2JAH - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   BIOCHEMICAL AND STRUCTURAL ANALYSIS OF THE CLAVULANIC ACID DEHYDEOGENASE (CAD) FROM STREPTOMYCES CLAVULIGERUS

Authors :   A. K. Mackenzie, N. J. Kershaw, H. Hernandez, C. V. Robinson, C. J. Schof I. Andersson

Date :   28 Nov 06 (Deposition) - 20 Feb 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Short-Chain Dehydrogenase/Reductase, Lactamase Inhibitor, Antibiotic Biosynthesis, Nadph, Oxidoreductase, Clavulanic Acid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. K. Mackenzie, N. J. Kershaw, H. Hernandez, C. V. Robinson, C. J. Schofield, I. Andersson
Clavulanic Acid Dehydrogenase: Structural And Biochemical Analysis Of The Final Step In The Biosynthesis Of The Beta-Lactamase Inhibitor Clavulanic Acid
Biochemistry V. 46 1523 2007
PubMed-ID: 17279617 | Reference-DOI: 10.1021/BI061978X

Molecule 1 - CLAVULANIC ACID DEHYDROGENASE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET24A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Scientific	:	STREPTOMYCES CLAVULIGERUS
	Organism Taxid	:	1901
	Strain	:	NRRL3585

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 28)

No.	Name	Count	Type	Full Name
1	MSE	24	Mod. Amino Acid	SELENOMETHIONINE
2	NDP	4	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:14 , SER A:16 , SER A:17 , GLY A:18 , ILE A:19 , ALA A:38 , ARG A:39 , ARG A:40 , LEU A:63 , ASP A:64 , VAL A:65 , ASN A:91 , ALA A:92 , GLY A:93 , THR A:114 , MSE A:140 , SER A:141 , SER A:142 , TYR A:155 , LYS A:159 , PRO A:185 , GLY A:186 , THR A:187 , THR A:188 , THR A:190 , GLU A:191 , LEU A:192 , HOH A:2045 , HOH A:2048 , HOH A:2137 , HOH A:2138 , HOH A:2139 , HOH A:2140 , HOH A:2141	BINDING SITE FOR RESIDUE NDP A1248
2	AC2	SOFTWARE	GLN A:69 , HOH A:2028 , GLY B:14 , SER B:16 , SER B:17 , GLY B:18 , ILE B:19 , ALA B:38 , ARG B:39 , ARG B:40 , LEU B:63 , ASP B:64 , VAL B:65 , ASN B:91 , ALA B:92 , GLY B:93 , THR B:114 , MSE B:140 , SER B:141 , SER B:142 , TYR B:155 , LYS B:159 , PRO B:185 , GLY B:186 , THR B:187 , THR B:188 , THR B:190 , GLU B:191 , LEU B:192 , HOH B:2021 , HOH B:2023 , HOH B:2049 , HOH B:2078 , HOH B:2104 , HOH B:2105	BINDING SITE FOR RESIDUE NDP B1248
3	AC3	SOFTWARE	GLY C:14 , SER C:16 , SER C:17 , GLY C:18 , ILE C:19 , ALA C:38 , ARG C:39 , ARG C:40 , LEU C:63 , ASP C:64 , VAL C:65 , ASN C:91 , ALA C:92 , GLY C:93 , THR C:114 , MSE C:140 , SER C:141 , SER C:142 , TYR C:155 , LYS C:159 , PRO C:185 , GLY C:186 , THR C:187 , THR C:188 , THR C:190 , GLU C:191 , LEU C:192 , HOH C:2004 , HOH C:2057 , HOH C:2080 , HOH C:2094 , HOH C:2103 , HOH C:2129 , HOH C:2130 , HOH C:2131	BINDING SITE FOR RESIDUE NDP C1248
4	AC4	SOFTWARE	GLY D:14 , SER D:16 , SER D:17 , GLY D:18 , ILE D:19 , ALA D:38 , ARG D:39 , ARG D:40 , LEU D:63 , ASP D:64 , VAL D:65 , ASN D:91 , ALA D:92 , GLY D:93 , THR D:114 , MSE D:140 , SER D:141 , SER D:142 , TYR D:155 , LYS D:159 , PRO D:185 , GLY D:186 , THR D:187 , THR D:188 , THR D:190 , GLU D:191 , LEU D:192 , HOH D:2003 , HOH D:2084 , HOH D:2088 , HOH D:2116 , HOH D:2117	BINDING SITE FOR RESIDUE NDP D1248

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

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

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

(no "PROSITE Motif" information available for 2JAH)

(no "Exon" information available for 2JAH)

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:245
 aligned with Q9LCV7_STRCL | Q9LCV7 from UniProtKB/TrEMBL  Length:247

    Alignment length:245
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242     
         Q9LCV7_STRCL     3 SALQGKVALITGASSGIGEATARALAAEGAAVAIAARRVEKLRALGDELTAAGAKVHVLELDVADRQGVDAAVASTVEALGGLDILVNNAGIMLLGPVEDADTTDWTRMIDTNLLGLMYMTRAALPHLLRSKGTVVQMSSIAGRVNVRNAAVYQATKFGVNAFSETLRQEVTERGVRVVVIEPGTTDTELRGHITHTATKEMYEQRISQIRKLQAQDIAEAVRYAVTAPHHATVHEIFIRPTDQV 247
               SCOP domains d2jaha_ A: automated matches                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhh...eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jah A   3 SALQGKVALITGASSGIGEATARALAAEGAAVAIAARRVEKLRALGDELTAAGAKVHVLELDVADRQGVDAAVASTVEALGGLDILVNNAGImLLGPVEDADTTDWTRmIDTNLLGLmYmTRAALPHLLRSKGTVVQmSSIAGRVNVRNAAVYQATKFGVNAFSETLRQEVTERGVRVVVIEPGTTDTELRGHITHTATKEmYEQRISQIRKLQAQDIAEAVRYAVTAPHHATVHEIFIRPTDQV 247
                                    12        22        32        42        52        62        72        82        92  |    102       112       122       132       142       152       162       172       182       192       202 |     212       222       232       242     
                                                                                                                       95-MSE         111-MSE  120-MSE             140-MSE                                                         204-MSE                                       
                                                                                                                                                 122-MSE

Chain B from PDB  Type:PROTEIN  Length:245
 aligned with Q9LCV7_STRCL | Q9LCV7 from UniProtKB/TrEMBL  Length:247

    Alignment length:245
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242     
         Q9LCV7_STRCL     3 SALQGKVALITGASSGIGEATARALAAEGAAVAIAARRVEKLRALGDELTAAGAKVHVLELDVADRQGVDAAVASTVEALGGLDILVNNAGIMLLGPVEDADTTDWTRMIDTNLLGLMYMTRAALPHLLRSKGTVVQMSSIAGRVNVRNAAVYQATKFGVNAFSETLRQEVTERGVRVVVIEPGTTDTELRGHITHTATKEMYEQRISQIRKLQAQDIAEAVRYAVTAPHHATVHEIFIRPTDQV 247
               SCOP domains d2jahb_ B: automated matches                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhh...eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jah B   3 SALQGKVALITGASSGIGEATARALAAEGAAVAIAARRVEKLRALGDELTAAGAKVHVLELDVADRQGVDAAVASTVEALGGLDILVNNAGImLLGPVEDADTTDWTRmIDTNLLGLmYmTRAALPHLLRSKGTVVQmSSIAGRVNVRNAAVYQATKFGVNAFSETLRQEVTERGVRVVVIEPGTTDTELRGHITHTATKEmYEQRISQIRKLQAQDIAEAVRYAVTAPHHATVHEIFIRPTDQV 247
                                    12        22        32        42        52        62        72        82        92  |    102       112       122       132       142       152       162       172       182       192       202 |     212       222       232       242     
                                                                                                                       95-MSE         111-MSE  120-MSE             140-MSE                                                         204-MSE                                       
                                                                                                                                                 122-MSE

Chain C from PDB  Type:PROTEIN  Length:246
 aligned with Q9LCV7_STRCL | Q9LCV7 from UniProtKB/TrEMBL  Length:247

    Alignment length:246
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241      
         Q9LCV7_STRCL     2 PSALQGKVALITGASSGIGEATARALAAEGAAVAIAARRVEKLRALGDELTAAGAKVHVLELDVADRQGVDAAVASTVEALGGLDILVNNAGIMLLGPVEDADTTDWTRMIDTNLLGLMYMTRAALPHLLRSKGTVVQMSSIAGRVNVRNAAVYQATKFGVNAFSETLRQEVTERGVRVVVIEPGTTDTELRGHITHTATKEMYEQRISQIRKLQAQDIAEAVRYAVTAPHHATVHEIFIRPTDQV 247
               SCOP domains d2jahc_ C: automated matches                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2jah C   2 PSALQGKVALITGASSGIGEATARALAAEGAAVAIAARRVEKLRALGDELTAAGAKVHVLELDVADRQGVDAAVASTVEALGGLDILVNNAGImLLGPVEDADTTDWTRmIDTNLLGLmYmTRAALPHLLRSKGTVVQmSSIAGRVNVRNAAVYQATKFGVNAFSETLRQEVTERGVRVVVIEPGTTDTELRGHITHTATKEmYEQRISQIRKLQAQDIAEAVRYAVTAPHHATVHEIFIRPTDQV 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      
                                                                                                                        95-MSE         111-MSE  120-MSE             140-MSE                                                         204-MSE                                       
                                                                                                                                                  122-MSE

Chain D from PDB  Type:PROTEIN  Length:245
 aligned with Q9LCV7_STRCL | Q9LCV7 from UniProtKB/TrEMBL  Length:247

    Alignment length:245
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242     
         Q9LCV7_STRCL     3 SALQGKVALITGASSGIGEATARALAAEGAAVAIAARRVEKLRALGDELTAAGAKVHVLELDVADRQGVDAAVASTVEALGGLDILVNNAGIMLLGPVEDADTTDWTRMIDTNLLGLMYMTRAALPHLLRSKGTVVQMSSIAGRVNVRNAAVYQATKFGVNAFSETLRQEVTERGVRVVVIEPGTTDTELRGHITHTATKEMYEQRISQIRKLQAQDIAEAVRYAVTAPHHATVHEIFIRPTDQV 247
               SCOP domains d2jahd_ D: automated matches                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhh...eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jah D   3 SALQGKVALITGASSGIGEATARALAAEGAAVAIAARRVEKLRALGDELTAAGAKVHVLELDVADRQGVDAAVASTVEALGGLDILVNNAGImLLGPVEDADTTDWTRmIDTNLLGLmYmTRAALPHLLRSKGTVVQmSSIAGRVNVRNAAVYQATKFGVNAFSETLRQEVTERGVRVVVIEPGTTDTELRGHITHTATKEmYEQRISQIRKLQAQDIAEAVRYAVTAPHHATVHEIFIRPTDQV 247
                                    12        22        32        42        52        62        72        82        92  |    102       112       122       132       142       152       162       172       182       192       202 |     212       222       232       242     
                                                                                                                       95-MSE         111-MSE  120-MSE             140-MSE                                                         204-MSE                                       
                                                                                                                                                 122-MSE

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: Alpha and beta proteins (a/b) (23833)

Fold: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: automated matches (447)

Protein domain: automated matches (447)

Streptomyces clavuligerus [TaxId: 1901] (2)

1a	d2jaha_	A:
1b	d2jahb_	B:
1c	d2jahc_	C:
1d	d2jahd_	D:

(no "CATH Domain" information available for 2JAH)

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (Q9LCV7_STRCL | Q9LCV7)

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.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NDP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2jah)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2jah
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	Q9LCV7_STRCL \| Q9LCV7
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	Q9LCV7_STRCL \| Q9LCV7
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	Q9LCV7_STRCL \| Q9LCV7	:	2jap

(no "Related Entries Specified in the PDB File" available for 2JAH)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 28)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (1, 1)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File