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Title :   STRUCTURE OF THE COVALENT ACYL-ADENYLATE FORM OF THE MOEB-MOAD PROTEIN COMPLEX

Authors :   M. W. Lake, M. M. Wuebbens, K. V. Rajagopalan, H. Schindelin

Date :   03 Sep 01 (Deposition) - 21 Nov 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Moeb: Modified Rossmann Fold; (2) Cys-X-X-Cys Zinc-Binding Motifs; Moad: Ubiquitin-Like Fold, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. W. Lake, M. M. Wuebbens, K. V. Rajagopalan, H. Schindelin
Mechanism Of Ubiquitin Activation Revealed By The Structure Of A Bacterial Moeb-Moad Complex.
Nature V. 414 325 2001
PubMed-ID: 11713534 | Reference-DOI: 10.1038/35104586

Molecule 1 - MOLYBDOPTERIN BIOSYNTHESIS MOEB PROTEIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	MOEB
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

Molecule 2 - MOLYBDOPTERIN [MPT] CONVERTING FACTOR, SUBUNIT 1
	Chains	:	D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	MOAD
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN D

		1	2
Asymmetric Unit	:	B	D
Biological Unit 1 (2x)	:	B	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	SO4	1	Ligand/Ion	SULFATE ION
3	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	AMP	2	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	SO4	2	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS B:172 , CYS B:175 , CYS B:244 , CYS B:247	BINDING SITE FOR RESIDUE ZN B 250
2	AC2	SOFTWARE	ARG B:14 , SER B:69 , ASN B:70 , ARG B:73 , HOH D:84	BINDING SITE FOR RESIDUE SO4 B 251
3	AC3	SOFTWARE	GLY B:38 , GLY B:40 , GLY B:41 , LEU B:61 , ASP B:62 , PHE B:63 , ASP B:64 , ARG B:73 , GLN B:74 , LYS B:86 , LEU B:109 , CYS B:128 , THR B:129 , ASP B:130 , ASN B:131 , VAL B:134 , HOH B:266 , HOH B:281 , HOH B:310 , GLY D:81 , HOH D:84 , HOH D:90 , HOH D:102 , HOH D:105	BINDING SITE FOR RESIDUE AMP D 82

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

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

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

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

(no "Exon" information available for 1JWB)

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
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Chain B from PDB  Type:PROTEIN  Length:240
 aligned with MOEB_ECOLI | P12282 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:247
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       
           MOEB_ECOLI     2 AELSDQEMLRYNRQIILRGFDFDGQEALKDSRVLIVGLGGLGCAASQYLASAGVGNLTLLDFDTVSLSNLQRQTLHSDATVGQPKVESARDALTRINPHIAITPVNALLDDAELAALIAEHDLVLDCTDNVAVRNQLNAGCFAAKVPLVSGAAIRMEGQITVFTYQDGEPCYRCLSRLFGENALTCVEAGVMAPLIGVIGSLQAMEAIKMLAGYGKPASGKIVMYDAMTCQFREMKLMRNPGCEVCG 248
               SCOP domains d1jwbb_ B: Molybdenum cofactor biosynthesis protein MoeB                                                                                                                                                                                                SCOP domains
               CATH domains 1jwbB00 B:2-248 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------ThiF-1jwbB01 B:30-164                                                                                                                  ---MoeZ_MoeB-1jwb       B02 B:168-248                                                Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh...hhhhhhhhhhhheeeee..hhhhhhhhhhhhhhh..eeeeee....hhhhhhh....hhhhh..hhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhh..eeeeeee..eeeeeee.......hhhhhhh...-------....hhhhhhhhhhhhhhhhhhhhhh.......eeeeee....eeeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jwb B   2 AELSDQEMLRYNRQIILRGFDFDGQEALKDSRVLIVGLGGLGCAASQYLASAGVGNLTLLDFDTVSLSNLQRQTLHSDATVGQPKVESARDALTRINPHIAITPVNALLDDAELAALIAEHDLVLDCTDNVAVRNQLNAGCFAAKVPLVSGAAIRMEGQITVFTYQDGEPCYRCLSRLFG-------EAGVMAPLIGVIGSLQAMEAIKMLAGYGKPASGKIVMYDAMTCQFREMKLMRNPGCEVCG 248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       
                                                                                                                                                                                                             181     189

Chain D from PDB  Type:PROTEIN  Length:80
 aligned with MOAD_ECOLI | P30748 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:80
                                    11        21        31        41        51        61        71        81
           MOAD_ECOLI     2 IKVLFFAQVRELVGTDATEVAADFPTVEALRQHMAAQSDRWALALEDGKLLAAVNQTLVSFDHPLTDGDEVAFFPPVTGG  81
               SCOP domains d1jwbd_ D: Molybdopterin synthase subunit MoaD                                   SCOP domains
               CATH domains 1jwbD00 D:2-81  [code=3.10.20.30, no name defined]                               CATH domains
               Pfam domains --ThiS-1jwbD01 D:4-81                                                            Pfam domains
         Sec.struct. author .eeeehhhhhhhhh..eee.......hhhhhhhhhh.hhhhhhhh.....eeee..eee...........eeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                 1jwb D   2 IKVLFFAQVRELVGTDATEVAADFPTVEALRQHMAAQSDRWALALEDGKLLAAVNQTLVSFDHPLTDGDEVAFFPPVTGG  81
                                    11        21        31        41        51        61        71        81

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: NAD(P)-binding Rossmann-like Domain (1244)

Escherichia coli. Organism_taxid: 562. (48)

1jwbB00

B:2-248

Architecture: Roll (3276)

Topology: Ubiquitin-like (UB roll) (674)

Homologous Superfamily: [code=3.10.20.30, no name defined] (153)

Escherichia coli. Organism_taxid: 562. (14)

1jwbD00

D:2-81

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: ThiF (14)

Escherichia coli (strain K12) (6)

ThiF-1jwbB01

B:30-164

Clan: Ubiquitin (279)

Family: ThiS (18)

Escherichia coli (strain K12) (5)

ThiS-1jwbD01

D:4-81

Clan: no clan defined [family: MoeZ_MoeB] (6)

Family: MoeZ_MoeB (6)

Escherichia coli (strain K12) (6)

MoeZ_MoeB-1jwbB02

B:168-248

Asymmetric Unit(hide GO term definitions)

Chain B (MOEB_ECOLI | P12282)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0061605	molybdopterin-synthase adenylyltransferase activity	Catalysis of the reaction: ATP [molybdopterin-synthase sulfur-carrier protein]-Gly-Gly = diphosphate [molybdopterin-synthase sulfur-carrier protein]-Gly-Gly-AMP.
	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:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0008641	small protein activating enzyme activity	Catalysis of the activation of small proteins, such as ubiquitin or ubiquitin-like proteins, through the formation of an ATP-dependent high-energy thiolester bond.
	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.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006777	Mo-molybdopterin cofactor biosynthetic process	The chemical reactions and pathways resulting in the formation of the Mo-molybdopterin cofactor, essential for the catalytic activity of some enzymes. The cofactor consists of a mononuclear molybdenum (Mo) ion coordinated by one or two molybdopterin ligands.
	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).
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain D (MOAD_ECOLI | P30748)

molecular function
	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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0006777	Mo-molybdopterin cofactor biosynthetic process	The chemical reactions and pathways resulting in the formation of the Mo-molybdopterin cofactor, essential for the catalytic activity of some enzymes. The cofactor consists of a mononuclear molybdenum (Mo) ion coordinated by one or two molybdopterin ligands.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric Unit
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	1jwb
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	MOAD_ECOLI \| P30748
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	MOEB_ECOLI \| P12282
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UniProtKB/Swiss-Prot
	MOAD_ECOLI \| P30748	:	1fm0 1fma 1jw9 1jwa 1nvi 3bii
	MOEB_ECOLI \| P12282	:	1jw9 1jwa

1fmo	STRUCTURE OF MOLYBDOPTERIN SYNTHASE (MOAD IN COMPLEX WITH MOAE)
1jw9	STRUCTURE OF THE NATIVE MOEB-MOAD PROTEIN COMPLEX
1jwa	STRUCTURE OF THE ATP-BOUND MOEB-MOAD PROTEIN COMPLEX

Description

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