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Title :   CRYSTAL STRUCTURE OF THE CATHODIC HEMOGLOBIN ISOLATED FROM THE ANTARCTIC FISH TREMATOMUS NEWNESI

Authors :   L. Mazzarella, G. Bonomi, M. C. Lubrano, A. Merlino, A. Riccio, A. Vergara, L. Vitagliano, C. Verde, G. Di Prisco

Date :   13 Jul 05 (Deposition) - 02 Aug 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Hemoglobin, Root Effect, Cooperativity, Antarctic Fish, Oxygen Storage/Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Mazzarella, G. Bonomi, M. C. Lubrano, A. Merlino, A. Riccio, A. Vergara, L. Vitagliano, C. Verde, G. Di Prisco
Minimal Structural Requirements For Root Effect: Crystal Structure Of The Cathodic Hemoglobin Isolated From The Antarctic Fish Trematomus Newnesi
Proteins V. 62 316 2006
PubMed-ID: 16299734 | Reference-DOI: 10.1002/PROT.20709
(for further references see the PDB file header)

Molecule 1 - HEMOGLOBIN ALPHA-1 CHAIN
	Chains	:	A, C
	Organism Common	:	DUSKY NOTOTHEN
	Organism Scientific	:	TREMATOMUS NEWNESI
	Organism Taxid	:	35730

Molecule 2 - HEMOGLOBIN BETA-C CHAIN
	Chains	:	B, D
	Organism Common	:	DUSKY NOTOTHEN
	Organism Scientific	:	TREMATOMUS NEWNESI
	Organism Taxid	:	35730

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 6)

No.	Name	Count	Type	Full Name
1	ACE	2	Mod. Amino Acid	ACETYL GROUP
2	HEM	4	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:42 , HIS A:45 , TRP A:46 , HIS A:59 , LYS A:62 , VAL A:63 , ILE A:67 , HIS A:88 , LEU A:92 , VAL A:94 , ASN A:98 , PHE A:99 , LEU A:102 , LEU A:137 , HOH A:1114 , HOH C:1180	BINDING SITE FOR RESIDUE HEM A 200
2	AC2	SOFTWARE	THR B:38 , PHE B:42 , HIS B:63 , ILE B:67 , LEU B:91 , HIS B:92 , LEU B:96 , VAL B:98 , ASN B:102 , PHE B:103 , LEU B:106 , LEU B:141	BINDING SITE FOR RESIDUE HEM B 400
3	AC3	SOFTWARE	MET C:32 , TYR C:42 , HIS C:45 , TRP C:46 , HIS C:59 , LYS C:62 , VAL C:63 , ILE C:67 , GLN C:87 , HIS C:88 , LEU C:92 , ASN C:98 , PHE C:99 , LEU C:102 , LEU C:137 , HOH C:1361	BINDING SITE FOR RESIDUE HEM C 600
4	AC4	SOFTWARE	THR D:38 , TYR D:41 , HIS D:63 , ILE D:67 , LEU D:91 , HIS D:92 , LEU D:96 , VAL D:98 , ASN D:102 , PHE D:103 , LEU D:106 , LEU D:141	BINDING SITE FOR RESIDUE HEM D 800

(no "SS Bond" information available for 2AA1)

(no "Cis Peptide Bond" information available for 2AA1)

(no "SAP(SNP)/Variant" information available for 2AA1)

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLOBIN	PS01033	Globin family profile.	HBA1_TRENE	2-142	2	A:2-142 C:2-142
1	GLOBIN	PS01033	Globin family profile.	HBBC_TRENE	4-146	2	B:4-146 D:4-146

(no "Exon" information available for 2AA1)

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:143
 aligned with HBA1_TRENE | P45718 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:143
                             1                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139   
           HBA1_TRENE     - -SLSDKDKAAVRALWSKIGKSSDAIGNDALSRMIVVYPQTKIYFSHWPDVTPGSPNIKAHGKKVMGGIALAVSKIDDLKTGLMELSEQHAYKLRVDPSNFKILNHCILVVISTMFPKEFTPEAHVSLDKFLSGVALALAERYR 142
               SCOP domains d2aa1a_ A: Hemoglobin, alpha-chain                                                                                                              SCOP domains
               CATH domains -2aa1A00 A:1-142 Globins                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GLOBIN  PDB: A:2-142 UniProt: 2-142                                                                                                           PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aa1 A   0 xSLSDKDKAAVRALWSKIGKSSDAIGNDALSRMIVVYPQTKIYFSHWPDVTPGSPNIKAHGKKVMGGIALAVSKIDDLKTGLMELSEQHAYKLRVDPSNFKILNHCILVVISTMFPKEFTPEAHVSLDKFLSGVALALAERYR 142
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139   
                            |                                                                                                                                              
                            0-ACE

Chain B from PDB  Type:PROTEIN  Length:146
 aligned with HBBC_TRENE | P45721 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      
           HBBC_TRENE     1 VEWTDFERATIKDIFSKLEYDVVGPATLARCLVVYPWTQRYFGKFGNLYNAAAIAQNAMVSKHGTTILNGLDRAVKNMDDITNTYAELSVLHSEKLHVDPDNFKLLADCLTIVVAARFGSAFTGEVQAAFQKFMAVVVSSLGKQYR 146
               SCOP domains d2aa1b1 B:1-146 Hemoglobin, beta-chain                                                                                                             SCOP domains
               CATH domains 2aa1B00 B:1-146 Globins                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---GLOBIN  PDB: B:4-146 UniProt: 4-146                                                                                                             PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aa1 B   1 VEWTDFERATIKDIFSKLEYDVVGPATLARCLVVYPWTQRYFGKFGNLYNAAAIAQNAMVSKHGTTILNGLDRAVKNMDDITNTYAELSVLHSEKLHVDPDNFKLLADCLTIVVAARFGSAFTGEVQAAFQKFMAVVVSSLGKQYR 146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain C from PDB  Type:PROTEIN  Length:143
 aligned with HBA1_TRENE | P45718 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:143
                             1                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139   
           HBA1_TRENE     - -SLSDKDKAAVRALWSKIGKSSDAIGNDALSRMIVVYPQTKIYFSHWPDVTPGSPNIKAHGKKVMGGIALAVSKIDDLKTGLMELSEQHAYKLRVDPSNFKILNHCILVVISTMFPKEFTPEAHVSLDKFLSGVALALAERYR 142
               SCOP domains d2aa1c_ C: Hemoglobin, alpha-chain                                                                                                              SCOP domains
               CATH domains -2aa1C00 C:1-142 Globins                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GLOBIN  PDB: C:2-142 UniProt: 2-142                                                                                                           PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aa1 C   0 xSLSDKDKAAVRALWSKIGKSSDAIGNDALSRMIVVYPQTKIYFSHWPDVTPGSPNIKAHGKKVMGGIALAVSKIDDLKTGLMELSEQHAYKLRVDPSNFKILNHCILVVISTMFPKEFTPEAHVSLDKFLSGVALALAERYR 142
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139   
                            0-ACE

Chain D from PDB  Type:PROTEIN  Length:146
 aligned with HBBC_TRENE | P45721 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      
           HBBC_TRENE     1 VEWTDFERATIKDIFSKLEYDVVGPATLARCLVVYPWTQRYFGKFGNLYNAAAIAQNAMVSKHGTTILNGLDRAVKNMDDITNTYAELSVLHSEKLHVDPDNFKLLADCLTIVVAARFGSAFTGEVQAAFQKFMAVVVSSLGKQYR 146
               SCOP domains d2aa1d_ D: Hemoglobin, beta-chain                                                                                                                  SCOP domains
               CATH domains 2aa1D00 D:1-146 Globins                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---GLOBIN  PDB: D:4-146 UniProt: 4-146                                                                                                             PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aa1 D   1 VEWTDFERATIKDIFSKLEYDVVGPATLARCLVVYPWTQRYFGKFGNLYNAAAIAQNAMVSKHGTTILNGLDRAVKNMDDITNTYAELSVLHSEKLHVDPDNFKLLADCLTIVVAARFGSAFTGEVQAAFQKFMAVVVSSLGKQYR 146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Globin-like (1351)

Superfamily: Globin-like (1308)

Family: Globins (1157)

Protein domain: Hemoglobin, alpha-chain (292)

Antarctic fish (Trematomus newnesi) [TaxId: 35730] (6)

1a	d2aa1a_	A:
1b	d2aa1c_	C:

Protein domain: Hemoglobin, beta-chain (292)

Antarctic fish (Trematomus newnesi) [TaxId: 35730] (6)

2a	d2aa1b1	B:1-146
2b	d2aa1d_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Globin-like (786)

Homologous Superfamily: Globins (743)

Dusky notothen (Trematomus newnesi) (3)

1a	2aa1B00	B:1-146
1b	2aa1D00	D:1-146
1c	2aa1A00	A:1-142
1d	2aa1C00	C:1-142

(no "Pfam Domain" information available for 2AA1)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,C (HBA1_TRENE | P45718)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0019825	oxygen binding	Interacting selectively and non-covalently with oxygen (O2).
	GO:0005344	oxygen transporter activity	Enables the directed movement of oxygen into, out of or within a cell, or between cells.
biological process
	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: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:0005833	hemoglobin complex	An iron-containing, oxygen carrying complex. In vertebrates it is made up of two pairs of associated globin polypeptide chains, each chain carrying a noncovalently bound heme prosthetic group.

Chain B,D (HBBC_TRENE | P45721)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0019825	oxygen binding	Interacting selectively and non-covalently with oxygen (O2).
	GO:0005344	oxygen transporter activity	Enables the directed movement of oxygen into, out of or within a cell, or between cells.
biological process
	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: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:0005833	hemoglobin complex	An iron-containing, oxygen carrying complex. In vertebrates it is made up of two pairs of associated globin polypeptide chains, each chain carrying a noncovalently bound heme prosthetic group.

Asymmetric/Biological Unit
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(no "Cis Peptide Bonds" information available for 2aa1)

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	HBA1_TRENE \| P45718	:	1la6 1t1n 3d1k 3nfe 3ng6

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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