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(-) Description

Title :  CRYSTALLOGRAPHIC ANALYSIS OF OXYGENATED AND DEOXYGENATED STATES OF ARTHROPOD HEMOCYANIN SHOWS UNUSUAL DIFFERENCES
 
Authors :  H. Ton-That, K. Magnus
Date :  06 Jan 95  (Deposition) - 27 Feb 95  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxygen Transport, Hemocyanin, Copper Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. A. Magnus, B. Hazes, H. Ton-That, C. Bonaventura, J. Bonaventura, W. G. Hol
Crystallographic Analysis Of Oxygenated And Deoxygenated States Of Arthropod Hemocyanin Shows Unusual Differences.
Proteins V. 19 302 1994
PubMed-ID: 7984626  |  Reference-DOI: 10.1002/PROT.340190405
(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  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CU2Ligand/IonCOPPER (II) ION
2OXY1Ligand/IonOXYGEN MOLECULE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:324 , HIS A:328 , HIS A:364 , CU A:630 , OXY A:631BINDING SITE FOR RESIDUE CU A 629
2AC2SOFTWAREHIS A:173 , HIS A:177 , HIS A:204 , CU A:629 , OXY A:631BINDING SITE FOR RESIDUE CU A 630
3AC3SOFTWAREPHE A:49 , HIS A:173 , HIS A:177 , HIS A:204 , HIS A:324 , HIS A:328 , PHE A:360 , HIS A:364 , CU A:629 , CU A:630BINDING SITE FOR RESIDUE OXY A 631

(-) SS Bonds  (2, 2)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:598 -Pro A:599

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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 1OXY)

(-) 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:573
 aligned with HCY2_LIMPO | P04253 from UniProtKB/Swiss-Prot  Length:628

    Alignment length:627
                                    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       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       
           HCY2_LIMPO     1 TLHDKQIRVCHLFEQLSSATVIGDGDKHKHSDRLKNVGKLQPGAIFSCFHPDHLEEARHLYEVFWEAGDFNDFIEIAKEARTFVNEGLFAFAAEVAVLHRDDCKGLYVPPVQEIFPDKFIPSAAINEAFKKAHVRPEFDESPILVDVQDTGNILDPEYRLAYYREDVGINAHHWHWHLVYPSTWNPKYFGKKKDRKGELFYYMHQQMCARYDCERLSNGMHRMLPFNNFDEPLAGYAPHLTHVASGKYYSPRPDGLKLRDLGDIEISEMVRMRERILDSIHLGYVISEDGSHKTLDELHGTDILGALVESSYESVNHEYYGNLHNWGHVTMARIHDPDGRFHEEPGVMSDTSTSLRDPIFYNWHRFIDNIFHEYKNTLKPYDHDVLNFPDIQVQDVTLHARVDNVVHFTMREQELELKHGINPGNARSIKARYYHLDHEPFSYAVNVQNNSASDKHATVRIFLAPKYDELGNEIKADELRRTAIELDKFKTDLHPGKNTVVRHSLDSSVTLSHQPTFEDLLHGVGLNEHKSEYCSCGWPSHLLVPKGNIKGMEYHLFVMLTDWDKDKVDGSESVACVDAVSYCGARDHKYPDKKPMGFPFDRPIHTEHISDFLTNNMFIKDIKIKFH 627
               SCOP domains d1oxya1 A:1-109 H               emocyanin, N-terminal domain                                                 d1oxya2 A:110-379 Arth                   ropod hemocyanin                                                                                                                                                                                                                     d1oxya3 A:380-627 Arthropod hemocyanin, C       -terminal domain                                                                                                                                                                                         SCOP domains
               CATH domains 1oxyA01 A:1-109 H               emocyanin, N-terminal domain                                                 1oxyA02 A:110-377 Di-c                   opper center containing domain from catechol oxidase                                                                                                                                                                               1oxyA03 A:378-627 E set domains                                                                                                                                                                                                                            CATH domains
               Pfam domains Hemocyanin_N-1oxy               A03 A:1-106                                                               ---Hemocyanin_M-1oxyA01 A                   :110-373                                                                                                                                                                                                                       -----Hemocyanin_C-1oxyA02 A:379-627                                                                                                                                                                                                                            Pfam domains
         Sec.struct. author ..hhhhhhhhhh.....---------------..................hhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhh.......hhhh.hhh...hhhhhhh...-------------------.....hhhhhhhhh..hhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhh................................................hhhhhhhhhhhhhhhhh.eee.....eee.....hhhhhhhhhh.......hhhh..hhhhhhhhhh.hhh..........hhh....hhh.hhhhhhhhhhhhhhhhhhhh.....hhhh....eeeeeeeee.....eeeeeeeeeeee....-------..............eeeeeeee.....eeeeeeeeeee..........hhhhhhh.eeeeeeeeee..eeeeeeeehhh..........hhhh.---------.........hhh.........eeeeeeeeeeehhhh...----......hhhh.........................hhhh............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------HEMOCYANIN_1        ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------HEMOCYANI-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYROSINASE_2------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oxy A   1 TLHDKQIRICHLFEQLS---------------RLKNVGKLQPGAIFSCFHPDHLEEARHLYEVFWEAGDFNDFIEIAKEARTFVNEGLFAFAAEVAVLHRDDCKGLYVPPVQEIFPDKFIPSAAINEAFKK-------------------GNILDPEYRLAYYREDVGINAHHWHWHLVYPSTWNPKYFGKKKDRKGELFYYMHQQMCARYDCERLSNGMHRMLPFNNFDEPLAGYAPHLTHVASGKYYSPRPDGLKLRDLGDIEISEMVRMRERILDSIHLGYVISEDGSHKTLDELHGTDILGALVESSYESVNHEYYGNLHNWGHVTMARIHDPDGRFHEEPGVMSDTSTSLRDPIFYNWHRFIDNIFHEYKNTLKPYDHDVLNFPDIQVQDVTLHARVDNVVHTFMREQELELKHG-------SIKAKYYHLDHEPFSYAVNVQNNSASDKHATVRIFLAPKYDELGNEIKADELRRTAIELDKFKTDLHPGKNTVVRHSLDSSVTLSHQPTFEDLL---------SEYCSCGWPSHLLVPKGNVAGMEYHLFVMLTDWDKDKVD----VACVDAVSYCGARDHKYPDKKPMGFPFDRPIHTEHISDFLTNNMFIKDIKIKFH 627
                                    10      |  -         -  |     40        50        60        70        80        90       100       110       120       130|        -         -|      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       420       430       440       450       460       470       480       490       500       510       520|        -|      540       550       560        |-   |   580       590       600       610       620       
                                           17              33                                                                                               131                 151                                                                                                                                                                                                                                                                          420     428                                                                                          521       531                                   569  574
   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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        HCY2_LIMPO | P04253: 1ll1 1lla 1nol

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