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Title :   THE THREE DIMENSIONAL STRUCTURE OF ADENOSYLCOBINAMIDE KINASE/ ADENOSYLCOBINAMIDE PHOSPHATE GUALYLYLTRANSFERASE (COBU) COMPLEXED WITH GMP: EVIDENCE FOR A SUBSTRATE INDUCED TRANSFERASE ACTIVE SITE

Authors :   T. B. Thompson, M. G. Thomas, J. C. Esclante-Semerena, I. Rayment

Date :   02 Aug 99 (Deposition) - 18 Aug 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Alpha/Beta Structure Rossmann Fold P-Loop, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. B. Thompson, M. G. Thomas, J. C. Escalante-Semerena, I. Rayment
Three-Dimensional Structure Of Adenosylcobinamide Kinase/Adenosylcobinamide Phosphate Guanylyltransferase (Cobu) Complexed With Gmp: Evidence For A Substrate-Induced Transferase Active Site.
Biochemistry V. 38 12995 1999
PubMed-ID: 10529169 | Reference-DOI: 10.1021/BI990910X
(for further references see the PDB file header)

Molecule 1 - ADENOSYLCOBINAMIDE KINASE
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	SALMONELLA TYPHIMURIUM
	Organism Taxid	:	602
	Synonym	:	COBU

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 7)

No.	Name	Count	Type	Full Name
1	5GP	3	Ligand/Ion	GUANOSINE-5'-MONOPHOSPHATE
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	PO4	2	Ligand/Ion	PHOSPHATE ION
4	POP	1	Ligand/Ion	PYROPHOSPHATE 2-

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:7 , ARG A:9 , SER A:10 , GLY A:11 , LYS A:12 , SER A:13 , HOH A:851	BINDING SITE FOR RESIDUE PO4 A 600
2	AC2	SOFTWARE	GLY B:7 , ARG B:9 , SER B:10 , GLY B:11 , LYS B:12 , SER B:13 , HOH B:725 , HOH B:749	BINDING SITE FOR RESIDUE PO4 B 601
3	AC3	SOFTWARE	SER C:13 , GLU C:80 , POP C:608	BINDING SITE FOR RESIDUE MG C 607
4	AC4	SOFTWARE	TYR A:28 , ALA A:30 , THR A:31 , SER A:32 , ILE A:34 , ILE A:43 , HIS A:46 , LYS A:47 , ARG A:50 , GLU A:58 , GLU A:80 , CYS A:81	BINDING SITE FOR RESIDUE 5GP A 604
5	AC5	SOFTWARE	SER B:13 , TYR B:28 , ALA B:30 , THR B:31 , SER B:32 , ILE B:43 , HIS B:46 , LYS B:47 , ARG B:50 , GLU B:58 , GLU B:80 , CYS B:81	BINDING SITE FOR RESIDUE 5GP B 605
6	AC6	SOFTWARE	GLY C:7 , ALA C:8 , ARG C:9 , SER C:10 , GLY C:11 , LYS C:12 , SER C:13 , MG C:607 , HOH C:739 , HOH C:898	BINDING SITE FOR RESIDUE POP C 608
7	AC7	SOFTWARE	TYR C:28 , ALA C:30 , THR C:31 , SER C:32 , ILE C:34 , LYS C:47 , ARG C:50 , GLU C:80 , CYS C:81 , THR C:84	BINDING SITE FOR RESIDUE 5GP C 606

(no "SS Bond" information available for 1C9K)

Asymmetric/Biological Unit

No.	Residues
1	Glu A:80	-	Cys A:81
2	Glu B:80	-	Cys B:81
3	Glu C:80	-	Cys C:81

(no "SAP(SNP)/Variant" information available for 1C9K)

(no "PROSITE Motif" information available for 1C9K)

(no "Exon" information available for 1C9K)

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:170
 aligned with COBU_SALTY | Q05599 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:180
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181
           COBU_SALTY     2 MILVTGGARSGKSRHAEALIGDAPQVLYIATSQILDDEMAARIQHHKDGRPAHWRTAECWRHLDTLITADLAPDDAILLECITTMVTNLLFALGGENDPEQWDYAAMERAIDDEIQILIAACQRCPAKVVLVTNEVGMGIVPENRLARHFRDIAGRVNQRLAAAADEVWLVVSGIGVKIK 181
               SCOP domains d1c9ka_ A: Adenosylcobinamide kina      se/adenosylcobinamide phosphate guanylyltransferase C    obU                                                                                 SCOP domains
               CATH domains 1c9kA00 A:1-180 P-loop containing       nucleotide triphosphate hydrolases                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhh....eeeee....------hhhhhhhhh....eeee....hhhhh.........eeeeehhhhhhhhhhhhh----.....hhhhhhhhhhhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhhhhhhhhhh.eeeeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1c9k A   1 MILVTGGARSGKSRHAEALIGDAPQVLYIATSQI------ARIQHHKDGRPAHWRTAECWRHLDTLITADLAPDDAILLECITTMVTNLLFAL----DPEQWDYAAMERAIDDEIQILIAACQRCPAKVVLVTNEVGMGIVPENRLARHFRDIAGRVNQRLAAAADEVWLVVSGIGVKIK 180
                                    10        20        30   |     -|       50        60        70        80        90  |    100       110       120       130       140       150       160       170       180
                                                            34     41                                                  93   98

Chain B from PDB  Type:PROTEIN  Length:180
 aligned with COBU_SALTY | Q05599 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:180
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181
           COBU_SALTY     2 MILVTGGARSGKSRHAEALIGDAPQVLYIATSQILDDEMAARIQHHKDGRPAHWRTAECWRHLDTLITADLAPDDAILLECITTMVTNLLFALGGENDPEQWDYAAMERAIDDEIQILIAACQRCPAKVVLVTNEVGMGIVPENRLARHFRDIAGRVNQRLAAAADEVWLVVSGIGVKIK 181
               SCOP domains d1c9kb_ B: Adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU                                                                                           SCOP domains
               CATH domains 1c9kB00 B:1-180 P-loop containing nucleotide triphosphate hydrolases                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhh...eeee....hhhhh.........eeeeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.........hhhhhhhhhhhhhhhhhhhhhh.eeeeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1c9k B   1 MILVTGGARSGKSRHAEALIGDAPQVLYIATSQILDDEMAARIQHHKDGRPAHWRTAECWRHLDTLITADLAPDDAILLECITTMVTNLLFALGGENDPEQWDYAAMERAIDDEIQILIAACQRCPAKVVLVTNEVGMGIVPENRLARHFRDIAGRVNQRLAAAADEVWLVVSGIGVKIK 180
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain C from PDB  Type:PROTEIN  Length:165
 aligned with COBU_SALTY | Q05599 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:180
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181
           COBU_SALTY     2 MILVTGGARSGKSRHAEALIGDAPQVLYIATSQILDDEMAARIQHHKDGRPAHWRTAECWRHLDTLITADLAPDDAILLECITTMVTNLLFALGGENDPEQWDYAAMERAIDDEIQILIAACQRCPAKVVLVTNEVGMGIVPENRLARHFRDIAGRVNQRLAAAADEVWLVVSGIGVKIK 181
               SCOP domains d1c9kc_ C: Adenosylcobinamide kinas         e/adenosylcob   inamide phosphate guanylyltransfer   ase CobU                                                                            SCOP domains
               CATH domains 1c9kC00 C:1-180 P-loop containing n         ucleotide tri   phosphate hydrolases                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhh....eeeee.....---------hhhhhh....eee---.hhhhh.........eeeeehhhhhhhhhhhhhh---.....hhhhhhhhhhhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhhhhhhhhhh.eeeeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1c9k C   1 MILVTGGARSGKSRHAEALIGDAPQVLYIATSQIL---------HHKDGRPAHWRTA---RHLDTLITADLAPDDAILLECITTMVTNLLFALG---DPEQWDYAAMERAIDDEIQILIAACQRCPAKVVLVTNEVGMGIVPENRLARHFRDIAGRVNQRLAAAADEVWLVVSGIGVKIK 180
                                    10        20        30    |    -    |   50      |  -|       70        80        90   |   100       110       120       130       140       150       160       170       180
                                                             35        45          57  61                               94  98

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Salmonella typhimurium. Organism_taxid: 602. (5)

1a	1c9kB00	B:1-180
1b	1c9kA00	A:1-180
1c	1c9kC00	C:1-180

(no "Pfam Domain" information available for 1C9K)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (COBU_SALTY | Q05599)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0043752	adenosylcobinamide kinase activity	Catalysis of the reaction: RTP + adenosylcobinamide = adenosylcobinamide phosphate + RDP (where RTP is either ATP or GTP).
	GO:0008820	cobinamide phosphate guanylyltransferase activity	Catalysis of the reaction: adenosylcobinamide phosphate + GTP + 2 H(+) = adenosylcobinamide-GDP + diphosphate.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0009236	cobalamin biosynthetic process	The chemical reactions and pathways resulting in the formation of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
	GO:0051188	cofactor biosynthetic process	The chemical reactions and pathways resulting in the formation of a cofactor, a substance that is required for the activity of an enzyme or other protein.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu A:80 - Cys A:81	[ RasMol ]
		Glu B:80 - Cys B:81	[ RasMol ]
		Glu C:80 - Cys C:81	[ RasMol ]

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	1c9k
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	COBU_SALTY \| Q05599	:	1cbu

1cbu	THE APO STRUCTURE OF COBU

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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