKFIPSAAINEAFKKAHVRPEFDESPILVDVQDTGNILDPEYRLAYYREDVGINAHHWHWHLVYPSTWNPKYFGKKKDRKGELFYYMHQQMCARYDCERLSNGMHRMLPFNNFDEPLAGYAPHLTHVASGKYYSPRPDGLKLRDLGDIEISEMVRMRERILDSIHLGYVISEDGSHKTLDELHGTDILGALVESSYESVNHEYYGNLHNWGHVTMARIHDPDGRFHEEPGVMSDTSTSLRDPIFYNWHRFIDNIFHEYKNTLKPYDHDVLNFPDIQVQDVTLHARVDNVVHFTMREQELELKHGINPGNARSIKARYYHLDHEPFSYAVNVQNNSASDKHATVRIFLAPKYDELGNEIKADELRRTAIELDKFKTDLHPGKNTVVRHSLDSSVTLSHQPTFEDLLHGVGLNEHKSEYCSCGWPSHLLVPKGNIKGMEYHLFVMLTDWDKDKVDGSESVACVDAVSYCGARDHKYPDKKPMGFPFDRPIHTEHISDFLTNNMFIKDIKIKFHE 628
               SCOP domains d1llaa1 A:2-109 Hem         ocyanin, N-terminal domain                                                      d1llaa2 A:110-379 Arth        ropod he  mocyanin                                                                                                                                                                                                                              d1llaa3 A:380-628 Arthropod hemocyanin, C-terminal domain                                                                                                                                                                                                 SCOP domains
               CATH domains 1llaA01 A:2-109 Hem         ocyanin, N-terminal domain                                                      1llaA03 A:110-377 Di-c        opper ce  nter containing domain from catechol oxidase                                                                                                                                                                                        1llaA02 A:378-628 E set domains                                                                                                                                                                                                                             CATH domains
               Pfam domains Hemocyanin_N-1llaA0         3 A:2-106                                                                    ---Hemocyanin_M-1llaA01 A        :110-373                                                                                                                                                                                                                                  -----Hemocyanin_C-1llaA02 A:379-627                                                                                                                                                                                                                           - Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh.---------..hhhhhh............hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhh--------...eeee.--.....hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..............................................hhhhhhhhhhhhhhhhhhheee.....eee....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh............hhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh...eeeeeeeee.....eeeeeeeeeeee............eeeeeeeeee...eeeeeeee.....eeeeeeeeeee.........hhhhhhhhheeeeeeeeee..eeeeeeee.hhh..ee....hhhhhhh....----.......ee.hhh........eeeeeeeeeeehhhhh.----......hhhhhh.......................hhhhh....eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------HEMOCYANIN_1        ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------HEMOCYANI--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYROSINASE_2-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lla A   2 LHDKQIRICHLFEQLSSAT---------HSDRLKNVGKLQPGAIFSCFHPDHLEEARHLYEVFWEAGDFNDFIEIAKEARTFVNEGLFAFAAEVAVLHRDDCKGLYVPPVQEIFPDKFIPSAAINEAFKK--------ESPILVDV--TGNILDPEYRLAYYREDVGINAHHWHWHLVYPSTWNPKYFGKKKDRKGELFYYMHQQMCARYDCERLSNGMHRMLPFNNFDEPLAGYAPHLTHVASGKYYSPRPDGLKLRDLGDIEISEMVRMRERILDSIHLGYVISEDGSHKTLDELHGTDILGALVESSYESVNHEYYGNLHNWGHVTMARIHDPDGRFHEEPGVMSDTSTSLRDPIFYNWHRFIDNIFHEYKNTLKPYDHDVLNFPDIQVQDVTLHARVDNVVHTFMREQELELKHGINPGNARSIKARYYHLDHEPFSYAVNVQNNSASDKHATVRIFLAPKYDELGNEIKADELRRTAIELDKFKTDLHPGKNTVVRHSLDSSVTLSHQPTFEDLLHGVGL----SEYCSCGWPSHLLVPKGNIKGMEYHLFVMLTDWDKDKV----SVACVDAVSYCGARDHKYPDKKPMGFPFDRPIHTEHISDFLTNNMFIKDIKIKFHE 628
                                    11        |-        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       471       481       491       501       511       521    |  531       541       551       561      |  - |     581       591       601       611       621       
                                             20        30                                                                                                  131      140    147  |                                                                                                                                                                                                                                                                                                                                                                                     526  531                                  568  573                                                       
                                                                                                                                                                              150
   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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: Di-copper (13)
(-)
Clan: no clan defined [family: Hemocyanin_C] (3)
(-)
Clan: no clan defined [family: Hemocyanin_N] (3)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (HCY2_LIMPO | P04253)
molecular function
    GO:0031404    chloride ion binding    Interacting selectively and non-covalently with chloride ions (Cl-).
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0005344    oxygen transporter activity    Enables the directed movement of oxygen into, out of or within a cell, or between cells.
biological process
    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.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0015671    oxygen transport    The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0051259    protein oligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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  1lla
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 Related Entries

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

UniProtKB/Swiss-Prot
        HCY2_LIMPO | P04253: 1ll1 1nol 1oxy

(-) Related Entries Specified in the PDB File

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