3A44 - JenaLib

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Title :   CRYSTAL STRUCTURE OF HYPA IN THE DIMERIC FORM

Authors :   S. Watanabe, T. Arai, R. Matsumi, H. Atomi, T. Imanaka, K. Miki

Date :   30 Jun 09 (Deposition) - 06 Oct 09 (Release) - 22 Feb 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.31

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   [Nife] Hydrogenase Maturation, Zinc-Finger, Nickel Binding, Domain Swapping, Metal-Binding, Nickel, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Watanabe, T. Arai, R. Matsumi, H. Atomi, T. Imanaka, K. Miki
Crystal Structure Of Hypa, A Nickel-Binding Metallochaperon For [Nife] Hydrogenase Maturation.
J. Mol. Biol. V. 394 448 2009
PubMed-ID: 19769985 | Reference-DOI: 10.1016/J.JMB.2009.09.030

Molecule 1 - HYDROGENASE NICKEL INCORPORATION PROTEIN HYPA
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21(+)A
	Expression System Strain	:	BL21-CODONPLUS(DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	HYPA
	Organism Common	:	THERMOCOCCUS KODAKARAENSIS
	Organism Scientific	:	PYROCOCCUS KODAKARAENSIS
	Organism Taxid	:	69014
	Strain	:	KOD1
	Synonym	:	HYPA

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	FME	1	Mod. Amino Acid	N-FORMYLMETHIONINE
2	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	FME	1	Mod. Amino Acid	N-FORMYLMETHIONINE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	FME	-1	Mod. Amino Acid	N-FORMYLMETHIONINE
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:73 , CYS A:76 , CYS B:110 , CYS B:113 , SER B:115	BINDING SITE FOR RESIDUE ZN A 140
2	AC2	SOFTWARE	CYS A:110 , CYS A:113 , CYS B:73 , CYS B:76	BINDING SITE FOR RESIDUE ZN B 140
3	AC3	SOFTWARE	CYS C:73 , CYS C:76 , CYS D:110 , CYS D:113	BINDING SITE FOR RESIDUE ZN C 140
4	AC4	SOFTWARE	CYS C:110 , CYS C:113 , SER C:115 , CYS D:73 , CYS D:76	BINDING SITE FOR RESIDUE ZN C 141

Asymmetric Unit

No.	Residues
1	A:113	-	B:76
2	B:73	-	B:76

(no "Cis Peptide Bond" information available for 3A44)

(no "SAP(SNP)/Variant" information available for 3A44)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HYPA	PS01249	Hydrogenases expression/synthesis hypA family signature.	HYPA_THEKO	34-76	4	A:34-76 B:34-76 C:34-76 D:34-76

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HYPA	PS01249	Hydrogenases expression/synthesis hypA family signature.	HYPA_THEKO	34-76	2	A:34-76 B:34-76 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HYPA	PS01249	Hydrogenases expression/synthesis hypA family signature.	HYPA_THEKO	34-76	2	- - C:34-76 D:34-76

(no "Exon" information available for 3A44)

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:137
 aligned with HYPA_THEKO | Q5JIH3 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:137
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       
           HYPA_THEKO     2 HEWALADAIVRTVLDYAQREGASRVKAVRVVLGELQDVAEDIVKFAMEQLFAGTIAEGAEIEFVEEEAVFKCRNCNYEWKLKEVKDKFDERIKEDIHFIPEVVHAFLACPKCGSHDFEVVKGRGVYVAGIKIEKEGG 138
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh....eeeeeeeeee.....hhhhhhhhhhhhhh.......eeeeeee..eee......eeehhhhhhhhhhhhh...hhhhhhhhhhh.........eeeee...eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------HYPA  PDB: A:34-76 UniProt: 34-76          -------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a44 A   2 HEWALADAIVRTVLDYAQREGASRVKAVRVVLGELQDVAEDIVKFAMEQLFAGTIAEGAEIEFVEEEAVFKCRNCNYEWKLKEVKDKFDERIKEDIHFIPEVVHAFLACPKCGSHDFEVVKGRGVYVAGIKIEKEGG 138
                                    11        21        31        41        51        61        71        81        91       101       111       121       131

Chain B from PDB  Type:PROTEIN  Length:132
 aligned with HYPA_THEKO | Q5JIH3 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:136
                                    10        20        30        40        50        60        70        80        90       100       110       120       130      
           HYPA_THEKO     1 MHEWALADAIVRTVLDYAQREGASRVKAVRVVLGELQDVAEDIVKFAMEQLFAGTIAEGAEIEFVEEEAVFKCRNCNYEWKLKEVKDKFDERIKEDIHFIPEVVHAFLACPKCGSHDFEVVKGRGVYVAGIKIEKE 136
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh....eeeeeeeeee.....hhhhhhhhhhhhhh.......eeeeeee..eeee.....eeehhhhhhhhhh.......----hhhhhh...........eee...eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------HYPA  PDB: B:34-76 UniProt: 34-76          ------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a44 B   1 mHEWALADAIVRTVLDYAQREGASRVKAVRVVLGELQDVAEDIVKFAMEQLFAGTIAEGAEIEFVEEEAVFKCRNCNYEWKLKEVKDKFDERIKEDIH----VVHAFLACPKCGSHDFEVVKGRGVYVAGIKIEKE 136
                            |       10        20        30        40        50        60        70        80        90       | -  |    110       120       130      
                            1-FME                                                                                           98  103

Chain C from PDB  Type:PROTEIN  Length:122
 aligned with HYPA_THEKO | Q5JIH3 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:136
                                    11        21        31        41        51        61        71        81        91       101       111       121       131      
           HYPA_THEKO     2 HEWALADAIVRTVLDYAQREGASRVKAVRVVLGELQDVAEDIVKFAMEQLFAGTIAEGAEIEFVEEEAVFKCRNCNYEWKLKEVKDKFDERIKEDIHFIPEVVHAFLACPKCGSHDFEVVKGRGVYVAGIKIEKEG 137
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh....eeeeeeeeee.....hhhhhhhhhhhhhh.......eeeeeee..eeee.....eee.hhhhhhh--------------...............eeee...eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------HYPA  PDB: C:34-76 UniProt: 34-76          ------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a44 C   2 HEWALADAIVRTVLDYAQREGASRVKAVRVVLGELQDVAEDIVKFAMEQLFAGTIAEGAEIEFVEEEAVFKCRNCNYEWKLKEVKDKF--------------VHAFLACPKCGSHDFEVVKGRGVYVAGIKIEKEG 137
                                    11        21        31        41        51        61        71        81       | -         -  |    111       121       131      
                                                                                                                  89            104

Chain D from PDB  Type:PROTEIN  Length:127
 aligned with HYPA_THEKO | Q5JIH3 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:135
                                    12        22        32        42        52        62        72        82        92       102       112       122       132     
           HYPA_THEKO     3 EWALADAIVRTVLDYAQREGASRVKAVRVVLGELQDVAEDIVKFAMEQLFAGTIAEGAEIEFVEEEAVFKCRNCNYEWKLKEVKDKFDERIKEDIHFIPEVVHAFLACPKCGSHDFEVVKGRGVYVAGIKIEKEG 137
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh....eeeeeeeeee.....hhhhhhhhhhhhhh.......eeeeeee..eee......eeehhhhhhhhhhhh--------..hhhhh.........eee.....eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------HYPA  PDB: D:34-76 UniProt: 34-76          ------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a44 D   3 EWALADAIVRTVLDYAQREGASRVKAVRVVLGELQDVAEDIVKFAMEQLFAGTIAEGAEIEFVEEEAVFKCRNCNYEWKLKEVKDKFDERI--------EVVHAFLACPKCGSHDFEVVKGRGVYVAGIKIEKEG 137
                                    12        22        32        42        52        62        72        82        92|      102       112       122       132     
                                                                                                                     93      102

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 '\|'

(no "SCOP Domain" information available for 3A44)

(no "CATH Domain" information available for 3A44)

(no "Pfam Domain" information available for 3A44)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (HYPA_THEKO | Q5JIH3)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016151	nickel cation binding	Interacting selectively and non-covalently with nickel (Ni) cations.
biological process
	GO:0006464	cellular protein modification process	The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).

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	3a44
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	HYPA_THEKO \| Q5JIH3	:	3a43 5aun 5auo 5aup

Description

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Ligands, Modified Residues, Ions (2, 5)

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SS Bonds (2, 2)

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