1KGN - JenaLib

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Title :   R2F FROM CORYNEBACTERIUM AMMONIAGENES IN ITS OXIDISED, FE CONTAINING, FORM

Authors :   M. Hogbom, Y. Huque, B. M. Sjoberg, P. Nordlund

Date :   28 Nov 01 (Deposition) - 21 Dec 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   Helix Bundle, Arm Exchange, Radical Protein, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Hogbom, Y. Huque, B. M. Sjoberg, P. Nordlund
Crystal Structure Of The Di-Iron/Radical Protein Of Ribonucleotide Reductase From Corynebacterium Ammoniagenes.
Biochemistry V. 41 1381 2002
PubMed-ID: 11802741 | Reference-DOI: 10.1021/BI011429L
(for further references see the PDB file header)

Molecule 1 - RIBONUCLEOTIDE REDUCTASE PROTEIN R2F
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PIG056
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	CORYNEBACTERIUM AMMONIAGENES
	Organism Taxid	:	1697

		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 (1, 8)

No.	Name	Count	Type	Full Name
1	FE	8	Ligand/Ion	FE (III) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	FE	-1	Ligand/Ion	FE (III) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	FE	-1	Ligand/Ion	FE (III) ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:77 , GLU A:108 , HIS A:111 , GLU A:202 , FE A:2001 , HOH A:2096 , HOH A:2147 , HOH A:2427	BINDING SITE FOR RESIDUE FE A 1001
2	AC2	SOFTWARE	ASP B:77 , GLU B:108 , HIS B:111 , GLU B:202 , FE B:2002 , HOH B:2064 , HOH B:2164 , HOH B:2364	BINDING SITE FOR RESIDUE FE B 1002
3	AC3	SOFTWARE	ASP D:77 , GLU D:108 , HIS D:111 , GLU D:202 , FE D:1004	BINDING SITE FOR RESIDUE FE D 1003
4	AC4	SOFTWARE	GLU D:108 , GLU D:168 , GLU D:202 , HIS D:205 , FE D:1003	BINDING SITE FOR RESIDUE FE D 1004
5	AC5	SOFTWARE	GLU A:108 , GLU A:168 , GLU A:202 , HIS A:205 , FE A:1001 , HOH A:2096 , HOH A:2427	BINDING SITE FOR RESIDUE FE A 2001
6	AC6	SOFTWARE	GLU B:108 , GLU B:168 , GLU B:202 , HIS B:205 , FE B:1002 , HOH B:2164 , HOH B:2364	BINDING SITE FOR RESIDUE FE B 2002
7	AC7	SOFTWARE	ASP C:77 , GLU C:108 , HIS C:111 , GLU C:202 , FE C:3002 , HOH C:3051 , HOH C:3060 , HOH C:3403	BINDING SITE FOR RESIDUE FE C 3001
8	AC8	SOFTWARE	GLU C:108 , GLU C:168 , GLU C:202 , HIS C:205 , FE C:3001 , HOH C:3051 , HOH C:3403	BINDING SITE FOR RESIDUE FE C 3002

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

(no "Cis Peptide Bond" information available for 1KGN)

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

(no "PROSITE Motif" information available for 1KGN)

(no "Exon" information available for 1KGN)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:296
 aligned with O69274_CORAM | O69274 from UniProtKB/TrEMBL  Length:329

    Alignment length:296
                                    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      
         O69274_CORAM     2 SNEYDEYIANHTDPVKAINWNVIPDEKDLEVWDRLTGNFWLPEKIPVSNDIQSWNKMTPQEQLATMRVFTGLTLLDTIQGTVGAISLLPDAETMHEEAVYTNIAFMESVHAKSYSNIFMTLASTPQINEAFRWSEENENLQRKAKIIMSYYNGDDPLKKKVASTLLESFLFYSGFYLPMYLSSRAKLTNTADIIRLIIRDESVHGYYIGYKYQQGVKKLSEAEQEEYKAYTFDLMYDLYENEIEYTEDIYDDLGWTEDVKRFLRYNANKALNNLGYEGLFPTDETKVSPAILSSLS 297
               SCOP domains d1kgna_ A: Ribonucleotide reductase R2                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1kgnA00 A:2-297 Ribonucleotide Reductase, subunit A                                                                                                                                                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh.............hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh......hhhhh..hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kgn A   2 SNEYDEYIANHTDPVKAINWNVIPDEKDLEVWDRLTGNFWLPEKIPVSNDIQSWNKMTPQEQLATMRVFTGLTLLDTIQGTVGAISLLPDAETMHEEAVYTNIAFMESVHAKSYSNIFMTLASTPQINEAFRWSEENENLQRKAKIIMSYYNGDDPLKKKVASTLLESFLFYSGFYLPMYLSSRAKLTNTADIIRLIIRDESVHGYYIGYKYQQGVKKLSEAEQEEYKAYTFDLMYDLYENEIEYTEDIYDDLGWTEDVKRFLRYNANKALNNLGYEGLFPTDETKVSPAILSSLS 297
                                    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

Chain B from PDB  Type:PROTEIN  Length:296
 aligned with O69274_CORAM | O69274 from UniProtKB/TrEMBL  Length:329

    Alignment length:296
                                    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      
         O69274_CORAM     2 SNEYDEYIANHTDPVKAINWNVIPDEKDLEVWDRLTGNFWLPEKIPVSNDIQSWNKMTPQEQLATMRVFTGLTLLDTIQGTVGAISLLPDAETMHEEAVYTNIAFMESVHAKSYSNIFMTLASTPQINEAFRWSEENENLQRKAKIIMSYYNGDDPLKKKVASTLLESFLFYSGFYLPMYLSSRAKLTNTADIIRLIIRDESVHGYYIGYKYQQGVKKLSEAEQEEYKAYTFDLMYDLYENEIEYTEDIYDDLGWTEDVKRFLRYNANKALNNLGYEGLFPTDETKVSPAILSSLS 297
               SCOP domains d1kgnb_ B: Ribonucleotide reductase R2                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1kgnB00 B:2-297 Ribonucleotide Reductase, subunit A                                                                                                                                                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh.............hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh......hhhhh..hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kgn B   2 SNEYDEYIANHTDPVKAINWNVIPDEKDLEVWDRLTGNFWLPEKIPVSNDIQSWNKMTPQEQLATMRVFTGLTLLDTIQGTVGAISLLPDAETMHEEAVYTNIAFMESVHAKSYSNIFMTLASTPQINEAFRWSEENENLQRKAKIIMSYYNGDDPLKKKVASTLLESFLFYSGFYLPMYLSSRAKLTNTADIIRLIIRDESVHGYYIGYKYQQGVKKLSEAEQEEYKAYTFDLMYDLYENEIEYTEDIYDDLGWTEDVKRFLRYNANKALNNLGYEGLFPTDETKVSPAILSSLS 297
                                    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

Chain C from PDB  Type:PROTEIN  Length:296
 aligned with O69274_CORAM | O69274 from UniProtKB/TrEMBL  Length:329

    Alignment length:296
                                    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      
         O69274_CORAM     2 SNEYDEYIANHTDPVKAINWNVIPDEKDLEVWDRLTGNFWLPEKIPVSNDIQSWNKMTPQEQLATMRVFTGLTLLDTIQGTVGAISLLPDAETMHEEAVYTNIAFMESVHAKSYSNIFMTLASTPQINEAFRWSEENENLQRKAKIIMSYYNGDDPLKKKVASTLLESFLFYSGFYLPMYLSSRAKLTNTADIIRLIIRDESVHGYYIGYKYQQGVKKLSEAEQEEYKAYTFDLMYDLYENEIEYTEDIYDDLGWTEDVKRFLRYNANKALNNLGYEGLFPTDETKVSPAILSSLS 297
               SCOP domains d1kgnc_ C: Ribonucleotide reductase R2                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1kgnC00 C:2-297 Ribonucleotide Reductase, subunit A                                                                                                                                                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh.............hhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh......hhhhh..hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kgn C   2 SNEYDEYIANHTDPVKAINWNVIPDEKDLEVWDRLTGNFWLPEKIPVSNDIQSWNKMTPQEQLATMRVFTGLTLLDTIQGTVGAISLLPDAETMHEEAVYTNIAFMESVHAKSYSNIFMTLASTPQINEAFRWSEENENLQRKAKIIMSYYNGDDPLKKKVASTLLESFLFYSGFYLPMYLSSRAKLTNTADIIRLIIRDESVHGYYIGYKYQQGVKKLSEAEQEEYKAYTFDLMYDLYENEIEYTEDIYDDLGWTEDVKRFLRYNANKALNNLGYEGLFPTDETKVSPAILSSLS 297
                                    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

Chain D from PDB  Type:PROTEIN  Length:296
 aligned with O69274_CORAM | O69274 from UniProtKB/TrEMBL  Length:329

    Alignment length:296
                                    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      
         O69274_CORAM     2 SNEYDEYIANHTDPVKAINWNVIPDEKDLEVWDRLTGNFWLPEKIPVSNDIQSWNKMTPQEQLATMRVFTGLTLLDTIQGTVGAISLLPDAETMHEEAVYTNIAFMESVHAKSYSNIFMTLASTPQINEAFRWSEENENLQRKAKIIMSYYNGDDPLKKKVASTLLESFLFYSGFYLPMYLSSRAKLTNTADIIRLIIRDESVHGYYIGYKYQQGVKKLSEAEQEEYKAYTFDLMYDLYENEIEYTEDIYDDLGWTEDVKRFLRYNANKALNNLGYEGLFPTDETKVSPAILSSLS 297
               SCOP domains d1kgnd_ D: Ribonucleotide reductase R2                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1kgnD00 D:2-297 Ribonucleotide Reductase, subunit A                                                                                                                                                                                                                                                      CATH domains
           Pfam domains (1) -----------Ribonuc_red_sm-1kgnD01 D:13-291                                                                                                                                                                                                                                                        ------ Pfam domains (1)
           Pfam domains (2) -----------Ribonuc_red_sm-1kgnD02 D:13-291                                                                                                                                                                                                                                                        ------ Pfam domains (2)
           Pfam domains (3) -----------Ribonuc_red_sm-1kgnD03 D:13-291                                                                                                                                                                                                                                                        ------ Pfam domains (3)
           Pfam domains (4) -----------Ribonuc_red_sm-1kgnD04 D:13-291                                                                                                                                                                                                                                                        ------ Pfam domains (4)
         Sec.struct. author ...hhhhhhh..............hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh......hhhhh..hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kgn D   2 SNEYDEYIANHTDPVKAINWNVIPDEKDLEVWDRLTGNFWLPEKIPVSNDIQSWNKMTPQEQLATMRVFTGLTLLDTIQGTVGAISLLPDAETMHEEAVYTNIAFMESVHAKSYSNIFMTLASTPQINEAFRWSEENENLQRKAKIIMSYYNGDDPLKKKVASTLLESFLFYSGFYLPMYLSSRAKLTNTADIIRLIIRDESVHGYYIGYKYQQGVKKLSEAEQEEYKAYTFDLMYDLYENEIEYTEDIYDDLGWTEDVKRFLRYNANKALNNLGYEGLFPTDETKVSPAILSSLS 297
                                    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

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Ferritin-like (533)

Superfamily: Ferritin-like (489)

Family: Ribonucleotide reductase-like (185)

Protein domain: Ribonucleotide reductase R2 (45)

Corynebacterium ammoniagenes [TaxId: 1697] (6)

1a	d1kgna_	A:
1b	d1kgnb_	B:
1c	d1kgnc_	C:
1d	d1kgnd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Ribonucleotide Reductase, subunit A (86)

Homologous Superfamily: Ribonucleotide Reductase, subunit A (86)

Corynebacterium ammoniagenes. Organism_taxid: 1697. (4)

1a	1kgnA00	A:2-297
1b	1kgnB00	B:2-297
1c	1kgnC00	C:2-297
1d	1kgnD00	D:2-297

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ferritin (185)

Family: Ribonuc_red_sm (41)

Corynebacterium ammoniagenes (Brevibacterium ammoniagenes) (5)

1a	Ribonuc_red_sm-1kgnD01	D:13-291
1b	Ribonuc_red_sm-1kgnD02	D:13-291
1c	Ribonuc_red_sm-1kgnD03	D:13-291
1d	Ribonuc_red_sm-1kgnD04	D:13-291

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (O69274_CORAM | O69274)

molecular function
	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:0004748	ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor	Catalysis of the reaction: 2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin. Thioredoxin disulfide is the oxidized form of thioredoxin.
biological process
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0009186	deoxyribonucleoside diphosphate metabolic process	The chemical reactions and pathways involving a deoxyribonucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with diphosphate on the sugar.
	GO:0009263	deoxyribonucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
	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.
cellular component
	GO:0005971	ribonucleoside-diphosphate reductase complex	An enzyme complex composed of 2-4 or more subunits, which usually contains nonheme iron and requires ATP for catalysis. Catalyzes the formation of 2'-deoxyribonucleoside diphosphate from ribonucleoside diphosphate, using either thioredoxin disulfide or glutaredoxin disulfide as an acceptor.

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1kgo	1KGO CONTAINS R2F WITH FE2+.
1kgp	1KGP CONTAINS R2F WITH MN2+.

Description

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Ligands, Modified Residues, Ions (1, 8)

Sites (8, 8)

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